Starting phenix.real_space_refine on Thu Sep 18 22:06:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5gaq_8015/09_2025/5gaq_8015.cif Found real_map, /net/cci-nas-00/data/ceres_data/5gaq_8015/09_2025/5gaq_8015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5gaq_8015/09_2025/5gaq_8015.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5gaq_8015/09_2025/5gaq_8015.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5gaq_8015/09_2025/5gaq_8015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5gaq_8015/09_2025/5gaq_8015.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 13032 2.51 5 N 3465 2.21 5 O 4005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20574 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2286 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 278} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: B, C, D, E, F, G, H, I Time building chain proxies: 1.78, per 1000 atoms: 0.09 Number of scatterers: 20574 At special positions: 0 Unit cell: (132.99, 134.42, 114.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 4005 8.00 N 3465 7.00 C 13032 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 755.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4770 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 1.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 240 through 243 removed outlier: 3.513A pdb=" N GLN A 243 " --> pdb=" O ASN A 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 240 through 243' Processing helix chain 'B' and resid 240 through 243 removed outlier: 3.513A pdb=" N GLN B 243 " --> pdb=" O ASN B 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 240 through 243' Processing helix chain 'C' and resid 240 through 243 removed outlier: 3.508A pdb=" N GLN C 243 " --> pdb=" O ASN C 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 240 through 243' Processing helix chain 'D' and resid 240 through 243 removed outlier: 3.507A pdb=" N GLN D 243 " --> pdb=" O ASN D 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 240 through 243' Processing helix chain 'E' and resid 240 through 243 removed outlier: 3.509A pdb=" N GLN E 243 " --> pdb=" O ASN E 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 240 through 243' Processing helix chain 'F' and resid 240 through 243 removed outlier: 3.515A pdb=" N GLN F 243 " --> pdb=" O ASN F 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 240 through 243' Processing helix chain 'G' and resid 240 through 243 removed outlier: 3.511A pdb=" N GLN G 243 " --> pdb=" O ASN G 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 240 through 243' Processing helix chain 'H' and resid 240 through 243 removed outlier: 3.506A pdb=" N GLN H 243 " --> pdb=" O ASN H 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 240 through 243' Processing helix chain 'I' and resid 240 through 243 removed outlier: 3.508A pdb=" N GLN I 243 " --> pdb=" O ASN I 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 240 through 243' No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.03 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6513 1.34 - 1.45: 2856 1.45 - 1.57: 11529 1.57 - 1.69: 0 1.69 - 1.81: 126 Bond restraints: 21024 Sorted by residual: bond pdb=" CA PRO A 108 " pdb=" C PRO A 108 " ideal model delta sigma weight residual 1.517 1.540 -0.023 9.30e-03 1.16e+04 6.09e+00 bond pdb=" CA PRO F 108 " pdb=" C PRO F 108 " ideal model delta sigma weight residual 1.517 1.540 -0.023 9.30e-03 1.16e+04 5.95e+00 bond pdb=" CA PRO D 108 " pdb=" C PRO D 108 " ideal model delta sigma weight residual 1.517 1.539 -0.022 9.30e-03 1.16e+04 5.79e+00 bond pdb=" CA PRO C 108 " pdb=" C PRO C 108 " ideal model delta sigma weight residual 1.517 1.539 -0.022 9.30e-03 1.16e+04 5.79e+00 bond pdb=" CA PRO G 108 " pdb=" C PRO G 108 " ideal model delta sigma weight residual 1.517 1.539 -0.022 9.30e-03 1.16e+04 5.70e+00 ... (remaining 21019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 23757 1.23 - 2.47: 3720 2.47 - 3.70: 829 3.70 - 4.93: 161 4.93 - 6.17: 27 Bond angle restraints: 28494 Sorted by residual: angle pdb=" N ASN G 248 " pdb=" CA ASN G 248 " pdb=" C ASN G 248 " ideal model delta sigma weight residual 111.36 116.08 -4.72 1.09e+00 8.42e-01 1.88e+01 angle pdb=" N ASN C 248 " pdb=" CA ASN C 248 " pdb=" C ASN C 248 " ideal model delta sigma weight residual 111.36 116.07 -4.71 1.09e+00 8.42e-01 1.87e+01 angle pdb=" N ASN B 248 " pdb=" CA ASN B 248 " pdb=" C ASN B 248 " ideal model delta sigma weight residual 111.36 116.07 -4.71 1.09e+00 8.42e-01 1.87e+01 angle pdb=" N ASN E 248 " pdb=" CA ASN E 248 " pdb=" C ASN E 248 " ideal model delta sigma weight residual 111.36 116.04 -4.68 1.09e+00 8.42e-01 1.84e+01 angle pdb=" N ASN I 248 " pdb=" CA ASN I 248 " pdb=" C ASN I 248 " ideal model delta sigma weight residual 111.36 116.01 -4.65 1.09e+00 8.42e-01 1.82e+01 ... (remaining 28489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.50: 11284 15.50 - 30.99: 911 30.99 - 46.49: 180 46.49 - 61.98: 36 61.98 - 77.48: 9 Dihedral angle restraints: 12420 sinusoidal: 4923 harmonic: 7497 Sorted by residual: dihedral pdb=" CA PHE E 70 " pdb=" C PHE E 70 " pdb=" N GLU E 71 " pdb=" CA GLU E 71 " ideal model delta harmonic sigma weight residual -180.00 -163.28 -16.72 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA PHE B 70 " pdb=" C PHE B 70 " pdb=" N GLU B 71 " pdb=" CA GLU B 71 " ideal model delta harmonic sigma weight residual 180.00 -163.30 -16.70 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA PHE I 70 " pdb=" C PHE I 70 " pdb=" N GLU I 71 " pdb=" CA GLU I 71 " ideal model delta harmonic sigma weight residual -180.00 -163.30 -16.70 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 12417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1571 0.049 - 0.098: 1044 0.098 - 0.147: 255 0.147 - 0.197: 195 0.197 - 0.246: 103 Chirality restraints: 3168 Sorted by residual: chirality pdb=" CA ILE A 127 " pdb=" N ILE A 127 " pdb=" C ILE A 127 " pdb=" CB ILE A 127 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ILE E 127 " pdb=" N ILE E 127 " pdb=" C ILE E 127 " pdb=" CB ILE E 127 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ILE I 127 " pdb=" N ILE I 127 " pdb=" C ILE I 127 " pdb=" CB ILE I 127 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 3165 not shown) Planarity restraints: 3600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR F 279 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.84e+00 pdb=" C THR F 279 " 0.029 2.00e-02 2.50e+03 pdb=" O THR F 279 " -0.011 2.00e-02 2.50e+03 pdb=" N ASN F 280 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 279 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C THR E 279 " 0.029 2.00e-02 2.50e+03 pdb=" O THR E 279 " -0.011 2.00e-02 2.50e+03 pdb=" N ASN E 280 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR I 279 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C THR I 279 " -0.029 2.00e-02 2.50e+03 pdb=" O THR I 279 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN I 280 " 0.010 2.00e-02 2.50e+03 ... (remaining 3597 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4989 2.81 - 3.33: 18259 3.33 - 3.86: 36101 3.86 - 4.38: 40324 4.38 - 4.90: 72865 Nonbonded interactions: 172538 Sorted by model distance: nonbonded pdb=" OG SER E 82 " pdb=" OG1 THR F 57 " model vdw 2.289 3.040 nonbonded pdb=" OG SER F 82 " pdb=" OG1 THR G 57 " model vdw 2.289 3.040 nonbonded pdb=" OG SER D 82 " pdb=" OG1 THR E 57 " model vdw 2.289 3.040 nonbonded pdb=" OG1 THR A 57 " pdb=" OG SER I 82 " model vdw 2.290 3.040 nonbonded pdb=" OG SER G 82 " pdb=" OG1 THR H 57 " model vdw 2.290 3.040 ... (remaining 172533 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 11.330 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4972 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 21024 Z= 0.436 Angle : 1.016 6.166 28494 Z= 0.654 Chirality : 0.081 0.246 3168 Planarity : 0.003 0.028 3600 Dihedral : 11.967 77.477 7650 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.80 % Allowed : 5.84 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.69 (0.14), residues: 2574 helix: None (None), residues: 0 sheet: -2.39 (0.12), residues: 1386 loop : -2.35 (0.15), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 169 TYR 0.016 0.002 TYR F 96 PHE 0.007 0.002 PHE D 266 TRP 0.012 0.003 TRP C 20 HIS 0.006 0.002 HIS G 103 Details of bonding type rmsd covalent geometry : bond 0.00630 (21024) covalent geometry : angle 1.01599 (28494) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 846 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7534 (pm20) REVERT: A 44 MET cc_start: 0.5888 (ttm) cc_final: 0.5543 (ttp) REVERT: A 66 THR cc_start: 0.6312 (p) cc_final: 0.6048 (p) REVERT: A 102 GLU cc_start: 0.5810 (mt-10) cc_final: 0.5502 (mt-10) REVERT: A 117 GLN cc_start: 0.5484 (tt0) cc_final: 0.5198 (tt0) REVERT: A 128 GLU cc_start: 0.7959 (pt0) cc_final: 0.7704 (pt0) REVERT: A 165 LYS cc_start: 0.8397 (tttt) cc_final: 0.7929 (tmtt) REVERT: A 176 LYS cc_start: 0.8041 (mttm) cc_final: 0.7791 (mmtt) REVERT: A 215 ASN cc_start: 0.7870 (m-40) cc_final: 0.7084 (p0) REVERT: A 217 MET cc_start: 0.8406 (mmt) cc_final: 0.8149 (mpp) REVERT: A 218 TYR cc_start: 0.5527 (m-80) cc_final: 0.5130 (m-10) REVERT: A 285 ASP cc_start: 0.8149 (m-30) cc_final: 0.7809 (m-30) REVERT: A 289 ASP cc_start: 0.5535 (m-30) cc_final: 0.5301 (m-30) REVERT: B 13 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7778 (pm20) REVERT: B 44 MET cc_start: 0.6042 (ttm) cc_final: 0.5803 (tpt) REVERT: B 63 THR cc_start: 0.5293 (p) cc_final: 0.4708 (t) REVERT: B 66 THR cc_start: 0.6471 (p) cc_final: 0.6241 (p) REVERT: B 85 GLU cc_start: 0.5991 (tt0) cc_final: 0.5763 (tm-30) REVERT: B 90 MET cc_start: 0.6274 (ttp) cc_final: 0.5882 (ttp) REVERT: B 94 GLU cc_start: 0.5317 (mt-10) cc_final: 0.4969 (mp0) REVERT: B 130 MET cc_start: 0.4971 (ttp) cc_final: 0.4712 (ttm) REVERT: B 165 LYS cc_start: 0.8160 (tttt) cc_final: 0.7691 (tptt) REVERT: B 167 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7366 (mm-30) REVERT: B 176 LYS cc_start: 0.8293 (mttm) cc_final: 0.8041 (mmtp) REVERT: B 204 GLU cc_start: 0.7897 (tt0) cc_final: 0.7626 (tp30) REVERT: B 215 ASN cc_start: 0.8041 (m-40) cc_final: 0.7217 (p0) REVERT: B 217 MET cc_start: 0.8470 (mmt) cc_final: 0.8175 (mpp) REVERT: B 218 TYR cc_start: 0.6565 (m-80) cc_final: 0.6122 (m-10) REVERT: B 249 LYS cc_start: 0.7976 (tttt) cc_final: 0.7701 (ttpt) REVERT: B 263 ASN cc_start: 0.5734 (t0) cc_final: 0.5491 (t0) REVERT: C 11 GLN cc_start: 0.7054 (pt0) cc_final: 0.6747 (pt0) REVERT: C 13 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8399 (pm20) REVERT: C 44 MET cc_start: 0.5681 (ttm) cc_final: 0.5323 (ttp) REVERT: C 45 LYS cc_start: 0.4770 (tttt) cc_final: 0.4542 (tttp) REVERT: C 66 THR cc_start: 0.6345 (p) cc_final: 0.6106 (p) REVERT: C 128 GLU cc_start: 0.7516 (pt0) cc_final: 0.7244 (pt0) REVERT: C 134 ASP cc_start: 0.6710 (m-30) cc_final: 0.6097 (m-30) REVERT: C 165 LYS cc_start: 0.7931 (tttt) cc_final: 0.7485 (tmtt) REVERT: C 176 LYS cc_start: 0.8229 (mttm) cc_final: 0.7965 (mmtp) REVERT: C 215 ASN cc_start: 0.7656 (m-40) cc_final: 0.7039 (p0) REVERT: D 13 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7875 (pm20) REVERT: D 44 MET cc_start: 0.5665 (ttm) cc_final: 0.5359 (ttp) REVERT: D 85 GLU cc_start: 0.5947 (tt0) cc_final: 0.5668 (tm-30) REVERT: D 94 GLU cc_start: 0.5781 (mt-10) cc_final: 0.5447 (mt-10) REVERT: D 97 GLU cc_start: 0.6367 (mt-10) cc_final: 0.6034 (mt-10) REVERT: D 130 MET cc_start: 0.5623 (ttp) cc_final: 0.5330 (ttm) REVERT: D 165 LYS cc_start: 0.8343 (tttt) cc_final: 0.7770 (tmmt) REVERT: D 210 ARG cc_start: 0.5599 (mtm180) cc_final: 0.5228 (mtm-85) REVERT: D 214 LEU cc_start: 0.7765 (mt) cc_final: 0.7545 (mp) REVERT: D 215 ASN cc_start: 0.7210 (m-40) cc_final: 0.6739 (p0) REVERT: D 217 MET cc_start: 0.8343 (mmt) cc_final: 0.8142 (mpp) REVERT: D 218 TYR cc_start: 0.5931 (m-80) cc_final: 0.5692 (m-10) REVERT: D 240 ASN cc_start: 0.5734 (t0) cc_final: 0.5396 (t0) REVERT: D 263 ASN cc_start: 0.5975 (t0) cc_final: 0.5669 (t0) REVERT: D 265 TYR cc_start: 0.6834 (t80) cc_final: 0.6574 (t80) REVERT: E 13 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7892 (pm20) REVERT: E 44 MET cc_start: 0.5977 (ttm) cc_final: 0.5751 (tpt) REVERT: E 46 ASN cc_start: 0.5553 (m-40) cc_final: 0.5296 (m110) REVERT: E 85 GLU cc_start: 0.6145 (tt0) cc_final: 0.5906 (tm-30) REVERT: E 90 MET cc_start: 0.6697 (ttp) cc_final: 0.6349 (tmm) REVERT: E 94 GLU cc_start: 0.5164 (mt-10) cc_final: 0.4958 (mt-10) REVERT: E 134 ASP cc_start: 0.6473 (m-30) cc_final: 0.6223 (m-30) REVERT: E 152 ARG cc_start: 0.6504 (mmt180) cc_final: 0.6014 (tpt90) REVERT: E 165 LYS cc_start: 0.8200 (tttt) cc_final: 0.7847 (tmmt) REVERT: E 167 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7488 (mm-30) REVERT: E 204 GLU cc_start: 0.8085 (tt0) cc_final: 0.7873 (pm20) REVERT: E 205 ASP cc_start: 0.7242 (t0) cc_final: 0.6745 (m-30) REVERT: E 214 LEU cc_start: 0.7736 (mt) cc_final: 0.7401 (mt) REVERT: E 215 ASN cc_start: 0.7819 (m-40) cc_final: 0.7361 (m-40) REVERT: E 217 MET cc_start: 0.8449 (mmt) cc_final: 0.7999 (mpp) REVERT: E 218 TYR cc_start: 0.5971 (m-80) cc_final: 0.5654 (m-10) REVERT: E 228 ASP cc_start: 0.9081 (t0) cc_final: 0.8846 (m-30) REVERT: F 11 GLN cc_start: 0.6711 (pt0) cc_final: 0.6478 (pt0) REVERT: F 13 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7608 (pm20) REVERT: F 46 ASN cc_start: 0.5153 (m-40) cc_final: 0.4919 (m110) REVERT: F 63 THR cc_start: 0.5947 (p) cc_final: 0.4919 (t) REVERT: F 85 GLU cc_start: 0.5986 (tt0) cc_final: 0.5735 (tm-30) REVERT: F 102 GLU cc_start: 0.5406 (mt-10) cc_final: 0.5205 (tt0) REVERT: F 152 ARG cc_start: 0.6824 (mmt180) cc_final: 0.6462 (mmm160) REVERT: F 165 LYS cc_start: 0.8083 (tttt) cc_final: 0.7575 (tmtt) REVERT: F 176 LYS cc_start: 0.8079 (mttm) cc_final: 0.7848 (mmtp) REVERT: F 215 ASN cc_start: 0.7615 (m-40) cc_final: 0.6879 (p0) REVERT: F 218 TYR cc_start: 0.4824 (m-80) cc_final: 0.4505 (m-10) REVERT: F 263 ASN cc_start: 0.5721 (t0) cc_final: 0.5219 (t0) REVERT: F 265 TYR cc_start: 0.7020 (t80) cc_final: 0.6807 (t80) REVERT: F 268 ARG cc_start: 0.6927 (mtm-85) cc_final: 0.6648 (mtm-85) REVERT: F 290 LYS cc_start: 0.6379 (mttt) cc_final: 0.6178 (mmtt) REVERT: G 13 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7662 (pm20) REVERT: G 36 GLN cc_start: 0.5845 (OUTLIER) cc_final: 0.5290 (tt0) REVERT: G 42 LYS cc_start: 0.6738 (tttt) cc_final: 0.6270 (mtmm) REVERT: G 46 ASN cc_start: 0.5280 (m-40) cc_final: 0.4989 (m-40) REVERT: G 117 GLN cc_start: 0.5693 (tt0) cc_final: 0.5338 (tt0) REVERT: G 128 GLU cc_start: 0.7320 (pt0) cc_final: 0.7111 (pt0) REVERT: G 165 LYS cc_start: 0.8095 (tttt) cc_final: 0.7761 (tmmt) REVERT: G 176 LYS cc_start: 0.8021 (mttm) cc_final: 0.7804 (mmtt) REVERT: G 194 HIS cc_start: 0.8174 (m90) cc_final: 0.7846 (m90) REVERT: G 205 ASP cc_start: 0.7309 (t0) cc_final: 0.7103 (m-30) REVERT: G 214 LEU cc_start: 0.8011 (mt) cc_final: 0.7705 (mp) REVERT: G 215 ASN cc_start: 0.7742 (m-40) cc_final: 0.7145 (p0) REVERT: G 217 MET cc_start: 0.8705 (mmt) cc_final: 0.8457 (mpp) REVERT: G 218 TYR cc_start: 0.5319 (m-80) cc_final: 0.4944 (m-10) REVERT: H 13 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8167 (pm20) REVERT: H 85 GLU cc_start: 0.6351 (tt0) cc_final: 0.6143 (tm-30) REVERT: H 90 MET cc_start: 0.6389 (ttp) cc_final: 0.6014 (tmm) REVERT: H 92 GLU cc_start: 0.6278 (mt-10) cc_final: 0.5914 (mt-10) REVERT: H 117 GLN cc_start: 0.5846 (tt0) cc_final: 0.5640 (tt0) REVERT: H 130 MET cc_start: 0.5331 (ttp) cc_final: 0.4936 (ttm) REVERT: H 134 ASP cc_start: 0.5997 (m-30) cc_final: 0.5641 (m-30) REVERT: H 165 LYS cc_start: 0.8479 (tttt) cc_final: 0.7972 (tmtt) REVERT: H 174 GLU cc_start: 0.8263 (mt-10) cc_final: 0.8029 (mp0) REVERT: H 176 LYS cc_start: 0.8132 (mttm) cc_final: 0.7919 (mmtp) REVERT: H 205 ASP cc_start: 0.7296 (t0) cc_final: 0.6829 (m-30) REVERT: H 206 TRP cc_start: 0.8687 (p-90) cc_final: 0.8253 (p90) REVERT: H 215 ASN cc_start: 0.7700 (m-40) cc_final: 0.7088 (p0) REVERT: H 217 MET cc_start: 0.8741 (mmt) cc_final: 0.8471 (mpp) REVERT: H 218 TYR cc_start: 0.6189 (m-80) cc_final: 0.5699 (m-10) REVERT: H 263 ASN cc_start: 0.5922 (t0) cc_final: 0.5613 (t0) REVERT: H 266 PHE cc_start: 0.4656 (m-80) cc_final: 0.4421 (m-10) REVERT: H 290 LYS cc_start: 0.6379 (mttt) cc_final: 0.6137 (mttt) REVERT: I 11 GLN cc_start: 0.6335 (pt0) cc_final: 0.6105 (pt0) REVERT: I 13 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7823 (mm-30) REVERT: I 44 MET cc_start: 0.5710 (ttm) cc_final: 0.5137 (tmm) REVERT: I 63 THR cc_start: 0.5651 (p) cc_final: 0.5140 (t) REVERT: I 66 THR cc_start: 0.5868 (p) cc_final: 0.5664 (p) REVERT: I 70 PHE cc_start: 0.4015 (t80) cc_final: 0.3717 (t80) REVERT: I 90 MET cc_start: 0.6686 (ttp) cc_final: 0.6347 (tmm) REVERT: I 97 GLU cc_start: 0.5843 (mt-10) cc_final: 0.5598 (mt-10) REVERT: I 121 ASP cc_start: 0.7415 (t70) cc_final: 0.7137 (m-30) REVERT: I 128 GLU cc_start: 0.7134 (pt0) cc_final: 0.6803 (pt0) REVERT: I 152 ARG cc_start: 0.6348 (mmt180) cc_final: 0.5859 (tpt90) REVERT: I 165 LYS cc_start: 0.8066 (tttt) cc_final: 0.7469 (tmtt) REVERT: I 175 ARG cc_start: 0.7116 (mmm160) cc_final: 0.6800 (mmm-85) REVERT: I 215 ASN cc_start: 0.8019 (m-40) cc_final: 0.7600 (m110) REVERT: I 218 TYR cc_start: 0.5370 (m-80) cc_final: 0.4833 (m-10) REVERT: I 285 ASP cc_start: 0.8373 (m-30) cc_final: 0.8116 (m-30) outliers start: 18 outliers final: 4 residues processed: 855 average time/residue: 0.1696 time to fit residues: 209.2778 Evaluate side-chains 502 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 497 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 36 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 247 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 81 HIS ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN A 243 GLN B 11 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN B 81 HIS B 243 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN C 81 HIS ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN C 243 GLN C 248 ASN C 263 ASN D 11 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 HIS ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 GLN D 143 GLN D 243 GLN E 11 GLN E 81 HIS ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 ASN E 243 GLN ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 ASN F 81 HIS F 103 HIS F 117 GLN F 147 GLN F 243 GLN F 255 HIS G 11 GLN G 36 GLN G 81 HIS G 103 HIS G 117 GLN G 243 GLN G 263 ASN H 36 GLN H 81 HIS H 103 HIS H 117 GLN H 243 GLN I 36 GLN I 81 HIS ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 243 GLN I 263 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.119256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.096987 restraints weight = 28333.409| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.41 r_work: 0.3193 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21024 Z= 0.175 Angle : 0.531 7.322 28494 Z= 0.289 Chirality : 0.049 0.169 3168 Planarity : 0.003 0.046 3600 Dihedral : 5.426 88.873 2855 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.97 % Allowed : 13.72 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.21 (0.15), residues: 2574 helix: None (None), residues: 0 sheet: -2.13 (0.12), residues: 1431 loop : -1.91 (0.15), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 287 TYR 0.011 0.001 TYR D 96 PHE 0.016 0.002 PHE A 209 TRP 0.027 0.002 TRP G 206 HIS 0.006 0.001 HIS C 194 Details of bonding type rmsd covalent geometry : bond 0.00419 (21024) covalent geometry : angle 0.53070 (28494) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 509 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8197 (pm20) REVERT: A 16 VAL cc_start: 0.8872 (t) cc_final: 0.8638 (p) REVERT: A 21 LYS cc_start: 0.8866 (tppt) cc_final: 0.8481 (tmtt) REVERT: A 44 MET cc_start: 0.8363 (ttm) cc_final: 0.7941 (ttp) REVERT: A 87 GLN cc_start: 0.8326 (tt0) cc_final: 0.8063 (tp40) REVERT: A 102 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8232 (mt-10) REVERT: A 165 LYS cc_start: 0.8479 (tttt) cc_final: 0.8266 (tmtt) REVERT: A 176 LYS cc_start: 0.9100 (mttm) cc_final: 0.8737 (mmmt) REVERT: A 235 ASP cc_start: 0.8332 (t70) cc_final: 0.8106 (t0) REVERT: A 239 ASP cc_start: 0.8626 (t0) cc_final: 0.7975 (t0) REVERT: A 285 ASP cc_start: 0.8550 (m-30) cc_final: 0.8157 (m-30) REVERT: A 292 ILE cc_start: 0.8954 (mt) cc_final: 0.8715 (tt) REVERT: B 13 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8121 (pm20) REVERT: B 19 VAL cc_start: 0.9197 (t) cc_final: 0.8948 (p) REVERT: B 44 MET cc_start: 0.8564 (ttm) cc_final: 0.8037 (ttp) REVERT: B 85 GLU cc_start: 0.7992 (tt0) cc_final: 0.7608 (tm-30) REVERT: B 90 MET cc_start: 0.9013 (ttp) cc_final: 0.8554 (ttp) REVERT: B 94 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7805 (mt-10) REVERT: B 167 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8252 (mp0) REVERT: B 176 LYS cc_start: 0.9122 (mttm) cc_final: 0.8801 (mmtp) REVERT: B 235 ASP cc_start: 0.8538 (t70) cc_final: 0.8125 (t70) REVERT: B 249 LYS cc_start: 0.8940 (tttt) cc_final: 0.8431 (ttpp) REVERT: B 292 ILE cc_start: 0.8861 (mt) cc_final: 0.8596 (tt) REVERT: B 293 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8665 (pp) REVERT: C 44 MET cc_start: 0.8431 (ttm) cc_final: 0.7966 (mpp) REVERT: C 45 LYS cc_start: 0.8900 (tttt) cc_final: 0.8234 (tttp) REVERT: C 94 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7885 (mt-10) REVERT: C 134 ASP cc_start: 0.8397 (m-30) cc_final: 0.8134 (m-30) REVERT: C 147 GLN cc_start: 0.8716 (tt0) cc_final: 0.8504 (tp40) REVERT: C 154 LYS cc_start: 0.8726 (mttt) cc_final: 0.8390 (mtpp) REVERT: C 175 ARG cc_start: 0.9102 (mmm160) cc_final: 0.8865 (mtp85) REVERT: C 176 LYS cc_start: 0.9176 (mttm) cc_final: 0.8805 (mmtp) REVERT: C 198 PHE cc_start: 0.8732 (m-80) cc_final: 0.8477 (m-80) REVERT: C 235 ASP cc_start: 0.8534 (t0) cc_final: 0.8309 (t0) REVERT: C 248 ASN cc_start: 0.8983 (p0) cc_final: 0.8593 (p0) REVERT: C 257 ASP cc_start: 0.8354 (m-30) cc_final: 0.7857 (m-30) REVERT: C 292 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8508 (tt) REVERT: D 13 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8419 (pm20) REVERT: D 34 VAL cc_start: 0.9541 (OUTLIER) cc_final: 0.9273 (m) REVERT: D 44 MET cc_start: 0.8518 (ttm) cc_final: 0.8043 (ttp) REVERT: D 85 GLU cc_start: 0.8022 (tt0) cc_final: 0.7753 (tm-30) REVERT: D 97 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8105 (mt-10) REVERT: D 154 LYS cc_start: 0.8860 (mttt) cc_final: 0.8432 (mtpp) REVERT: D 165 LYS cc_start: 0.8544 (tttt) cc_final: 0.8192 (tmmt) REVERT: D 263 ASN cc_start: 0.8747 (t0) cc_final: 0.8387 (t0) REVERT: D 290 LYS cc_start: 0.8714 (mttt) cc_final: 0.8240 (mmtp) REVERT: E 13 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8389 (pm20) REVERT: E 44 MET cc_start: 0.8552 (ttm) cc_final: 0.8302 (tpp) REVERT: E 85 GLU cc_start: 0.8155 (tt0) cc_final: 0.7905 (tm-30) REVERT: E 90 MET cc_start: 0.8962 (ttp) cc_final: 0.8573 (tmm) REVERT: E 110 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8417 (p) REVERT: E 130 MET cc_start: 0.8630 (ttp) cc_final: 0.8393 (ttm) REVERT: E 154 LYS cc_start: 0.8898 (mttt) cc_final: 0.8312 (mtpt) REVERT: E 165 LYS cc_start: 0.8574 (tttt) cc_final: 0.8190 (tmmt) REVERT: E 167 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8147 (mp0) REVERT: E 174 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8449 (mp0) REVERT: E 248 ASN cc_start: 0.8904 (p0) cc_final: 0.8346 (p0) REVERT: F 13 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8175 (pm20) REVERT: F 46 ASN cc_start: 0.8757 (m-40) cc_final: 0.8512 (m110) REVERT: F 85 GLU cc_start: 0.8143 (tt0) cc_final: 0.7751 (tm-30) REVERT: F 90 MET cc_start: 0.9034 (ttp) cc_final: 0.8615 (tmm) REVERT: F 94 GLU cc_start: 0.8143 (tt0) cc_final: 0.7784 (mt-10) REVERT: F 155 ILE cc_start: 0.9037 (mt) cc_final: 0.8776 (pt) REVERT: F 165 LYS cc_start: 0.8630 (tttt) cc_final: 0.8256 (tmmt) REVERT: F 176 LYS cc_start: 0.8950 (mttm) cc_final: 0.8578 (mmtp) REVERT: F 263 ASN cc_start: 0.8840 (t0) cc_final: 0.8519 (t0) REVERT: F 290 LYS cc_start: 0.8757 (mttt) cc_final: 0.8262 (mmtt) REVERT: F 292 ILE cc_start: 0.8923 (mt) cc_final: 0.8636 (tt) REVERT: G 13 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8129 (pm20) REVERT: G 36 GLN cc_start: 0.8839 (tt0) cc_final: 0.8497 (tt0) REVERT: G 42 LYS cc_start: 0.9187 (tttt) cc_final: 0.8707 (mtmm) REVERT: G 94 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8069 (mt-10) REVERT: G 165 LYS cc_start: 0.8527 (tttt) cc_final: 0.8141 (tmmt) REVERT: G 167 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8360 (mt-10) REVERT: G 176 LYS cc_start: 0.9006 (mttm) cc_final: 0.8550 (mmtt) REVERT: G 187 TRP cc_start: 0.8155 (m100) cc_final: 0.7929 (m100) REVERT: G 218 TYR cc_start: 0.8162 (m-80) cc_final: 0.7931 (m-80) REVERT: G 236 GLN cc_start: 0.8819 (mp10) cc_final: 0.8382 (mp10) REVERT: H 85 GLU cc_start: 0.8202 (tt0) cc_final: 0.7871 (tm-30) REVERT: H 90 MET cc_start: 0.9038 (ttp) cc_final: 0.8762 (tmm) REVERT: H 92 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8139 (mt-10) REVERT: H 110 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8500 (p) REVERT: H 117 GLN cc_start: 0.9098 (tt0) cc_final: 0.8749 (tt0) REVERT: H 121 ASP cc_start: 0.8631 (t70) cc_final: 0.8144 (m-30) REVERT: H 175 ARG cc_start: 0.8893 (mmm160) cc_final: 0.8661 (mmm-85) REVERT: H 176 LYS cc_start: 0.8969 (mttm) cc_final: 0.8625 (mmtp) REVERT: H 221 TYR cc_start: 0.9173 (m-80) cc_final: 0.8866 (m-10) REVERT: H 236 GLN cc_start: 0.8905 (mp10) cc_final: 0.8255 (mp10) REVERT: H 290 LYS cc_start: 0.8976 (mttt) cc_final: 0.8519 (mtmm) REVERT: I 11 GLN cc_start: 0.9014 (pt0) cc_final: 0.8721 (pt0) REVERT: I 13 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8261 (pm20) REVERT: I 70 PHE cc_start: 0.7237 (t80) cc_final: 0.6872 (t80) REVERT: I 121 ASP cc_start: 0.8412 (t70) cc_final: 0.8033 (m-30) REVERT: I 147 GLN cc_start: 0.8557 (tt0) cc_final: 0.8311 (tt0) REVERT: I 154 LYS cc_start: 0.8717 (mttt) cc_final: 0.8226 (mtpp) REVERT: I 165 LYS cc_start: 0.8480 (tttt) cc_final: 0.8043 (tmmt) REVERT: I 187 TRP cc_start: 0.8345 (m100) cc_final: 0.8103 (m100) REVERT: I 221 TYR cc_start: 0.9204 (m-80) cc_final: 0.8894 (m-10) REVERT: I 249 LYS cc_start: 0.8662 (ttmt) cc_final: 0.8378 (tttm) REVERT: I 257 ASP cc_start: 0.8546 (t70) cc_final: 0.7833 (m-30) outliers start: 67 outliers final: 28 residues processed: 560 average time/residue: 0.1317 time to fit residues: 116.0544 Evaluate side-chains 474 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 441 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 46 ASN Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 293 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 138 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 249 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN A 215 ASN A 243 GLN B 11 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN B 263 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN ** C 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN C 119 ASN C 215 ASN C 243 GLN C 263 ASN D 11 GLN D 48 ASN D 58 HIS ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 GLN E 11 GLN ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 HIS ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN E 215 ASN E 243 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 HIS F 117 GLN F 215 ASN F 243 GLN G 11 GLN G 46 ASN G 48 ASN G 117 GLN G 143 GLN G 263 ASN H 48 ASN H 243 GLN H 263 ASN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 ASN ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 ASN I 243 GLN ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 263 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.114899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.092924 restraints weight = 28736.499| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.38 r_work: 0.3152 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 21024 Z= 0.262 Angle : 0.551 8.283 28494 Z= 0.299 Chirality : 0.049 0.165 3168 Planarity : 0.003 0.041 3600 Dihedral : 4.471 29.248 2846 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.56 % Allowed : 16.29 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.89 (0.15), residues: 2574 helix: None (None), residues: 0 sheet: -1.97 (0.13), residues: 1305 loop : -1.72 (0.14), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 287 TYR 0.014 0.001 TYR D 96 PHE 0.029 0.002 PHE G 209 TRP 0.030 0.002 TRP G 206 HIS 0.007 0.002 HIS B 103 Details of bonding type rmsd covalent geometry : bond 0.00602 (21024) covalent geometry : angle 0.55082 (28494) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 465 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8128 (pm20) REVERT: A 21 LYS cc_start: 0.8910 (tppt) cc_final: 0.8565 (tmtt) REVERT: A 44 MET cc_start: 0.8391 (ttm) cc_final: 0.8072 (ptm) REVERT: A 87 GLN cc_start: 0.8318 (tt0) cc_final: 0.8118 (tp40) REVERT: A 102 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8349 (mt-10) REVERT: A 176 LYS cc_start: 0.9012 (mttm) cc_final: 0.8614 (mmmt) REVERT: A 221 TYR cc_start: 0.9194 (m-80) cc_final: 0.8974 (m-80) REVERT: A 239 ASP cc_start: 0.8594 (t0) cc_final: 0.7939 (t0) REVERT: B 13 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8139 (pm20) REVERT: B 19 VAL cc_start: 0.9322 (t) cc_final: 0.9075 (p) REVERT: B 44 MET cc_start: 0.8575 (ttm) cc_final: 0.8359 (ttm) REVERT: B 85 GLU cc_start: 0.8147 (tt0) cc_final: 0.7803 (tm-30) REVERT: B 90 MET cc_start: 0.9011 (ttp) cc_final: 0.8613 (ttp) REVERT: B 94 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7877 (mt-10) REVERT: B 167 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8325 (mp0) REVERT: B 176 LYS cc_start: 0.9130 (mttm) cc_final: 0.8855 (mmtp) REVERT: B 212 LYS cc_start: 0.8622 (tttt) cc_final: 0.8367 (ttpp) REVERT: B 257 ASP cc_start: 0.9016 (t70) cc_final: 0.8775 (m-30) REVERT: B 292 ILE cc_start: 0.8956 (mt) cc_final: 0.8696 (tt) REVERT: B 293 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8854 (pp) REVERT: C 44 MET cc_start: 0.8501 (ttm) cc_final: 0.8097 (mpp) REVERT: C 45 LYS cc_start: 0.9002 (tttt) cc_final: 0.8549 (tttp) REVERT: C 52 ARG cc_start: 0.8116 (ttt-90) cc_final: 0.7908 (ttt180) REVERT: C 154 LYS cc_start: 0.8832 (mttt) cc_final: 0.8242 (mtpp) REVERT: C 159 ARG cc_start: 0.8810 (ttm110) cc_final: 0.8374 (ttp80) REVERT: C 174 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8561 (mp0) REVERT: C 175 ARG cc_start: 0.9103 (mmm160) cc_final: 0.8881 (mtp85) REVERT: C 176 LYS cc_start: 0.9181 (mttm) cc_final: 0.8717 (mmtp) REVERT: C 236 GLN cc_start: 0.8746 (mp10) cc_final: 0.7861 (mp10) REVERT: C 243 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7928 (pt0) REVERT: C 257 ASP cc_start: 0.8560 (m-30) cc_final: 0.8189 (m-30) REVERT: C 292 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8529 (tt) REVERT: C 293 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9038 (pp) REVERT: D 13 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8306 (pm20) REVERT: D 34 VAL cc_start: 0.9567 (OUTLIER) cc_final: 0.9297 (m) REVERT: D 85 GLU cc_start: 0.8211 (tt0) cc_final: 0.7929 (tm-30) REVERT: D 94 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7683 (mp0) REVERT: D 154 LYS cc_start: 0.8873 (mttt) cc_final: 0.8445 (mtpp) REVERT: D 240 ASN cc_start: 0.8364 (t0) cc_final: 0.7775 (t0) REVERT: D 243 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8101 (pt0) REVERT: D 257 ASP cc_start: 0.9198 (m-30) cc_final: 0.8979 (m-30) REVERT: D 263 ASN cc_start: 0.8922 (t0) cc_final: 0.8563 (t0) REVERT: E 13 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8398 (pm20) REVERT: E 21 LYS cc_start: 0.9039 (ttmm) cc_final: 0.8821 (ttmm) REVERT: E 44 MET cc_start: 0.8609 (ttm) cc_final: 0.8372 (tpp) REVERT: E 85 GLU cc_start: 0.8198 (tt0) cc_final: 0.7963 (tm-30) REVERT: E 90 MET cc_start: 0.8991 (ttp) cc_final: 0.8566 (tmm) REVERT: E 110 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8517 (p) REVERT: E 154 LYS cc_start: 0.9038 (mttt) cc_final: 0.8456 (mtpp) REVERT: E 165 LYS cc_start: 0.8475 (tttt) cc_final: 0.8199 (tmmt) REVERT: E 167 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8171 (mp0) REVERT: E 174 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8590 (mt-10) REVERT: E 176 LYS cc_start: 0.9052 (mmtt) cc_final: 0.8825 (mmmt) REVERT: E 248 ASN cc_start: 0.9137 (p0) cc_final: 0.8547 (p0) REVERT: F 52 ARG cc_start: 0.8276 (ttt-90) cc_final: 0.7938 (mtp85) REVERT: F 85 GLU cc_start: 0.8332 (tt0) cc_final: 0.7934 (tm-30) REVERT: F 90 MET cc_start: 0.9060 (ttp) cc_final: 0.8658 (tmm) REVERT: F 94 GLU cc_start: 0.8271 (tt0) cc_final: 0.7911 (mt-10) REVERT: F 155 ILE cc_start: 0.9072 (mt) cc_final: 0.8748 (pt) REVERT: F 165 LYS cc_start: 0.8527 (tttt) cc_final: 0.8249 (tmmt) REVERT: F 176 LYS cc_start: 0.8999 (mttm) cc_final: 0.8655 (mmtp) REVERT: F 240 ASN cc_start: 0.8310 (t0) cc_final: 0.8036 (t0) REVERT: F 257 ASP cc_start: 0.8418 (m-30) cc_final: 0.7849 (m-30) REVERT: F 263 ASN cc_start: 0.8933 (t0) cc_final: 0.8637 (t0) REVERT: F 292 ILE cc_start: 0.9062 (mt) cc_final: 0.8698 (tt) REVERT: G 13 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8367 (pm20) REVERT: G 42 LYS cc_start: 0.9199 (tttt) cc_final: 0.8677 (mtmm) REVERT: G 94 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8104 (mt-10) REVERT: G 117 GLN cc_start: 0.9112 (tt0) cc_final: 0.8831 (tt0) REVERT: G 165 LYS cc_start: 0.8502 (tttt) cc_final: 0.8171 (tmmt) REVERT: G 167 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8361 (mt-10) REVERT: G 176 LYS cc_start: 0.9016 (mttm) cc_final: 0.8622 (mmtt) REVERT: G 187 TRP cc_start: 0.8204 (m100) cc_final: 0.7941 (m100) REVERT: G 192 LEU cc_start: 0.9287 (mt) cc_final: 0.9067 (mt) REVERT: G 239 ASP cc_start: 0.8724 (t0) cc_final: 0.8506 (t0) REVERT: H 85 GLU cc_start: 0.8445 (tt0) cc_final: 0.8104 (tm-30) REVERT: H 90 MET cc_start: 0.9024 (ttp) cc_final: 0.8806 (tmm) REVERT: H 92 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8140 (mt-10) REVERT: H 110 THR cc_start: 0.9018 (OUTLIER) cc_final: 0.8671 (p) REVERT: H 176 LYS cc_start: 0.8855 (mttm) cc_final: 0.8478 (mmtp) REVERT: H 178 TYR cc_start: 0.8534 (m-80) cc_final: 0.8193 (m-80) REVERT: H 236 GLN cc_start: 0.8975 (mp10) cc_final: 0.8690 (mp10) REVERT: H 290 LYS cc_start: 0.9018 (mttt) cc_final: 0.8586 (mtmm) REVERT: I 13 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8236 (pm20) REVERT: I 21 LYS cc_start: 0.8921 (ttmm) cc_final: 0.8616 (tmtt) REVERT: I 87 GLN cc_start: 0.8293 (tt0) cc_final: 0.8003 (tp40) REVERT: I 90 MET cc_start: 0.9146 (ttp) cc_final: 0.8895 (tmm) REVERT: I 119 ASN cc_start: 0.8808 (OUTLIER) cc_final: 0.8286 (t0) REVERT: I 121 ASP cc_start: 0.8428 (t70) cc_final: 0.8047 (m-30) REVERT: I 147 GLN cc_start: 0.8654 (tt0) cc_final: 0.8394 (tt0) REVERT: I 154 LYS cc_start: 0.8809 (mttt) cc_final: 0.8289 (mtpp) REVERT: I 165 LYS cc_start: 0.8489 (tttt) cc_final: 0.8132 (tmmt) REVERT: I 187 TRP cc_start: 0.8396 (m100) cc_final: 0.8170 (m100) REVERT: I 249 LYS cc_start: 0.8834 (ttmt) cc_final: 0.8525 (tttm) REVERT: I 263 ASN cc_start: 0.9039 (t0) cc_final: 0.8745 (t0) outliers start: 103 outliers final: 55 residues processed: 540 average time/residue: 0.1323 time to fit residues: 111.8623 Evaluate side-chains 486 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 421 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 243 GLN Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 46 ASN Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 119 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 186 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 ASN A 243 GLN A 263 ASN B 11 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN B 263 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN C 263 ASN D 11 GLN D 58 HIS ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 GLN E 11 GLN ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 ASN E 58 HIS ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 ASN F 58 HIS F 215 ASN F 243 GLN G 11 GLN G 143 GLN G 147 GLN G 243 GLN G 263 ASN H 48 ASN H 117 GLN H 263 ASN I 11 GLN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 243 GLN ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.113660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.091827 restraints weight = 28997.905| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.39 r_work: 0.3133 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 21024 Z= 0.273 Angle : 0.547 8.356 28494 Z= 0.295 Chirality : 0.048 0.191 3168 Planarity : 0.003 0.032 3600 Dihedral : 4.397 28.857 2846 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.47 % Allowed : 17.62 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.82 (0.15), residues: 2574 helix: None (None), residues: 0 sheet: -1.96 (0.13), residues: 1287 loop : -1.63 (0.15), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 115 TYR 0.013 0.001 TYR H 178 PHE 0.029 0.002 PHE A 209 TRP 0.031 0.002 TRP G 206 HIS 0.006 0.002 HIS B 103 Details of bonding type rmsd covalent geometry : bond 0.00624 (21024) covalent geometry : angle 0.54711 (28494) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 454 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8122 (pm20) REVERT: A 21 LYS cc_start: 0.8925 (tppt) cc_final: 0.8568 (tmtt) REVERT: A 44 MET cc_start: 0.8373 (ttm) cc_final: 0.8171 (ptt) REVERT: A 87 GLN cc_start: 0.8326 (tt0) cc_final: 0.8092 (tp40) REVERT: A 102 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8330 (mt-10) REVERT: A 165 LYS cc_start: 0.8365 (tmmt) cc_final: 0.8015 (tmmt) REVERT: A 176 LYS cc_start: 0.8989 (mttm) cc_final: 0.8603 (mmmt) REVERT: A 240 ASN cc_start: 0.8460 (t0) cc_final: 0.8253 (t0) REVERT: A 249 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8722 (ttpt) REVERT: B 13 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8148 (pm20) REVERT: B 19 VAL cc_start: 0.9280 (t) cc_final: 0.9031 (p) REVERT: B 44 MET cc_start: 0.8567 (ttm) cc_final: 0.8308 (ttm) REVERT: B 85 GLU cc_start: 0.8217 (tt0) cc_final: 0.7831 (tm-30) REVERT: B 94 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7989 (mt-10) REVERT: B 167 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8265 (mp0) REVERT: B 176 LYS cc_start: 0.9151 (mttm) cc_final: 0.8820 (mmtp) REVERT: B 212 LYS cc_start: 0.8632 (tttt) cc_final: 0.8356 (ttpp) REVERT: B 292 ILE cc_start: 0.8899 (mt) cc_final: 0.8638 (tt) REVERT: B 293 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8891 (pp) REVERT: C 44 MET cc_start: 0.8495 (ttm) cc_final: 0.8112 (mpp) REVERT: C 45 LYS cc_start: 0.8979 (tttt) cc_final: 0.8498 (tttp) REVERT: C 52 ARG cc_start: 0.8103 (ttt-90) cc_final: 0.7902 (ttt180) REVERT: C 154 LYS cc_start: 0.8957 (mttt) cc_final: 0.8494 (mtpp) REVERT: C 159 ARG cc_start: 0.8850 (ttm110) cc_final: 0.8335 (ttp80) REVERT: C 174 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8335 (mp0) REVERT: C 175 ARG cc_start: 0.9154 (mmm160) cc_final: 0.8945 (mtp85) REVERT: C 176 LYS cc_start: 0.9164 (mttm) cc_final: 0.8684 (mmtp) REVERT: C 236 GLN cc_start: 0.8762 (mp10) cc_final: 0.7866 (mp10) REVERT: C 240 ASN cc_start: 0.8316 (t0) cc_final: 0.8074 (t0) REVERT: C 257 ASP cc_start: 0.8489 (m-30) cc_final: 0.8119 (m-30) REVERT: C 292 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8526 (tt) REVERT: D 13 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8241 (pm20) REVERT: D 85 GLU cc_start: 0.8260 (tt0) cc_final: 0.7933 (tm-30) REVERT: D 94 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: D 154 LYS cc_start: 0.8886 (mttt) cc_final: 0.8553 (mttm) REVERT: D 240 ASN cc_start: 0.8420 (t0) cc_final: 0.8098 (t0) REVERT: D 257 ASP cc_start: 0.9024 (m-30) cc_final: 0.8778 (m-30) REVERT: D 265 TYR cc_start: 0.8990 (t80) cc_final: 0.8067 (t80) REVERT: E 11 GLN cc_start: 0.8803 (pt0) cc_final: 0.8574 (pt0) REVERT: E 44 MET cc_start: 0.8605 (ttm) cc_final: 0.8340 (tpp) REVERT: E 85 GLU cc_start: 0.8280 (tt0) cc_final: 0.8044 (tm-30) REVERT: E 90 MET cc_start: 0.9002 (ttp) cc_final: 0.8643 (tmm) REVERT: E 110 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8388 (p) REVERT: E 154 LYS cc_start: 0.9033 (mttt) cc_final: 0.8498 (mtpt) REVERT: E 165 LYS cc_start: 0.8577 (tttt) cc_final: 0.8239 (tmmt) REVERT: E 167 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8131 (mp0) REVERT: E 176 LYS cc_start: 0.9051 (mmtt) cc_final: 0.8812 (mmmt) REVERT: E 192 LEU cc_start: 0.9266 (mt) cc_final: 0.8995 (mt) REVERT: E 248 ASN cc_start: 0.9189 (p0) cc_final: 0.8491 (p0) REVERT: F 52 ARG cc_start: 0.8429 (ttt-90) cc_final: 0.7973 (mtp85) REVERT: F 90 MET cc_start: 0.9051 (ttp) cc_final: 0.8651 (tmm) REVERT: F 94 GLU cc_start: 0.8270 (tt0) cc_final: 0.7907 (mt-10) REVERT: F 155 ILE cc_start: 0.9085 (mt) cc_final: 0.8748 (pt) REVERT: F 165 LYS cc_start: 0.8497 (tttt) cc_final: 0.8270 (tmmt) REVERT: F 176 LYS cc_start: 0.8999 (mttm) cc_final: 0.8648 (mmtt) REVERT: F 240 ASN cc_start: 0.8172 (t0) cc_final: 0.7908 (t0) REVERT: F 257 ASP cc_start: 0.8558 (m-30) cc_final: 0.7938 (m-30) REVERT: F 263 ASN cc_start: 0.8907 (t0) cc_final: 0.8645 (t0) REVERT: F 292 ILE cc_start: 0.9060 (mt) cc_final: 0.8851 (mt) REVERT: G 42 LYS cc_start: 0.9205 (tttt) cc_final: 0.8942 (ttmm) REVERT: G 94 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8112 (mt-10) REVERT: G 155 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8622 (pt) REVERT: G 165 LYS cc_start: 0.8509 (tttt) cc_final: 0.8294 (tmmt) REVERT: G 176 LYS cc_start: 0.9001 (mttm) cc_final: 0.8644 (mmtt) REVERT: G 235 ASP cc_start: 0.8608 (t0) cc_final: 0.8384 (t0) REVERT: H 85 GLU cc_start: 0.8447 (tt0) cc_final: 0.8108 (tm-30) REVERT: H 90 MET cc_start: 0.9020 (ttp) cc_final: 0.8784 (tmm) REVERT: H 92 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8054 (mt-10) REVERT: H 110 THR cc_start: 0.9018 (OUTLIER) cc_final: 0.8680 (p) REVERT: H 165 LYS cc_start: 0.8520 (ptpt) cc_final: 0.7746 (tmtt) REVERT: H 176 LYS cc_start: 0.8859 (mttm) cc_final: 0.8469 (mmtp) REVERT: H 178 TYR cc_start: 0.8618 (m-80) cc_final: 0.8250 (m-80) REVERT: H 206 TRP cc_start: 0.8167 (p-90) cc_final: 0.7765 (p-90) REVERT: H 236 GLN cc_start: 0.9062 (mp10) cc_final: 0.8576 (mp10) REVERT: H 260 THR cc_start: 0.8750 (p) cc_final: 0.8505 (t) REVERT: H 290 LYS cc_start: 0.9029 (mttt) cc_final: 0.8577 (mtmm) REVERT: I 13 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8100 (pm20) REVERT: I 21 LYS cc_start: 0.8940 (ttmm) cc_final: 0.8626 (tmtt) REVERT: I 87 GLN cc_start: 0.8282 (tt0) cc_final: 0.7988 (tp-100) REVERT: I 119 ASN cc_start: 0.8831 (t0) cc_final: 0.8184 (t0) REVERT: I 121 ASP cc_start: 0.8470 (t70) cc_final: 0.8016 (m-30) REVERT: I 147 GLN cc_start: 0.8747 (tt0) cc_final: 0.8464 (tt0) REVERT: I 154 LYS cc_start: 0.8777 (mttt) cc_final: 0.8325 (mtpp) REVERT: I 165 LYS cc_start: 0.8577 (tttt) cc_final: 0.8330 (tmmt) REVERT: I 240 ASN cc_start: 0.8568 (t0) cc_final: 0.8229 (t0) outliers start: 101 outliers final: 64 residues processed: 523 average time/residue: 0.1379 time to fit residues: 112.3898 Evaluate side-chains 478 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 407 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain C residue 11 GLN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 215 ASN Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 46 ASN Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 186 SER Chi-restraints excluded: chain I residue 228 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 137 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 83 optimal weight: 0.0980 chunk 136 optimal weight: 0.4980 chunk 249 optimal weight: 0.7980 chunk 235 optimal weight: 0.0570 chunk 49 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 ASN A 243 GLN A 255 HIS B 11 GLN B 243 GLN B 255 HIS B 263 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN C 263 ASN D 48 ASN D 243 GLN ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 GLN E 147 GLN E 255 HIS ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 GLN F 243 GLN G 11 GLN G 263 ASN H 48 ASN H 263 ASN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 243 GLN I 255 HIS I 263 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.120321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.098585 restraints weight = 27939.097| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.38 r_work: 0.3227 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21024 Z= 0.102 Angle : 0.463 7.708 28494 Z= 0.250 Chirality : 0.047 0.174 3168 Planarity : 0.003 0.028 3600 Dihedral : 3.957 27.220 2846 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.94 % Allowed : 17.44 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.66 (0.15), residues: 2574 helix: None (None), residues: 0 sheet: -1.79 (0.14), residues: 1287 loop : -1.62 (0.15), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 159 TYR 0.010 0.001 TYR B 218 PHE 0.022 0.001 PHE G 209 TRP 0.034 0.002 TRP G 206 HIS 0.005 0.001 HIS E 81 Details of bonding type rmsd covalent geometry : bond 0.00238 (21024) covalent geometry : angle 0.46314 (28494) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 496 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8711 (mt-10) cc_final: 0.7983 (pm20) REVERT: A 21 LYS cc_start: 0.8796 (tppt) cc_final: 0.8468 (tmtt) REVERT: A 44 MET cc_start: 0.8179 (ttm) cc_final: 0.7898 (ptm) REVERT: A 87 GLN cc_start: 0.8230 (tt0) cc_final: 0.8001 (tp40) REVERT: A 102 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8287 (mt-10) REVERT: A 165 LYS cc_start: 0.8330 (tmmt) cc_final: 0.8022 (tmmt) REVERT: A 176 LYS cc_start: 0.8956 (mttm) cc_final: 0.8545 (mmmt) REVERT: A 240 ASN cc_start: 0.8430 (t0) cc_final: 0.8119 (t0) REVERT: A 257 ASP cc_start: 0.8629 (m-30) cc_final: 0.7956 (m-30) REVERT: B 13 GLU cc_start: 0.8485 (mt-10) cc_final: 0.7799 (pm20) REVERT: B 19 VAL cc_start: 0.9154 (t) cc_final: 0.8792 (p) REVERT: B 44 MET cc_start: 0.8388 (ttm) cc_final: 0.7920 (tpp) REVERT: B 70 PHE cc_start: 0.7814 (t80) cc_final: 0.7465 (t80) REVERT: B 85 GLU cc_start: 0.8080 (tt0) cc_final: 0.7660 (tm-30) REVERT: B 94 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7968 (mt-10) REVERT: B 167 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8104 (mp0) REVERT: B 176 LYS cc_start: 0.9162 (mttm) cc_final: 0.8852 (mmtp) REVERT: B 212 LYS cc_start: 0.8552 (tttt) cc_final: 0.8297 (ttpp) REVERT: B 257 ASP cc_start: 0.8987 (OUTLIER) cc_final: 0.8712 (m-30) REVERT: B 265 TYR cc_start: 0.9071 (t80) cc_final: 0.8275 (t80) REVERT: B 292 ILE cc_start: 0.8798 (mt) cc_final: 0.8557 (tt) REVERT: B 293 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8706 (pp) REVERT: C 44 MET cc_start: 0.8290 (ttm) cc_final: 0.7851 (mpp) REVERT: C 45 LYS cc_start: 0.8870 (tttt) cc_final: 0.8457 (tttp) REVERT: C 52 ARG cc_start: 0.7837 (ttt-90) cc_final: 0.7625 (ttt180) REVERT: C 97 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8139 (mt-10) REVERT: C 154 LYS cc_start: 0.8946 (mttt) cc_final: 0.8383 (mtpp) REVERT: C 159 ARG cc_start: 0.8720 (ttm110) cc_final: 0.8208 (ttp80) REVERT: C 165 LYS cc_start: 0.8530 (tmtt) cc_final: 0.8257 (tmmt) REVERT: C 174 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8514 (mp0) REVERT: C 176 LYS cc_start: 0.9191 (mttm) cc_final: 0.8737 (mmtp) REVERT: C 236 GLN cc_start: 0.8846 (mp10) cc_final: 0.8191 (mp10) REVERT: C 257 ASP cc_start: 0.8534 (m-30) cc_final: 0.8159 (m-30) REVERT: C 292 ILE cc_start: 0.8809 (mt) cc_final: 0.8488 (tt) REVERT: D 13 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8193 (pm20) REVERT: D 19 VAL cc_start: 0.9239 (t) cc_final: 0.8848 (p) REVERT: D 44 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8001 (tpp) REVERT: D 85 GLU cc_start: 0.8170 (tt0) cc_final: 0.7780 (tm-30) REVERT: D 90 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8567 (tmm) REVERT: D 94 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: D 154 LYS cc_start: 0.8844 (mttt) cc_final: 0.8359 (mtpp) REVERT: D 179 MET cc_start: 0.8918 (ttm) cc_final: 0.8666 (ttt) REVERT: D 186 SER cc_start: 0.9210 (OUTLIER) cc_final: 0.8876 (p) REVERT: D 240 ASN cc_start: 0.8450 (t0) cc_final: 0.7824 (t0) REVERT: D 265 TYR cc_start: 0.8946 (t80) cc_final: 0.8439 (t80) REVERT: E 13 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8302 (pm20) REVERT: E 35 ASP cc_start: 0.8663 (t70) cc_final: 0.8418 (t0) REVERT: E 44 MET cc_start: 0.8416 (ttm) cc_final: 0.8088 (tpp) REVERT: E 85 GLU cc_start: 0.8170 (tt0) cc_final: 0.7875 (tm-30) REVERT: E 90 MET cc_start: 0.8861 (ttp) cc_final: 0.8537 (tmm) REVERT: E 110 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8274 (p) REVERT: E 154 LYS cc_start: 0.8953 (mttt) cc_final: 0.8338 (mtpp) REVERT: E 165 LYS cc_start: 0.8507 (tttt) cc_final: 0.8214 (tmmt) REVERT: E 167 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8004 (mp0) REVERT: E 176 LYS cc_start: 0.9046 (mmtt) cc_final: 0.8782 (mmmt) REVERT: E 192 LEU cc_start: 0.9196 (mt) cc_final: 0.8907 (mt) REVERT: E 209 PHE cc_start: 0.9227 (m-80) cc_final: 0.8763 (m-80) REVERT: E 292 ILE cc_start: 0.8966 (mt) cc_final: 0.8639 (tt) REVERT: F 52 ARG cc_start: 0.8145 (ttt-90) cc_final: 0.7824 (mtp85) REVERT: F 90 MET cc_start: 0.8930 (ttp) cc_final: 0.8536 (tmm) REVERT: F 94 GLU cc_start: 0.7852 (tt0) cc_final: 0.7436 (mt-10) REVERT: F 155 ILE cc_start: 0.9077 (mt) cc_final: 0.8754 (pt) REVERT: F 165 LYS cc_start: 0.8512 (tttt) cc_final: 0.8233 (tmmt) REVERT: F 176 LYS cc_start: 0.8958 (mttm) cc_final: 0.8620 (mmtp) REVERT: F 257 ASP cc_start: 0.8490 (m-30) cc_final: 0.7910 (m-30) REVERT: F 265 TYR cc_start: 0.9005 (t80) cc_final: 0.8724 (t80) REVERT: F 292 ILE cc_start: 0.9027 (mt) cc_final: 0.8670 (tt) REVERT: G 42 LYS cc_start: 0.9200 (tttt) cc_final: 0.8568 (mtmm) REVERT: G 94 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7770 (mp0) REVERT: G 165 LYS cc_start: 0.8560 (tttt) cc_final: 0.8349 (tmmt) REVERT: G 176 LYS cc_start: 0.8988 (mttm) cc_final: 0.8618 (mmtt) REVERT: G 235 ASP cc_start: 0.8468 (t0) cc_final: 0.8231 (t0) REVERT: G 239 ASP cc_start: 0.8667 (t0) cc_final: 0.8447 (t0) REVERT: G 257 ASP cc_start: 0.8835 (m-30) cc_final: 0.8183 (m-30) REVERT: H 85 GLU cc_start: 0.8492 (tt0) cc_final: 0.8064 (tm-30) REVERT: H 90 MET cc_start: 0.8907 (ttp) cc_final: 0.8540 (tmm) REVERT: H 119 ASN cc_start: 0.8963 (t0) cc_final: 0.8640 (t0) REVERT: H 154 LYS cc_start: 0.8872 (mttt) cc_final: 0.8397 (mtpp) REVERT: H 174 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8476 (mt-10) REVERT: H 176 LYS cc_start: 0.9002 (mttm) cc_final: 0.8607 (mmtp) REVERT: H 206 TRP cc_start: 0.8099 (p-90) cc_final: 0.7781 (p-90) REVERT: H 236 GLN cc_start: 0.9088 (mp10) cc_final: 0.8858 (mp10) REVERT: H 290 LYS cc_start: 0.8808 (mttt) cc_final: 0.8435 (mmtp) REVERT: H 292 ILE cc_start: 0.8951 (mt) cc_final: 0.8697 (tt) REVERT: I 13 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8082 (pm20) REVERT: I 21 LYS cc_start: 0.8849 (ttmm) cc_final: 0.8419 (tptt) REVERT: I 90 MET cc_start: 0.9104 (ttp) cc_final: 0.8796 (tmm) REVERT: I 128 GLU cc_start: 0.8322 (pt0) cc_final: 0.7932 (tt0) REVERT: I 147 GLN cc_start: 0.8633 (tt0) cc_final: 0.8357 (tt0) REVERT: I 165 LYS cc_start: 0.8585 (tttt) cc_final: 0.8248 (tmmt) REVERT: I 221 TYR cc_start: 0.9182 (m-80) cc_final: 0.8719 (m-80) REVERT: I 236 GLN cc_start: 0.8926 (mp10) cc_final: 0.8367 (mp10) REVERT: I 240 ASN cc_start: 0.8456 (t0) cc_final: 0.7992 (t0) REVERT: I 265 TYR cc_start: 0.8975 (t80) cc_final: 0.8764 (t80) outliers start: 89 outliers final: 43 residues processed: 554 average time/residue: 0.1330 time to fit residues: 114.9406 Evaluate side-chains 477 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 426 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 46 ASN Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 296 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 7 optimal weight: 8.9990 chunk 163 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 248 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 ASN A 243 GLN B 11 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN C 263 ASN D 243 GLN ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 GLN ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN E 160 GLN E 243 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 HIS F 147 GLN F 215 ASN F 243 GLN F 263 ASN G 11 GLN ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 263 ASN H 243 GLN ** H 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 263 ASN I 11 GLN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 243 GLN I 263 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.115487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.093400 restraints weight = 28161.269| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.38 r_work: 0.3167 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 21024 Z= 0.218 Angle : 0.502 8.239 28494 Z= 0.270 Chirality : 0.048 0.196 3168 Planarity : 0.003 0.039 3600 Dihedral : 4.004 28.660 2845 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.07 % Allowed : 17.84 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.62 (0.15), residues: 2574 helix: None (None), residues: 0 sheet: -1.78 (0.14), residues: 1287 loop : -1.56 (0.15), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 175 TYR 0.016 0.001 TYR H 178 PHE 0.019 0.002 PHE D 209 TRP 0.036 0.002 TRP E 206 HIS 0.006 0.001 HIS B 103 Details of bonding type rmsd covalent geometry : bond 0.00501 (21024) covalent geometry : angle 0.50226 (28494) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 433 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8028 (pm20) REVERT: A 21 LYS cc_start: 0.8863 (tppt) cc_final: 0.8483 (tmtt) REVERT: A 60 ILE cc_start: 0.8765 (mp) cc_final: 0.8293 (tt) REVERT: A 87 GLN cc_start: 0.8263 (tt0) cc_final: 0.8005 (tp40) REVERT: A 102 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8237 (mt-10) REVERT: A 159 ARG cc_start: 0.8673 (ttp-110) cc_final: 0.8322 (ttp-110) REVERT: A 165 LYS cc_start: 0.8368 (tmmt) cc_final: 0.8008 (tmmt) REVERT: A 176 LYS cc_start: 0.8972 (mttm) cc_final: 0.8546 (mmmt) REVERT: A 240 ASN cc_start: 0.8437 (t0) cc_final: 0.8135 (t0) REVERT: A 257 ASP cc_start: 0.8822 (m-30) cc_final: 0.7921 (m-30) REVERT: B 13 GLU cc_start: 0.8598 (mt-10) cc_final: 0.7901 (pm20) REVERT: B 19 VAL cc_start: 0.9274 (t) cc_final: 0.8942 (p) REVERT: B 44 MET cc_start: 0.8459 (ttm) cc_final: 0.8140 (ttm) REVERT: B 70 PHE cc_start: 0.7862 (t80) cc_final: 0.7515 (t80) REVERT: B 77 VAL cc_start: 0.9040 (t) cc_final: 0.8807 (p) REVERT: B 85 GLU cc_start: 0.8210 (tt0) cc_final: 0.7745 (tm-30) REVERT: B 94 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8143 (mt-10) REVERT: B 127 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7915 (mm) REVERT: B 167 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8240 (mp0) REVERT: B 176 LYS cc_start: 0.9150 (mttm) cc_final: 0.8858 (mmtp) REVERT: B 212 LYS cc_start: 0.8546 (tttt) cc_final: 0.8276 (ttpp) REVERT: B 265 TYR cc_start: 0.9090 (t80) cc_final: 0.8364 (t80) REVERT: B 292 ILE cc_start: 0.8890 (mt) cc_final: 0.8583 (tt) REVERT: B 293 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8819 (pp) REVERT: C 14 VAL cc_start: 0.8637 (OUTLIER) cc_final: 0.8415 (p) REVERT: C 44 MET cc_start: 0.8318 (ttm) cc_final: 0.7894 (mpp) REVERT: C 45 LYS cc_start: 0.8915 (tttt) cc_final: 0.8562 (tttp) REVERT: C 52 ARG cc_start: 0.7966 (ttt-90) cc_final: 0.7757 (ttt180) REVERT: C 94 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7560 (mp0) REVERT: C 128 GLU cc_start: 0.8302 (pt0) cc_final: 0.8024 (pt0) REVERT: C 147 GLN cc_start: 0.8834 (tt0) cc_final: 0.8546 (tp40) REVERT: C 154 LYS cc_start: 0.8968 (mttt) cc_final: 0.8411 (mtpp) REVERT: C 159 ARG cc_start: 0.8829 (ttm110) cc_final: 0.8269 (ttp80) REVERT: C 174 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8262 (mp0) REVERT: C 176 LYS cc_start: 0.9146 (mttm) cc_final: 0.8650 (mmtp) REVERT: C 236 GLN cc_start: 0.8699 (mp10) cc_final: 0.7835 (mp10) REVERT: C 240 ASN cc_start: 0.8353 (t0) cc_final: 0.8095 (t0) REVERT: C 243 GLN cc_start: 0.8613 (pt0) cc_final: 0.8406 (pt0) REVERT: C 257 ASP cc_start: 0.8471 (m-30) cc_final: 0.7795 (m-30) REVERT: C 275 ASP cc_start: 0.8565 (m-30) cc_final: 0.8359 (m-30) REVERT: C 292 ILE cc_start: 0.8879 (mt) cc_final: 0.8510 (tt) REVERT: D 13 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8074 (pm20) REVERT: D 44 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8119 (tpp) REVERT: D 85 GLU cc_start: 0.8252 (tt0) cc_final: 0.7885 (tm-30) REVERT: D 94 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7701 (mp0) REVERT: D 154 LYS cc_start: 0.8849 (mttt) cc_final: 0.8437 (mttm) REVERT: D 186 SER cc_start: 0.9123 (OUTLIER) cc_final: 0.8801 (p) REVERT: D 240 ASN cc_start: 0.8349 (t0) cc_final: 0.7962 (t0) REVERT: D 263 ASN cc_start: 0.8738 (t0) cc_final: 0.8073 (t0) REVERT: D 265 TYR cc_start: 0.8994 (t80) cc_final: 0.7831 (t80) REVERT: E 35 ASP cc_start: 0.8723 (t70) cc_final: 0.8488 (t0) REVERT: E 44 MET cc_start: 0.8518 (ttm) cc_final: 0.8085 (tpp) REVERT: E 70 PHE cc_start: 0.7736 (OUTLIER) cc_final: 0.6882 (t80) REVERT: E 85 GLU cc_start: 0.8260 (tt0) cc_final: 0.8007 (tm-30) REVERT: E 90 MET cc_start: 0.8951 (ttp) cc_final: 0.8552 (tmm) REVERT: E 110 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8359 (p) REVERT: E 154 LYS cc_start: 0.8981 (mttt) cc_final: 0.8483 (mttm) REVERT: E 165 LYS cc_start: 0.8491 (tttt) cc_final: 0.8215 (tmmt) REVERT: E 167 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8114 (mp0) REVERT: E 176 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8745 (mmmt) REVERT: E 192 LEU cc_start: 0.9189 (mt) cc_final: 0.8901 (mt) REVERT: F 52 ARG cc_start: 0.8301 (ttt-90) cc_final: 0.7908 (mtp85) REVERT: F 90 MET cc_start: 0.8993 (ttp) cc_final: 0.8572 (tmm) REVERT: F 94 GLU cc_start: 0.8172 (tt0) cc_final: 0.7773 (mt-10) REVERT: F 155 ILE cc_start: 0.9044 (mt) cc_final: 0.8711 (pt) REVERT: F 165 LYS cc_start: 0.8427 (tttt) cc_final: 0.8172 (tmmt) REVERT: F 176 LYS cc_start: 0.8979 (mttm) cc_final: 0.8639 (mmtt) REVERT: F 240 ASN cc_start: 0.8470 (t0) cc_final: 0.8129 (t0) REVERT: F 263 ASN cc_start: 0.8985 (t0) cc_final: 0.8748 (t0) REVERT: F 292 ILE cc_start: 0.8993 (mt) cc_final: 0.8771 (mt) REVERT: G 42 LYS cc_start: 0.9220 (tttt) cc_final: 0.8564 (mtmm) REVERT: G 60 ILE cc_start: 0.8782 (mp) cc_final: 0.8376 (tt) REVERT: G 94 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7791 (mp0) REVERT: G 165 LYS cc_start: 0.8591 (tttt) cc_final: 0.8277 (tmmt) REVERT: G 167 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8280 (mm-30) REVERT: G 176 LYS cc_start: 0.8994 (mttm) cc_final: 0.8616 (mmtt) REVERT: G 236 GLN cc_start: 0.8859 (mp10) cc_final: 0.8585 (mp10) REVERT: H 85 GLU cc_start: 0.8571 (tt0) cc_final: 0.8167 (tm-30) REVERT: H 90 MET cc_start: 0.8943 (ttp) cc_final: 0.8622 (tmm) REVERT: H 127 ILE cc_start: 0.8686 (mt) cc_final: 0.8421 (mm) REVERT: H 154 LYS cc_start: 0.8906 (mttt) cc_final: 0.8455 (mtpp) REVERT: H 176 LYS cc_start: 0.8852 (mttm) cc_final: 0.8437 (mmtp) REVERT: H 178 TYR cc_start: 0.8688 (m-80) cc_final: 0.8385 (m-80) REVERT: H 206 TRP cc_start: 0.8134 (p-90) cc_final: 0.7829 (p-90) REVERT: H 236 GLN cc_start: 0.9052 (mp10) cc_final: 0.8823 (mp10) REVERT: H 260 THR cc_start: 0.8779 (p) cc_final: 0.8477 (t) REVERT: H 290 LYS cc_start: 0.8815 (mttt) cc_final: 0.8389 (mtmm) REVERT: H 292 ILE cc_start: 0.8909 (mt) cc_final: 0.8596 (tt) REVERT: I 13 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8071 (pm20) REVERT: I 21 LYS cc_start: 0.8893 (ttmm) cc_final: 0.8479 (tptt) REVERT: I 35 ASP cc_start: 0.8324 (t0) cc_final: 0.7922 (t0) REVERT: I 90 MET cc_start: 0.9095 (ttp) cc_final: 0.8775 (tmm) REVERT: I 147 GLN cc_start: 0.8677 (tt0) cc_final: 0.8371 (tt0) REVERT: I 154 LYS cc_start: 0.8692 (mttt) cc_final: 0.8159 (mtpp) REVERT: I 165 LYS cc_start: 0.8478 (tttt) cc_final: 0.8257 (tmmt) REVERT: I 236 GLN cc_start: 0.8938 (mp10) cc_final: 0.8543 (mp10) REVERT: I 240 ASN cc_start: 0.8481 (t0) cc_final: 0.8003 (t0) outliers start: 92 outliers final: 62 residues processed: 499 average time/residue: 0.1285 time to fit residues: 101.0983 Evaluate side-chains 477 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 406 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain C residue 11 GLN Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 46 ASN Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 121 ASP Chi-restraints excluded: chain I residue 186 SER Chi-restraints excluded: chain I residue 296 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 155 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 219 optimal weight: 0.8980 chunk 245 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 198 optimal weight: 0.6980 chunk 125 optimal weight: 0.6980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN D 243 GLN ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 GLN ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 HIS F 147 GLN F 215 ASN F 243 GLN G 11 GLN G 117 GLN G 263 ASN H 48 ASN H 263 ASN I 11 GLN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 243 GLN I 263 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.117202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.095250 restraints weight = 28026.840| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.38 r_work: 0.3185 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21024 Z= 0.176 Angle : 0.480 7.241 28494 Z= 0.259 Chirality : 0.047 0.266 3168 Planarity : 0.003 0.035 3600 Dihedral : 3.924 27.872 2845 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.98 % Allowed : 18.33 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.57 (0.15), residues: 2574 helix: None (None), residues: 0 sheet: -1.73 (0.14), residues: 1287 loop : -1.55 (0.15), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 175 TYR 0.013 0.001 TYR E 178 PHE 0.020 0.001 PHE I 198 TRP 0.042 0.002 TRP G 206 HIS 0.005 0.001 HIS E 81 Details of bonding type rmsd covalent geometry : bond 0.00404 (21024) covalent geometry : angle 0.47964 (28494) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 425 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8088 (pm20) REVERT: A 21 LYS cc_start: 0.8842 (tppt) cc_final: 0.8466 (tmtt) REVERT: A 44 MET cc_start: 0.8518 (ptt) cc_final: 0.8302 (ptm) REVERT: A 60 ILE cc_start: 0.8697 (mp) cc_final: 0.8202 (tt) REVERT: A 87 GLN cc_start: 0.8256 (tt0) cc_final: 0.7987 (tp40) REVERT: A 102 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8221 (mt-10) REVERT: A 165 LYS cc_start: 0.8436 (tmmt) cc_final: 0.8044 (tmmt) REVERT: A 176 LYS cc_start: 0.8976 (mttm) cc_final: 0.8546 (mmmt) REVERT: A 240 ASN cc_start: 0.8456 (t0) cc_final: 0.8200 (t0) REVERT: A 257 ASP cc_start: 0.8873 (m-30) cc_final: 0.7928 (m-30) REVERT: B 13 GLU cc_start: 0.8552 (mt-10) cc_final: 0.7775 (pm20) REVERT: B 19 VAL cc_start: 0.9267 (t) cc_final: 0.8933 (p) REVERT: B 44 MET cc_start: 0.8391 (ttm) cc_final: 0.8066 (ttm) REVERT: B 70 PHE cc_start: 0.7839 (t80) cc_final: 0.7546 (t80) REVERT: B 77 VAL cc_start: 0.9095 (t) cc_final: 0.8879 (p) REVERT: B 85 GLU cc_start: 0.8204 (tt0) cc_final: 0.7737 (tm-30) REVERT: B 94 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8120 (mt-10) REVERT: B 127 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7920 (mm) REVERT: B 167 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8104 (mp0) REVERT: B 176 LYS cc_start: 0.9182 (mttm) cc_final: 0.8882 (mmtp) REVERT: B 212 LYS cc_start: 0.8519 (tttt) cc_final: 0.8265 (ttpp) REVERT: B 292 ILE cc_start: 0.8872 (mt) cc_final: 0.8566 (tt) REVERT: B 293 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8826 (pp) REVERT: C 14 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8387 (p) REVERT: C 45 LYS cc_start: 0.8923 (tttt) cc_final: 0.8588 (tttp) REVERT: C 52 ARG cc_start: 0.7915 (ttt-90) cc_final: 0.7700 (ttt180) REVERT: C 94 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7526 (mp0) REVERT: C 128 GLU cc_start: 0.8291 (pt0) cc_final: 0.7990 (pt0) REVERT: C 147 GLN cc_start: 0.8821 (tt0) cc_final: 0.8540 (tp40) REVERT: C 154 LYS cc_start: 0.9011 (mttt) cc_final: 0.8453 (mtpp) REVERT: C 174 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8273 (mp0) REVERT: C 176 LYS cc_start: 0.9127 (mttm) cc_final: 0.8611 (mmtp) REVERT: C 236 GLN cc_start: 0.9016 (mp10) cc_final: 0.8489 (mp10) REVERT: C 257 ASP cc_start: 0.8524 (m-30) cc_final: 0.7863 (m-30) REVERT: C 275 ASP cc_start: 0.8585 (m-30) cc_final: 0.8381 (m-30) REVERT: C 292 ILE cc_start: 0.8910 (mt) cc_final: 0.8520 (tt) REVERT: D 13 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8064 (pm20) REVERT: D 44 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8106 (tpp) REVERT: D 85 GLU cc_start: 0.8233 (tt0) cc_final: 0.7887 (tm-30) REVERT: D 94 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7710 (mp0) REVERT: D 154 LYS cc_start: 0.8852 (mttt) cc_final: 0.8432 (mttm) REVERT: D 186 SER cc_start: 0.9116 (OUTLIER) cc_final: 0.8786 (p) REVERT: D 240 ASN cc_start: 0.8340 (t0) cc_final: 0.7921 (t0) REVERT: D 265 TYR cc_start: 0.8994 (t80) cc_final: 0.7906 (t80) REVERT: D 268 ARG cc_start: 0.8683 (mtm-85) cc_final: 0.8395 (ttm110) REVERT: E 35 ASP cc_start: 0.8713 (t70) cc_final: 0.8462 (t0) REVERT: E 44 MET cc_start: 0.8512 (ttm) cc_final: 0.8088 (tpp) REVERT: E 70 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7058 (t80) REVERT: E 85 GLU cc_start: 0.8222 (tt0) cc_final: 0.7981 (tm-30) REVERT: E 90 MET cc_start: 0.8934 (ttp) cc_final: 0.8555 (tmm) REVERT: E 110 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8352 (p) REVERT: E 154 LYS cc_start: 0.8979 (mttt) cc_final: 0.8487 (mttm) REVERT: E 165 LYS cc_start: 0.8493 (tttt) cc_final: 0.8208 (tmmt) REVERT: E 167 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8090 (mp0) REVERT: E 176 LYS cc_start: 0.8988 (mmtt) cc_final: 0.8739 (mmmt) REVERT: E 192 LEU cc_start: 0.9190 (mt) cc_final: 0.8874 (mt) REVERT: F 52 ARG cc_start: 0.8270 (ttt-90) cc_final: 0.7884 (mtp85) REVERT: F 90 MET cc_start: 0.8972 (ttp) cc_final: 0.8544 (tmm) REVERT: F 94 GLU cc_start: 0.8114 (tt0) cc_final: 0.7701 (mt-10) REVERT: F 155 ILE cc_start: 0.9027 (mt) cc_final: 0.8704 (pt) REVERT: F 165 LYS cc_start: 0.8420 (tttt) cc_final: 0.8172 (tmmt) REVERT: F 176 LYS cc_start: 0.8973 (mttm) cc_final: 0.8626 (mmtt) REVERT: F 240 ASN cc_start: 0.8435 (t0) cc_final: 0.8105 (t0) REVERT: F 292 ILE cc_start: 0.8963 (mt) cc_final: 0.8753 (mt) REVERT: G 42 LYS cc_start: 0.9208 (tttt) cc_final: 0.8495 (mtmm) REVERT: G 60 ILE cc_start: 0.8743 (mp) cc_final: 0.8357 (tt) REVERT: G 94 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7780 (mp0) REVERT: G 165 LYS cc_start: 0.8592 (tttt) cc_final: 0.8376 (tmmt) REVERT: G 167 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8224 (mm-30) REVERT: G 176 LYS cc_start: 0.8993 (mttm) cc_final: 0.8616 (mmtt) REVERT: H 85 GLU cc_start: 0.8564 (tt0) cc_final: 0.8171 (tm-30) REVERT: H 90 MET cc_start: 0.8953 (ttp) cc_final: 0.8616 (tmm) REVERT: H 92 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7993 (mt-10) REVERT: H 154 LYS cc_start: 0.8907 (mttt) cc_final: 0.8366 (mtpp) REVERT: H 176 LYS cc_start: 0.8853 (mttm) cc_final: 0.8438 (mmtp) REVERT: H 178 TYR cc_start: 0.8705 (m-80) cc_final: 0.8382 (m-80) REVERT: H 206 TRP cc_start: 0.8148 (p-90) cc_final: 0.7870 (p-90) REVERT: H 236 GLN cc_start: 0.9089 (mp10) cc_final: 0.8417 (mp10) REVERT: H 260 THR cc_start: 0.8761 (p) cc_final: 0.8465 (t) REVERT: H 290 LYS cc_start: 0.8806 (mttt) cc_final: 0.8384 (mtmm) REVERT: H 292 ILE cc_start: 0.8985 (mt) cc_final: 0.8682 (tt) REVERT: I 13 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8043 (pm20) REVERT: I 21 LYS cc_start: 0.8873 (ttmm) cc_final: 0.8460 (tptt) REVERT: I 35 ASP cc_start: 0.8297 (t0) cc_final: 0.7900 (t0) REVERT: I 90 MET cc_start: 0.9073 (ttp) cc_final: 0.8765 (tmm) REVERT: I 128 GLU cc_start: 0.8395 (pt0) cc_final: 0.7970 (tt0) REVERT: I 147 GLN cc_start: 0.8642 (tt0) cc_final: 0.8349 (tt0) REVERT: I 154 LYS cc_start: 0.8665 (mttt) cc_final: 0.8162 (mtpp) REVERT: I 165 LYS cc_start: 0.8548 (tttt) cc_final: 0.8303 (tmmt) REVERT: I 240 ASN cc_start: 0.8502 (t0) cc_final: 0.8051 (t0) REVERT: I 257 ASP cc_start: 0.8599 (t70) cc_final: 0.7963 (m-30) REVERT: I 293 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9021 (pp) outliers start: 90 outliers final: 68 residues processed: 490 average time/residue: 0.1295 time to fit residues: 100.0043 Evaluate side-chains 486 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 408 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain C residue 11 GLN Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 46 ASN Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 121 ASP Chi-restraints excluded: chain I residue 186 SER Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 296 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 93 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 175 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 chunk 231 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 ASN A 243 GLN B 11 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN C 263 ASN ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 GLN ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 GLN F 263 ASN G 11 GLN H 263 ASN I 11 GLN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 243 GLN I 263 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.119182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.097559 restraints weight = 28106.681| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.31 r_work: 0.3193 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21024 Z= 0.167 Angle : 0.479 6.826 28494 Z= 0.259 Chirality : 0.047 0.318 3168 Planarity : 0.003 0.034 3600 Dihedral : 3.887 28.046 2845 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.98 % Allowed : 18.50 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.64 (0.15), residues: 2574 helix: None (None), residues: 0 sheet: -1.79 (0.14), residues: 1332 loop : -1.55 (0.15), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 175 TYR 0.011 0.001 TYR H 178 PHE 0.017 0.002 PHE B 209 TRP 0.045 0.002 TRP E 206 HIS 0.005 0.001 HIS E 81 Details of bonding type rmsd covalent geometry : bond 0.00386 (21024) covalent geometry : angle 0.47885 (28494) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 423 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8081 (pm20) REVERT: A 21 LYS cc_start: 0.8830 (tppt) cc_final: 0.8454 (tmtt) REVERT: A 44 MET cc_start: 0.8450 (ptt) cc_final: 0.8246 (ptm) REVERT: A 60 ILE cc_start: 0.8686 (mp) cc_final: 0.8191 (tt) REVERT: A 87 GLN cc_start: 0.8261 (tt0) cc_final: 0.8000 (tp40) REVERT: A 102 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8217 (mt-10) REVERT: A 165 LYS cc_start: 0.8358 (tmmt) cc_final: 0.8101 (tmmt) REVERT: A 176 LYS cc_start: 0.9094 (mttm) cc_final: 0.8673 (mmmt) REVERT: A 240 ASN cc_start: 0.8462 (t0) cc_final: 0.8193 (t0) REVERT: A 257 ASP cc_start: 0.8917 (m-30) cc_final: 0.8008 (m-30) REVERT: B 13 GLU cc_start: 0.8551 (mt-10) cc_final: 0.7767 (pm20) REVERT: B 19 VAL cc_start: 0.9233 (t) cc_final: 0.8899 (p) REVERT: B 21 LYS cc_start: 0.8807 (ttmm) cc_final: 0.8338 (tmtt) REVERT: B 44 MET cc_start: 0.8374 (ttm) cc_final: 0.8041 (ttm) REVERT: B 52 ARG cc_start: 0.7877 (tpt-90) cc_final: 0.7371 (mtp85) REVERT: B 77 VAL cc_start: 0.9107 (t) cc_final: 0.8907 (p) REVERT: B 85 GLU cc_start: 0.8216 (tt0) cc_final: 0.7716 (tm-30) REVERT: B 94 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7925 (mt-10) REVERT: B 167 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8088 (mp0) REVERT: B 176 LYS cc_start: 0.9185 (mttm) cc_final: 0.8878 (mmtp) REVERT: B 209 PHE cc_start: 0.7977 (m-10) cc_final: 0.7672 (m-10) REVERT: B 212 LYS cc_start: 0.8512 (tttt) cc_final: 0.8267 (ttpp) REVERT: B 217 MET cc_start: 0.8602 (pmm) cc_final: 0.8393 (ptp) REVERT: B 292 ILE cc_start: 0.8858 (mt) cc_final: 0.8560 (tt) REVERT: B 293 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8827 (pp) REVERT: C 14 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8351 (p) REVERT: C 44 MET cc_start: 0.8306 (ttm) cc_final: 0.7903 (mpp) REVERT: C 45 LYS cc_start: 0.8903 (tttt) cc_final: 0.8571 (tttp) REVERT: C 52 ARG cc_start: 0.7906 (ttt-90) cc_final: 0.7704 (ttt180) REVERT: C 90 MET cc_start: 0.8992 (ttp) cc_final: 0.8558 (tmm) REVERT: C 94 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7514 (mp0) REVERT: C 128 GLU cc_start: 0.8270 (pt0) cc_final: 0.7965 (pt0) REVERT: C 147 GLN cc_start: 0.8771 (tt0) cc_final: 0.8513 (tp40) REVERT: C 154 LYS cc_start: 0.9016 (mttt) cc_final: 0.8475 (mtpp) REVERT: C 159 ARG cc_start: 0.8884 (ttm110) cc_final: 0.8534 (ttp80) REVERT: C 174 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8267 (mp0) REVERT: C 176 LYS cc_start: 0.9125 (mttm) cc_final: 0.8605 (mmtp) REVERT: C 236 GLN cc_start: 0.8835 (mp10) cc_final: 0.8302 (mp10) REVERT: C 257 ASP cc_start: 0.8510 (m-30) cc_final: 0.7843 (m-30) REVERT: C 292 ILE cc_start: 0.8894 (mt) cc_final: 0.8514 (tt) REVERT: D 13 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8064 (pm20) REVERT: D 44 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8097 (tpp) REVERT: D 85 GLU cc_start: 0.8228 (tt0) cc_final: 0.7905 (tm-30) REVERT: D 94 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7687 (mp0) REVERT: D 154 LYS cc_start: 0.8855 (mttt) cc_final: 0.8429 (mttm) REVERT: D 186 SER cc_start: 0.9091 (OUTLIER) cc_final: 0.8750 (p) REVERT: D 240 ASN cc_start: 0.8470 (t0) cc_final: 0.8019 (t0) REVERT: D 257 ASP cc_start: 0.8914 (m-30) cc_final: 0.8479 (m-30) REVERT: D 265 TYR cc_start: 0.8996 (t80) cc_final: 0.7857 (t80) REVERT: D 268 ARG cc_start: 0.8700 (mtm-85) cc_final: 0.8420 (ttm110) REVERT: E 35 ASP cc_start: 0.8703 (t70) cc_final: 0.8455 (t0) REVERT: E 44 MET cc_start: 0.8526 (ttm) cc_final: 0.8090 (tpp) REVERT: E 70 PHE cc_start: 0.7898 (OUTLIER) cc_final: 0.7145 (t80) REVERT: E 85 GLU cc_start: 0.8236 (tt0) cc_final: 0.7993 (tm-30) REVERT: E 90 MET cc_start: 0.8913 (ttp) cc_final: 0.8560 (tmm) REVERT: E 110 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8342 (p) REVERT: E 134 ASP cc_start: 0.8738 (m-30) cc_final: 0.8329 (m-30) REVERT: E 154 LYS cc_start: 0.8970 (mttt) cc_final: 0.8482 (mttm) REVERT: E 165 LYS cc_start: 0.8487 (tttt) cc_final: 0.8212 (tmmt) REVERT: E 167 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7915 (mp0) REVERT: E 176 LYS cc_start: 0.8995 (mmtt) cc_final: 0.8739 (mmmt) REVERT: E 262 MET cc_start: 0.8406 (mmm) cc_final: 0.8161 (mmm) REVERT: F 52 ARG cc_start: 0.8257 (ttt-90) cc_final: 0.7905 (mtp85) REVERT: F 90 MET cc_start: 0.9010 (ttp) cc_final: 0.8564 (tmm) REVERT: F 94 GLU cc_start: 0.8133 (tt0) cc_final: 0.7678 (mt-10) REVERT: F 155 ILE cc_start: 0.9080 (mt) cc_final: 0.8753 (pt) REVERT: F 165 LYS cc_start: 0.8421 (tttt) cc_final: 0.8171 (tmmt) REVERT: F 176 LYS cc_start: 0.8976 (mttm) cc_final: 0.8608 (mmtt) REVERT: F 240 ASN cc_start: 0.8423 (t0) cc_final: 0.8085 (t0) REVERT: F 263 ASN cc_start: 0.8860 (t0) cc_final: 0.8460 (t0) REVERT: F 265 TYR cc_start: 0.8996 (t80) cc_final: 0.7946 (t80) REVERT: F 266 PHE cc_start: 0.8046 (m-80) cc_final: 0.7098 (m-80) REVERT: F 292 ILE cc_start: 0.8905 (mt) cc_final: 0.8540 (tt) REVERT: G 36 GLN cc_start: 0.8974 (tt0) cc_final: 0.8514 (tt0) REVERT: G 42 LYS cc_start: 0.9177 (tttt) cc_final: 0.8521 (mtmm) REVERT: G 60 ILE cc_start: 0.8736 (mp) cc_final: 0.8363 (tt) REVERT: G 94 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7904 (mp0) REVERT: G 176 LYS cc_start: 0.8997 (mttm) cc_final: 0.8617 (mmtt) REVERT: H 85 GLU cc_start: 0.8569 (tt0) cc_final: 0.8178 (tm-30) REVERT: H 90 MET cc_start: 0.8915 (ttp) cc_final: 0.8559 (tmm) REVERT: H 92 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7960 (mt-10) REVERT: H 154 LYS cc_start: 0.8923 (mttt) cc_final: 0.8411 (mtpp) REVERT: H 176 LYS cc_start: 0.8852 (mttm) cc_final: 0.8427 (mmtp) REVERT: H 178 TYR cc_start: 0.8678 (m-80) cc_final: 0.8355 (m-80) REVERT: H 206 TRP cc_start: 0.8161 (p-90) cc_final: 0.7884 (p-90) REVERT: H 236 GLN cc_start: 0.9093 (mp10) cc_final: 0.8401 (mp10) REVERT: H 260 THR cc_start: 0.8787 (p) cc_final: 0.8497 (t) REVERT: H 282 TYR cc_start: 0.7661 (m-80) cc_final: 0.7437 (m-80) REVERT: H 288 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7276 (mt-10) REVERT: H 290 LYS cc_start: 0.8781 (mttt) cc_final: 0.8348 (mtmm) REVERT: H 292 ILE cc_start: 0.8987 (mt) cc_final: 0.8703 (tt) REVERT: I 13 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8068 (pm20) REVERT: I 21 LYS cc_start: 0.8862 (ttmm) cc_final: 0.8445 (tptt) REVERT: I 35 ASP cc_start: 0.8335 (t0) cc_final: 0.7891 (t0) REVERT: I 90 MET cc_start: 0.9080 (ttp) cc_final: 0.8782 (tmm) REVERT: I 128 GLU cc_start: 0.8377 (pt0) cc_final: 0.7958 (tt0) REVERT: I 147 GLN cc_start: 0.8623 (tt0) cc_final: 0.8337 (tt0) REVERT: I 154 LYS cc_start: 0.8685 (mttt) cc_final: 0.8163 (mtpp) REVERT: I 165 LYS cc_start: 0.8540 (tttt) cc_final: 0.8288 (tmmt) REVERT: I 236 GLN cc_start: 0.8959 (mp10) cc_final: 0.8609 (mp10) REVERT: I 240 ASN cc_start: 0.8473 (t0) cc_final: 0.7880 (t0) REVERT: I 257 ASP cc_start: 0.8541 (t70) cc_final: 0.8135 (m-30) outliers start: 90 outliers final: 67 residues processed: 489 average time/residue: 0.1333 time to fit residues: 102.3054 Evaluate side-chains 496 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 421 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain C residue 11 GLN Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 46 ASN Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 121 ASP Chi-restraints excluded: chain I residue 186 SER Chi-restraints excluded: chain I residue 296 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 178 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 chunk 250 optimal weight: 10.0000 chunk 174 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN B 11 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN C 263 ASN ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 GLN ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 HIS F 147 GLN G 11 GLN G 263 ASN H 263 ASN I 11 GLN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 243 GLN I 263 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.119323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.098803 restraints weight = 28199.909| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.26 r_work: 0.3210 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 21024 Z= 0.194 Angle : 0.502 9.712 28494 Z= 0.270 Chirality : 0.048 0.303 3168 Planarity : 0.003 0.033 3600 Dihedral : 3.950 28.439 2845 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.72 % Allowed : 18.73 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.65 (0.15), residues: 2574 helix: None (None), residues: 0 sheet: -1.83 (0.14), residues: 1350 loop : -1.49 (0.15), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 159 TYR 0.012 0.001 TYR I 26 PHE 0.016 0.002 PHE D 209 TRP 0.047 0.002 TRP E 206 HIS 0.005 0.001 HIS E 81 Details of bonding type rmsd covalent geometry : bond 0.00446 (21024) covalent geometry : angle 0.50198 (28494) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 416 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8111 (pm20) REVERT: A 21 LYS cc_start: 0.8818 (tppt) cc_final: 0.8453 (tmtt) REVERT: A 44 MET cc_start: 0.8504 (ptt) cc_final: 0.8287 (ptm) REVERT: A 60 ILE cc_start: 0.8695 (mp) cc_final: 0.8204 (tt) REVERT: A 84 GLU cc_start: 0.8231 (tt0) cc_final: 0.7769 (mt-10) REVERT: A 87 GLN cc_start: 0.8275 (tt0) cc_final: 0.7986 (tp40) REVERT: A 130 MET cc_start: 0.8683 (ttm) cc_final: 0.8444 (ttm) REVERT: A 165 LYS cc_start: 0.8362 (tmmt) cc_final: 0.8124 (tmmt) REVERT: A 176 LYS cc_start: 0.9100 (mttm) cc_final: 0.8682 (mmmt) REVERT: A 240 ASN cc_start: 0.8400 (t0) cc_final: 0.8123 (t0) REVERT: A 257 ASP cc_start: 0.8956 (m-30) cc_final: 0.7982 (m-30) REVERT: B 13 GLU cc_start: 0.8588 (mt-10) cc_final: 0.7782 (pm20) REVERT: B 19 VAL cc_start: 0.9256 (t) cc_final: 0.8913 (p) REVERT: B 44 MET cc_start: 0.8334 (ttm) cc_final: 0.7992 (ttm) REVERT: B 85 GLU cc_start: 0.8230 (tt0) cc_final: 0.7733 (tm-30) REVERT: B 94 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7895 (mt-10) REVERT: B 167 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8070 (mp0) REVERT: B 176 LYS cc_start: 0.9173 (mttm) cc_final: 0.8869 (mmtp) REVERT: B 212 LYS cc_start: 0.8536 (tttt) cc_final: 0.8229 (ttpp) REVERT: B 292 ILE cc_start: 0.8882 (mt) cc_final: 0.8584 (tt) REVERT: B 293 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8853 (pp) REVERT: C 14 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.8335 (p) REVERT: C 44 MET cc_start: 0.8325 (ttm) cc_final: 0.7889 (mpp) REVERT: C 45 LYS cc_start: 0.8899 (tttt) cc_final: 0.8571 (tttp) REVERT: C 52 ARG cc_start: 0.7954 (ttt-90) cc_final: 0.7750 (ttt180) REVERT: C 94 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7548 (mp0) REVERT: C 128 GLU cc_start: 0.8320 (pt0) cc_final: 0.8007 (pt0) REVERT: C 154 LYS cc_start: 0.9063 (mttt) cc_final: 0.8521 (mtpp) REVERT: C 159 ARG cc_start: 0.8930 (ttm110) cc_final: 0.8512 (ttp80) REVERT: C 174 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8236 (mp0) REVERT: C 176 LYS cc_start: 0.9115 (mttm) cc_final: 0.8581 (mmtp) REVERT: C 229 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7696 (tm-30) REVERT: C 236 GLN cc_start: 0.8837 (mp10) cc_final: 0.8281 (mp10) REVERT: C 257 ASP cc_start: 0.8544 (m-30) cc_final: 0.8158 (m-30) REVERT: C 292 ILE cc_start: 0.8916 (mt) cc_final: 0.8535 (tt) REVERT: D 13 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8048 (pm20) REVERT: D 44 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8073 (tpp) REVERT: D 85 GLU cc_start: 0.8306 (tt0) cc_final: 0.7973 (tm-30) REVERT: D 94 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7692 (mp0) REVERT: D 154 LYS cc_start: 0.8860 (mttt) cc_final: 0.8428 (mttm) REVERT: D 186 SER cc_start: 0.9093 (OUTLIER) cc_final: 0.8756 (p) REVERT: D 240 ASN cc_start: 0.8468 (t0) cc_final: 0.8020 (t0) REVERT: D 257 ASP cc_start: 0.8864 (m-30) cc_final: 0.8388 (m-30) REVERT: D 265 TYR cc_start: 0.9029 (t80) cc_final: 0.7926 (t80) REVERT: D 268 ARG cc_start: 0.8704 (mtm-85) cc_final: 0.8436 (ttm110) REVERT: E 44 MET cc_start: 0.8551 (ttm) cc_final: 0.7994 (tpp) REVERT: E 70 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.6571 (t80) REVERT: E 85 GLU cc_start: 0.8295 (tt0) cc_final: 0.8045 (tm-30) REVERT: E 90 MET cc_start: 0.8940 (ttp) cc_final: 0.8546 (tmm) REVERT: E 110 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8362 (p) REVERT: E 134 ASP cc_start: 0.8739 (m-30) cc_final: 0.8292 (m-30) REVERT: E 154 LYS cc_start: 0.8978 (mttt) cc_final: 0.8474 (mttm) REVERT: E 165 LYS cc_start: 0.8506 (tttt) cc_final: 0.8218 (tmmt) REVERT: E 167 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8074 (mp0) REVERT: E 176 LYS cc_start: 0.9003 (mmtt) cc_final: 0.8754 (mmmt) REVERT: F 52 ARG cc_start: 0.8289 (ttt-90) cc_final: 0.7974 (mtp85) REVERT: F 94 GLU cc_start: 0.8113 (tt0) cc_final: 0.7690 (mt-10) REVERT: F 155 ILE cc_start: 0.9110 (mt) cc_final: 0.8763 (pt) REVERT: F 165 LYS cc_start: 0.8384 (tttt) cc_final: 0.8160 (tmmt) REVERT: F 176 LYS cc_start: 0.8985 (mttm) cc_final: 0.8622 (mmtt) REVERT: F 240 ASN cc_start: 0.8381 (t0) cc_final: 0.8058 (t0) REVERT: F 292 ILE cc_start: 0.8903 (mt) cc_final: 0.8537 (tt) REVERT: G 36 GLN cc_start: 0.8968 (tt0) cc_final: 0.8480 (tt0) REVERT: G 42 LYS cc_start: 0.9182 (tttt) cc_final: 0.8489 (mtmm) REVERT: G 60 ILE cc_start: 0.8707 (mp) cc_final: 0.8368 (tt) REVERT: G 94 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7891 (mp0) REVERT: G 165 LYS cc_start: 0.8162 (tmmt) cc_final: 0.7877 (tmmt) REVERT: G 176 LYS cc_start: 0.8989 (mttm) cc_final: 0.8615 (mmtt) REVERT: G 240 ASN cc_start: 0.8185 (t0) cc_final: 0.7907 (t0) REVERT: H 85 GLU cc_start: 0.8623 (tt0) cc_final: 0.8244 (tm-30) REVERT: H 90 MET cc_start: 0.8871 (ttp) cc_final: 0.8543 (tmm) REVERT: H 92 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7950 (mt-10) REVERT: H 154 LYS cc_start: 0.8960 (mttt) cc_final: 0.8440 (mtpp) REVERT: H 176 LYS cc_start: 0.8874 (mttm) cc_final: 0.8430 (mmtp) REVERT: H 178 TYR cc_start: 0.8713 (m-80) cc_final: 0.8381 (m-80) REVERT: H 206 TRP cc_start: 0.8173 (p-90) cc_final: 0.7888 (p-90) REVERT: H 236 GLN cc_start: 0.9081 (mp10) cc_final: 0.8379 (mp10) REVERT: H 288 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7300 (mt-10) REVERT: H 290 LYS cc_start: 0.8766 (mttt) cc_final: 0.8337 (mtmm) REVERT: H 292 ILE cc_start: 0.8948 (mt) cc_final: 0.8629 (tt) REVERT: I 13 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8067 (pm20) REVERT: I 21 LYS cc_start: 0.8864 (ttmm) cc_final: 0.8456 (tptt) REVERT: I 35 ASP cc_start: 0.8354 (t0) cc_final: 0.7907 (t0) REVERT: I 128 GLU cc_start: 0.8367 (pt0) cc_final: 0.7930 (tt0) REVERT: I 147 GLN cc_start: 0.8684 (tt0) cc_final: 0.8430 (tt0) REVERT: I 154 LYS cc_start: 0.8726 (mttt) cc_final: 0.8190 (mtpp) REVERT: I 236 GLN cc_start: 0.8983 (mp10) cc_final: 0.8573 (mp10) REVERT: I 240 ASN cc_start: 0.8462 (t0) cc_final: 0.7931 (t0) REVERT: I 257 ASP cc_start: 0.8574 (t70) cc_final: 0.8170 (m-30) REVERT: I 275 ASP cc_start: 0.8877 (t0) cc_final: 0.8656 (m-30) outliers start: 84 outliers final: 71 residues processed: 478 average time/residue: 0.1356 time to fit residues: 102.3281 Evaluate side-chains 482 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 403 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain C residue 11 GLN Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 46 ASN Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 121 ASP Chi-restraints excluded: chain I residue 186 SER Chi-restraints excluded: chain I residue 228 ASP Chi-restraints excluded: chain I residue 296 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 193 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 202 optimal weight: 8.9990 chunk 235 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 213 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 230 optimal weight: 0.0970 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 GLN B 11 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 GLN ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN E 263 ASN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 HIS F 147 GLN F 263 ASN G 11 GLN G 263 ASN H 263 ASN I 11 GLN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 215 ASN I 263 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.119751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.099307 restraints weight = 28182.564| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.29 r_work: 0.3250 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21024 Z= 0.128 Angle : 0.487 9.420 28494 Z= 0.263 Chirality : 0.048 0.382 3168 Planarity : 0.003 0.040 3600 Dihedral : 3.816 27.416 2845 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.28 % Allowed : 19.70 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.57 (0.15), residues: 2574 helix: None (None), residues: 0 sheet: -1.77 (0.14), residues: 1368 loop : -1.44 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 159 TYR 0.014 0.001 TYR D 26 PHE 0.022 0.001 PHE I 209 TRP 0.047 0.002 TRP F 206 HIS 0.005 0.001 HIS E 81 Details of bonding type rmsd covalent geometry : bond 0.00298 (21024) covalent geometry : angle 0.48695 (28494) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 424 time to evaluate : 0.857 Fit side-chains REVERT: A 13 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8069 (pm20) REVERT: A 21 LYS cc_start: 0.8759 (tppt) cc_final: 0.8412 (tmtt) REVERT: A 44 MET cc_start: 0.8416 (ptt) cc_final: 0.8173 (ptm) REVERT: A 60 ILE cc_start: 0.8668 (mp) cc_final: 0.8177 (tt) REVERT: A 84 GLU cc_start: 0.8198 (tt0) cc_final: 0.7717 (mt-10) REVERT: A 87 GLN cc_start: 0.8264 (tt0) cc_final: 0.8011 (tp40) REVERT: A 176 LYS cc_start: 0.9090 (mttm) cc_final: 0.8666 (mmmt) REVERT: A 240 ASN cc_start: 0.8469 (t0) cc_final: 0.8174 (t0) REVERT: A 257 ASP cc_start: 0.8919 (m-30) cc_final: 0.8031 (m-30) REVERT: B 13 GLU cc_start: 0.8567 (mt-10) cc_final: 0.7747 (pm20) REVERT: B 19 VAL cc_start: 0.9169 (t) cc_final: 0.8814 (p) REVERT: B 21 LYS cc_start: 0.8769 (ttmm) cc_final: 0.8330 (tmtt) REVERT: B 44 MET cc_start: 0.8264 (ttm) cc_final: 0.7937 (ttm) REVERT: B 52 ARG cc_start: 0.7840 (tpt-90) cc_final: 0.7337 (mtp85) REVERT: B 85 GLU cc_start: 0.8178 (tt0) cc_final: 0.7692 (tm-30) REVERT: B 94 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7838 (mt-10) REVERT: B 167 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8032 (mp0) REVERT: B 176 LYS cc_start: 0.9231 (mttm) cc_final: 0.8844 (mmtp) REVERT: B 212 LYS cc_start: 0.8506 (tttt) cc_final: 0.8258 (ttpp) REVERT: B 268 ARG cc_start: 0.8873 (mtm110) cc_final: 0.8613 (ttm-80) REVERT: B 292 ILE cc_start: 0.8848 (mt) cc_final: 0.8556 (tt) REVERT: B 293 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8800 (pp) REVERT: C 14 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8308 (p) REVERT: C 44 MET cc_start: 0.8275 (ttm) cc_final: 0.7866 (mpp) REVERT: C 45 LYS cc_start: 0.8900 (tttt) cc_final: 0.8559 (tttp) REVERT: C 52 ARG cc_start: 0.7865 (ttt-90) cc_final: 0.7665 (ttt180) REVERT: C 94 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7583 (mp0) REVERT: C 128 GLU cc_start: 0.8281 (pt0) cc_final: 0.7943 (pt0) REVERT: C 154 LYS cc_start: 0.9038 (mttt) cc_final: 0.8486 (mtpp) REVERT: C 159 ARG cc_start: 0.8941 (ttm110) cc_final: 0.8590 (ttp80) REVERT: C 174 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8254 (mp0) REVERT: C 176 LYS cc_start: 0.9148 (mttm) cc_final: 0.8639 (mmtp) REVERT: C 198 PHE cc_start: 0.8715 (m-80) cc_final: 0.8481 (m-80) REVERT: C 229 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7701 (tm-30) REVERT: C 236 GLN cc_start: 0.9035 (mp10) cc_final: 0.8477 (mp10) REVERT: C 257 ASP cc_start: 0.8551 (m-30) cc_final: 0.7902 (m-30) REVERT: C 292 ILE cc_start: 0.8914 (mt) cc_final: 0.8534 (tt) REVERT: C 293 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9018 (pp) REVERT: D 13 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8014 (pm20) REVERT: D 19 VAL cc_start: 0.9211 (t) cc_final: 0.8830 (p) REVERT: D 44 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.7951 (tpp) REVERT: D 85 GLU cc_start: 0.8262 (tt0) cc_final: 0.7947 (tm-30) REVERT: D 94 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: D 154 LYS cc_start: 0.8865 (mttt) cc_final: 0.8412 (mttm) REVERT: D 186 SER cc_start: 0.9058 (OUTLIER) cc_final: 0.8697 (p) REVERT: D 240 ASN cc_start: 0.8455 (t0) cc_final: 0.7972 (t0) REVERT: D 257 ASP cc_start: 0.8839 (m-30) cc_final: 0.8356 (m-30) REVERT: D 265 TYR cc_start: 0.9009 (t80) cc_final: 0.7929 (t80) REVERT: D 268 ARG cc_start: 0.8692 (mtm-85) cc_final: 0.8419 (ttm110) REVERT: E 44 MET cc_start: 0.8333 (ttm) cc_final: 0.7782 (tpp) REVERT: E 70 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.6593 (t80) REVERT: E 85 GLU cc_start: 0.8231 (tt0) cc_final: 0.8008 (tm-30) REVERT: E 90 MET cc_start: 0.8852 (ttp) cc_final: 0.8464 (tmm) REVERT: E 110 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8308 (p) REVERT: E 134 ASP cc_start: 0.8695 (m-30) cc_final: 0.8283 (m-30) REVERT: E 154 LYS cc_start: 0.8966 (mttt) cc_final: 0.8459 (mttm) REVERT: E 165 LYS cc_start: 0.8480 (tttt) cc_final: 0.8212 (tmmt) REVERT: E 167 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7927 (mp0) REVERT: E 176 LYS cc_start: 0.9008 (mmtt) cc_final: 0.8747 (mmmt) REVERT: E 192 LEU cc_start: 0.9226 (mt) cc_final: 0.8966 (mt) REVERT: E 292 ILE cc_start: 0.9120 (mt) cc_final: 0.8684 (tt) REVERT: F 52 ARG cc_start: 0.8151 (ttt-90) cc_final: 0.7914 (mtp85) REVERT: F 90 MET cc_start: 0.8957 (ttp) cc_final: 0.8488 (tmm) REVERT: F 94 GLU cc_start: 0.7909 (tt0) cc_final: 0.7462 (mt-10) REVERT: F 155 ILE cc_start: 0.9101 (mt) cc_final: 0.8774 (pt) REVERT: F 165 LYS cc_start: 0.8411 (tttt) cc_final: 0.8174 (tmmt) REVERT: F 176 LYS cc_start: 0.8985 (mttm) cc_final: 0.8641 (mmtt) REVERT: F 240 ASN cc_start: 0.8412 (t0) cc_final: 0.8038 (t0) REVERT: F 263 ASN cc_start: 0.9026 (t0) cc_final: 0.8627 (t0) REVERT: F 265 TYR cc_start: 0.8995 (t80) cc_final: 0.7949 (t80) REVERT: F 266 PHE cc_start: 0.8070 (m-80) cc_final: 0.7281 (m-80) REVERT: F 292 ILE cc_start: 0.8888 (mt) cc_final: 0.8508 (tt) REVERT: G 36 GLN cc_start: 0.8887 (tt0) cc_final: 0.8473 (tt0) REVERT: G 42 LYS cc_start: 0.9169 (tttt) cc_final: 0.8487 (mtmm) REVERT: G 60 ILE cc_start: 0.8684 (mp) cc_final: 0.8347 (tt) REVERT: G 84 GLU cc_start: 0.8056 (tt0) cc_final: 0.7696 (mt-10) REVERT: G 94 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7879 (mp0) REVERT: G 176 LYS cc_start: 0.9114 (mttm) cc_final: 0.8764 (mmtt) REVERT: G 240 ASN cc_start: 0.8188 (t0) cc_final: 0.7886 (t0) REVERT: G 263 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8167 (m-40) REVERT: H 85 GLU cc_start: 0.8534 (tt0) cc_final: 0.8151 (tm-30) REVERT: H 90 MET cc_start: 0.8861 (ttp) cc_final: 0.8484 (tmm) REVERT: H 154 LYS cc_start: 0.8985 (mttt) cc_final: 0.8464 (mtpp) REVERT: H 176 LYS cc_start: 0.8868 (mttm) cc_final: 0.8453 (mmtp) REVERT: H 178 TYR cc_start: 0.8808 (m-80) cc_final: 0.8487 (m-80) REVERT: H 206 TRP cc_start: 0.8121 (p-90) cc_final: 0.7841 (p-90) REVERT: H 236 GLN cc_start: 0.9181 (mp10) cc_final: 0.8489 (mp10) REVERT: H 290 LYS cc_start: 0.8750 (mttt) cc_final: 0.8381 (mtmm) REVERT: H 292 ILE cc_start: 0.8957 (mt) cc_final: 0.8693 (tt) REVERT: I 13 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7924 (pm20) REVERT: I 21 LYS cc_start: 0.8740 (ttmm) cc_final: 0.8333 (tptt) REVERT: I 35 ASP cc_start: 0.8287 (t0) cc_final: 0.8055 (t70) REVERT: I 90 MET cc_start: 0.9023 (ttp) cc_final: 0.8652 (tmm) REVERT: I 128 GLU cc_start: 0.8289 (pt0) cc_final: 0.7910 (tt0) REVERT: I 147 GLN cc_start: 0.8630 (tt0) cc_final: 0.8372 (tt0) REVERT: I 154 LYS cc_start: 0.8752 (mttt) cc_final: 0.8230 (mtpp) REVERT: I 165 LYS cc_start: 0.8821 (tmtt) cc_final: 0.8490 (ptpt) REVERT: I 175 ARG cc_start: 0.9024 (mmm160) cc_final: 0.8541 (mmm-85) REVERT: I 204 GLU cc_start: 0.7188 (tp30) cc_final: 0.6896 (tm-30) REVERT: I 236 GLN cc_start: 0.9000 (mp10) cc_final: 0.8581 (mp10) REVERT: I 240 ASN cc_start: 0.8453 (t0) cc_final: 0.7884 (t0) REVERT: I 257 ASP cc_start: 0.8539 (t70) cc_final: 0.8206 (m-30) REVERT: I 275 ASP cc_start: 0.8870 (t0) cc_final: 0.8659 (m-30) outliers start: 74 outliers final: 57 residues processed: 475 average time/residue: 0.1405 time to fit residues: 104.4920 Evaluate side-chains 480 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 414 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 263 ASN Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 46 ASN Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 186 SER Chi-restraints excluded: chain I residue 296 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 247 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 249 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN B 11 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN C 263 ASN D 143 GLN E 11 GLN ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 ASN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 HIS F 147 GLN F 215 ASN G 11 GLN G 147 GLN H 119 ASN H 263 ASN I 11 GLN ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 215 ASN I 263 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.116788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.095719 restraints weight = 28415.816| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.33 r_work: 0.3176 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 21024 Z= 0.283 Angle : 0.564 9.253 28494 Z= 0.304 Chirality : 0.049 0.399 3168 Planarity : 0.003 0.044 3600 Dihedral : 4.117 29.547 2845 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.85 % Allowed : 19.43 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.67 (0.15), residues: 2574 helix: None (None), residues: 0 sheet: -1.88 (0.14), residues: 1350 loop : -1.46 (0.15), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 159 TYR 0.022 0.002 TYR D 26 PHE 0.031 0.002 PHE I 209 TRP 0.048 0.003 TRP E 206 HIS 0.006 0.001 HIS B 103 Details of bonding type rmsd covalent geometry : bond 0.00646 (21024) covalent geometry : angle 0.56357 (28494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5115.98 seconds wall clock time: 88 minutes 36.16 seconds (5316.16 seconds total)