Starting phenix.real_space_refine on Mon Feb 10 23:26:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xvu_38719/02_2025/8xvu_38719.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xvu_38719/02_2025/8xvu_38719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xvu_38719/02_2025/8xvu_38719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xvu_38719/02_2025/8xvu_38719.map" model { file = "/net/cci-nas-00/data/ceres_data/8xvu_38719/02_2025/8xvu_38719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xvu_38719/02_2025/8xvu_38719.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.000 sd= 1.000 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 28 5.16 5 C 2151 2.51 5 N 556 2.21 5 O 553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3288 Number of models: 1 Model: "" Number of chains: 3 Chain: "R" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2367 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 288} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 496 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 63} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 425 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 55} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 2.47, per 1000 atoms: 0.75 Number of scatterers: 3288 At special positions: 0 Unit cell: (69.5125, 77.8125, 94.4125, 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 28 16.00 O 553 8.00 N 556 7.00 C 2151 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 39 " - pdb=" SG CYS R 286 " distance=2.03 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 35 " distance=2.03 Simple disulfide: pdb=" SG CYS D 11 " - pdb=" SG CYS D 51 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 35 " distance=2.03 Simple disulfide: pdb=" SG CYS E 11 " - pdb=" SG CYS E 51 " distance=2.03 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: 0.75 Conformation dependent library (CDL) restraints added in 363.8 milliseconds 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 816 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 65.1% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'R' and resid 44 through 76 removed outlier: 3.601A pdb=" N PHE R 50 " --> pdb=" O ILE R 46 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL R 52 " --> pdb=" O LYS R 48 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE R 53 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER R 76 " --> pdb=" O VAL R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 111 Proline residue: R 102 - end of helix Processing helix chain 'R' and resid 115 through 149 Processing helix chain 'R' and resid 153 through 160 removed outlier: 3.832A pdb=" N THR R 156 " --> pdb=" O ARG R 153 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR R 160 " --> pdb=" O GLN R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 177 Processing helix chain 'R' and resid 177 through 183 removed outlier: 3.588A pdb=" N LEU R 181 " --> pdb=" O ALA R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 212 Processing helix chain 'R' and resid 212 through 218 Processing helix chain 'R' and resid 220 through 240 removed outlier: 3.662A pdb=" N LYS R 240 " --> pdb=" O ARG R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 279 Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 285 through 304 Processing helix chain 'R' and resid 305 through 315 Proline residue: R 311 - end of helix Processing helix chain 'R' and resid 318 through 330 removed outlier: 3.849A pdb=" N ALA R 330 " --> pdb=" O LEU R 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 21 No H-bonds generated for 'chain 'D' and resid 19 through 21' Processing helix chain 'D' and resid 56 through 69 removed outlier: 3.807A pdb=" N LYS D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 68 removed outlier: 3.914A pdb=" N LYS E 60 " --> pdb=" O SER E 56 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 184 through 187 Processing sheet with id=AA2, first strand: chain 'D' and resid 49 through 52 removed outlier: 4.240A pdb=" N VAL D 40 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR E 43 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL E 26 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE E 41 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL E 28 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLU E 39 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL E 40 " --> pdb=" O LEU E 52 " (cutoff:3.500A) 217 hydrogen bonds defined for protein. 636 hydrogen bond angles 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: 0.87 Time building geometry restraints manager: 0.89 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: 1028 1.34 - 1.46: 732 1.46 - 1.58: 1553 1.58 - 1.70: 0 1.70 - 1.82: 39 Bond restraints: 3352 Sorted by residual: bond pdb=" N GLN E 13 " pdb=" CA GLN E 13 " ideal model delta sigma weight residual 1.455 1.482 -0.027 1.25e-02 6.40e+03 4.51e+00 bond pdb=" C GLN E 13 " pdb=" O GLN E 13 " ideal model delta sigma weight residual 1.235 1.253 -0.018 1.22e-02 6.72e+03 2.15e+00 bond pdb=" CA GLN E 13 " pdb=" C GLN E 13 " ideal model delta sigma weight residual 1.521 1.534 -0.014 1.24e-02 6.50e+03 1.20e+00 bond pdb=" CB VAL R 162 " pdb=" CG1 VAL R 162 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.07e-01 bond pdb=" CA LEU E 12 " pdb=" CB LEU E 12 " ideal model delta sigma weight residual 1.535 1.521 0.014 1.69e-02 3.50e+03 7.04e-01 ... (remaining 3347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.88: 4274 0.88 - 1.77: 232 1.77 - 2.65: 33 2.65 - 3.54: 12 3.54 - 4.42: 10 Bond angle restraints: 4561 Sorted by residual: angle pdb=" O LEU E 12 " pdb=" C LEU E 12 " pdb=" N GLN E 13 " ideal model delta sigma weight residual 121.92 124.45 -2.53 1.30e+00 5.92e-01 3.79e+00 angle pdb=" N ASN R 110 " pdb=" CA ASN R 110 " pdb=" C ASN R 110 " ideal model delta sigma weight residual 112.30 114.89 -2.59 1.36e+00 5.41e-01 3.64e+00 angle pdb=" C LEU E 12 " pdb=" N GLN E 13 " pdb=" CA GLN E 13 " ideal model delta sigma weight residual 122.73 119.71 3.02 1.62e+00 3.81e-01 3.48e+00 angle pdb=" CA LEU E 12 " pdb=" C LEU E 12 " pdb=" N GLN E 13 " ideal model delta sigma weight residual 117.88 115.40 2.48 1.40e+00 5.10e-01 3.13e+00 angle pdb=" CA ASN R 310 " pdb=" C ASN R 310 " pdb=" N PRO R 311 " ideal model delta sigma weight residual 120.77 119.14 1.63 9.70e-01 1.06e+00 2.82e+00 ... (remaining 4556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 1867 17.97 - 35.93: 136 35.93 - 53.90: 22 53.90 - 71.87: 10 71.87 - 89.83: 3 Dihedral angle restraints: 2038 sinusoidal: 786 harmonic: 1252 Sorted by residual: dihedral pdb=" CA PHE R 220 " pdb=" C PHE R 220 " pdb=" N ILE R 221 " pdb=" CA ILE R 221 " ideal model delta harmonic sigma weight residual 180.00 -164.56 -15.44 0 5.00e+00 4.00e-02 9.54e+00 dihedral pdb=" CB MET D 58 " pdb=" CG MET D 58 " pdb=" SD MET D 58 " pdb=" CE MET D 58 " ideal model delta sinusoidal sigma weight residual -60.00 -116.07 56.07 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" CG ARG R 322 " pdb=" CD ARG R 322 " pdb=" NE ARG R 322 " pdb=" CZ ARG R 322 " ideal model delta sinusoidal sigma weight residual 90.00 131.26 -41.26 2 1.50e+01 4.44e-03 9.28e+00 ... (remaining 2035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 334 0.025 - 0.050: 138 0.050 - 0.075: 57 0.075 - 0.100: 21 0.100 - 0.125: 17 Chirality restraints: 567 Sorted by residual: chirality pdb=" CA ILE R 282 " pdb=" N ILE R 282 " pdb=" C ILE R 282 " pdb=" CB ILE R 282 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA ILE E 41 " pdb=" N ILE E 41 " pdb=" C ILE E 41 " pdb=" CB ILE E 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.49e-01 chirality pdb=" CA ILE E 18 " pdb=" N ILE E 18 " pdb=" C ILE E 18 " pdb=" CB ILE E 18 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.32e-01 ... (remaining 564 not shown) Planarity restraints: 556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS R 119 " 0.005 2.00e-02 2.50e+03 9.23e-03 8.52e-01 pdb=" C CYS R 119 " -0.016 2.00e-02 2.50e+03 pdb=" O CYS R 119 " 0.006 2.00e-02 2.50e+03 pdb=" N LYS R 120 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 214 " 0.014 5.00e-02 4.00e+02 2.14e-02 7.32e-01 pdb=" N PRO R 215 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO R 215 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO R 215 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 310 " 0.013 5.00e-02 4.00e+02 1.91e-02 5.81e-01 pdb=" N PRO R 311 " -0.033 5.00e-02 4.00e+02 pdb=" CA PRO R 311 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO R 311 " 0.011 5.00e-02 4.00e+02 ... (remaining 553 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 1188 2.88 - 3.39: 3317 3.39 - 3.89: 5236 3.89 - 4.40: 5667 4.40 - 4.90: 10128 Nonbonded interactions: 25536 Sorted by model distance: nonbonded pdb=" O GLY R 201 " pdb=" OG1 THR R 204 " model vdw 2.377 3.040 nonbonded pdb=" NE ARG R 185 " pdb=" OD2 ASP R 199 " model vdw 2.396 3.120 nonbonded pdb=" OD1 ASP R 143 " pdb=" NH1 ARG R 159 " model vdw 2.446 3.120 nonbonded pdb=" O PHE R 97 " pdb=" OG1 THR R 100 " model vdw 2.468 3.040 nonbonded pdb=" O LEU R 125 " pdb=" ND2 ASN R 129 " model vdw 2.481 3.120 ... (remaining 25531 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 9 through 11 or (resid 12 through 13 and (name N or name C \ A or name C or name O or name CB )) or resid 14 through 36 or (resid 37 and (nam \ e N or name CA or name C or name O or name CB )) or resid 38 through 68)) selection = (chain 'E' and (resid 9 through 63 or (resid 64 through 65 and (name N or name C \ A or name C or name O or name CB )) or resid 66 through 67 or (resid 68 and (nam \ e N or name CA or name C or name O or name CB )))) } 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: 0.590 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.020 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 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 : 0.004 0.028 3352 Z= 0.238 Angle : 0.511 4.423 4561 Z= 0.289 Chirality : 0.038 0.125 567 Planarity : 0.003 0.021 556 Dihedral : 13.713 89.833 1204 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.41), residues: 421 helix: 2.07 (0.32), residues: 261 sheet: 0.88 (0.75), residues: 51 loop : -0.08 (0.58), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 112 HIS 0.007 0.001 HIS R 150 PHE 0.010 0.001 PHE R 50 TYR 0.005 0.001 TYR R 267 ARG 0.003 0.000 ARG R 159 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.403 Fit side-chains REVERT: R 48 LYS cc_start: 0.7110 (mttt) cc_final: 0.6814 (ttpp) REVERT: R 126 LYS cc_start: 0.8060 (tttt) cc_final: 0.7728 (ttpp) REVERT: R 243 MET cc_start: 0.7082 (mtm) cc_final: 0.6683 (mtt) REVERT: R 245 GLN cc_start: 0.8399 (mp10) cc_final: 0.7178 (tt0) REVERT: R 320 LYS cc_start: 0.8337 (ttmt) cc_final: 0.8104 (ttmm) REVERT: D 43 THR cc_start: 0.9014 (m) cc_final: 0.8637 (t) REVERT: D 53 ASN cc_start: 0.8942 (t0) cc_final: 0.8688 (t0) REVERT: E 27 LYS cc_start: 0.8584 (tttt) cc_final: 0.8258 (ttpp) REVERT: E 46 ASN cc_start: 0.8763 (p0) cc_final: 0.8291 (p0) REVERT: E 53 ASN cc_start: 0.8217 (t0) cc_final: 0.7936 (t0) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1580 time to fit residues: 23.7625 Evaluate side-chains 90 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 ASN R 157 GLN R 323 HIS D 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.126111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.099699 restraints weight = 5272.207| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.42 r_work: 0.3084 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 3352 Z= 0.309 Angle : 0.619 8.056 4561 Z= 0.311 Chirality : 0.042 0.131 567 Planarity : 0.004 0.022 556 Dihedral : 3.820 18.380 453 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.79 % Allowed : 13.65 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.41), residues: 421 helix: 1.94 (0.32), residues: 257 sheet: 0.81 (0.73), residues: 51 loop : -0.07 (0.59), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 112 HIS 0.014 0.002 HIS R 323 PHE 0.012 0.002 PHE R 97 TYR 0.011 0.002 TYR R 160 ARG 0.003 0.001 ARG R 212 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: R 126 LYS cc_start: 0.8763 (tttt) cc_final: 0.8532 (ttpp) REVERT: R 160 TYR cc_start: 0.6411 (m-80) cc_final: 0.6182 (m-80) REVERT: R 245 GLN cc_start: 0.8648 (mp10) cc_final: 0.7272 (tt0) REVERT: R 276 LEU cc_start: 0.9355 (mt) cc_final: 0.9137 (mt) REVERT: R 280 GLN cc_start: 0.8084 (tm-30) cc_final: 0.7859 (tm-30) REVERT: R 320 LYS cc_start: 0.8473 (ttmt) cc_final: 0.8271 (ttmm) REVERT: D 30 SER cc_start: 0.8986 (OUTLIER) cc_final: 0.8553 (p) REVERT: D 39 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8462 (mt-10) REVERT: D 43 THR cc_start: 0.9105 (m) cc_final: 0.8797 (t) REVERT: D 53 ASN cc_start: 0.9015 (t0) cc_final: 0.8758 (t0) REVERT: D 58 MET cc_start: 0.8704 (mpp) cc_final: 0.8408 (tpt) REVERT: D 62 ILE cc_start: 0.9440 (mt) cc_final: 0.9063 (mt) REVERT: E 44 LEU cc_start: 0.8876 (mp) cc_final: 0.8445 (mm) REVERT: E 53 ASN cc_start: 0.8369 (t0) cc_final: 0.7971 (t0) outliers start: 10 outliers final: 2 residues processed: 97 average time/residue: 0.1601 time to fit residues: 18.7809 Evaluate side-chains 89 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 30 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 35 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.127899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.100572 restraints weight = 5191.777| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.17 r_work: 0.3121 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3352 Z= 0.201 Angle : 0.552 5.479 4561 Z= 0.286 Chirality : 0.040 0.131 567 Planarity : 0.003 0.023 556 Dihedral : 4.075 24.389 453 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.95 % Allowed : 13.65 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.42), residues: 421 helix: 2.01 (0.32), residues: 262 sheet: 0.60 (0.74), residues: 52 loop : 0.08 (0.65), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 112 HIS 0.003 0.001 HIS R 150 PHE 0.008 0.001 PHE R 97 TYR 0.006 0.001 TYR R 86 ARG 0.002 0.000 ARG R 288 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.397 Fit side-chains REVERT: R 245 GLN cc_start: 0.8639 (mp10) cc_final: 0.7257 (tt0) REVERT: R 280 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7790 (tm-30) REVERT: D 13 GLN cc_start: 0.8535 (mt0) cc_final: 0.8190 (mp10) REVERT: D 43 THR cc_start: 0.9092 (m) cc_final: 0.8824 (t) REVERT: D 53 ASN cc_start: 0.8900 (t0) cc_final: 0.8684 (t0) REVERT: D 58 MET cc_start: 0.8533 (mpp) cc_final: 0.8239 (tpt) REVERT: D 62 ILE cc_start: 0.9318 (mt) cc_final: 0.8992 (mt) REVERT: E 44 LEU cc_start: 0.8890 (mp) cc_final: 0.8485 (mm) REVERT: E 48 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7948 (mp10) REVERT: E 53 ASN cc_start: 0.8333 (t0) cc_final: 0.7966 (t0) outliers start: 7 outliers final: 3 residues processed: 89 average time/residue: 0.1658 time to fit residues: 17.7489 Evaluate side-chains 88 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 307 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.0570 chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 31 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 30 optimal weight: 0.0980 chunk 33 optimal weight: 3.9990 overall best weight: 0.4300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.129029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.103232 restraints weight = 5251.046| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.30 r_work: 0.3132 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3352 Z= 0.161 Angle : 0.511 5.438 4561 Z= 0.265 Chirality : 0.038 0.119 567 Planarity : 0.003 0.022 556 Dihedral : 3.832 24.424 453 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.11 % Allowed : 14.48 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.42), residues: 421 helix: 2.37 (0.32), residues: 256 sheet: 0.77 (0.75), residues: 52 loop : -0.01 (0.61), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 112 HIS 0.002 0.001 HIS R 150 PHE 0.007 0.001 PHE R 97 TYR 0.006 0.001 TYR R 86 ARG 0.002 0.000 ARG R 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: R 245 GLN cc_start: 0.8586 (mp10) cc_final: 0.7152 (tt0) REVERT: R 280 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7667 (tm-30) REVERT: D 13 GLN cc_start: 0.8492 (mt0) cc_final: 0.8194 (mp10) REVERT: D 43 THR cc_start: 0.9101 (m) cc_final: 0.8825 (t) REVERT: D 53 ASN cc_start: 0.8924 (t0) cc_final: 0.8630 (t0) REVERT: D 58 MET cc_start: 0.8575 (mpp) cc_final: 0.8360 (tpt) REVERT: E 27 LYS cc_start: 0.8786 (ttpp) cc_final: 0.8578 (ttpp) REVERT: E 44 LEU cc_start: 0.8896 (mp) cc_final: 0.8491 (mm) REVERT: E 53 ASN cc_start: 0.8324 (t0) cc_final: 0.7994 (t0) outliers start: 4 outliers final: 3 residues processed: 93 average time/residue: 0.1599 time to fit residues: 18.0050 Evaluate side-chains 88 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain D residue 30 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.0270 chunk 38 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 overall best weight: 1.1040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 306 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.126672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.100550 restraints weight = 5275.268| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.45 r_work: 0.3095 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3352 Z= 0.238 Angle : 0.544 5.233 4561 Z= 0.285 Chirality : 0.040 0.122 567 Planarity : 0.003 0.023 556 Dihedral : 3.931 23.377 453 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.67 % Allowed : 15.32 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.42), residues: 421 helix: 2.02 (0.32), residues: 260 sheet: 0.76 (0.75), residues: 52 loop : 0.13 (0.62), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 112 HIS 0.004 0.001 HIS R 150 PHE 0.010 0.001 PHE R 233 TYR 0.004 0.001 TYR R 131 ARG 0.002 0.000 ARG R 212 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 245 GLN cc_start: 0.8589 (mp10) cc_final: 0.7202 (tt0) REVERT: R 277 MET cc_start: 0.9336 (ttp) cc_final: 0.8875 (ttp) REVERT: R 280 GLN cc_start: 0.8214 (tm-30) cc_final: 0.7697 (tm-30) REVERT: D 43 THR cc_start: 0.9125 (m) cc_final: 0.8833 (t) REVERT: D 53 ASN cc_start: 0.8979 (t0) cc_final: 0.8742 (t0) REVERT: E 44 LEU cc_start: 0.8842 (mp) cc_final: 0.8457 (mm) REVERT: E 53 ASN cc_start: 0.8377 (t0) cc_final: 0.7999 (t0) outliers start: 6 outliers final: 4 residues processed: 88 average time/residue: 0.1592 time to fit residues: 16.9544 Evaluate side-chains 87 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain D residue 30 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.0270 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.127248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.101519 restraints weight = 5444.218| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.40 r_work: 0.3118 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3352 Z= 0.190 Angle : 0.532 5.498 4561 Z= 0.276 Chirality : 0.039 0.123 567 Planarity : 0.003 0.021 556 Dihedral : 3.901 21.688 453 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.95 % Allowed : 15.88 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.42), residues: 421 helix: 2.23 (0.32), residues: 256 sheet: 0.82 (0.77), residues: 52 loop : -0.11 (0.61), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 112 HIS 0.003 0.001 HIS R 150 PHE 0.007 0.001 PHE R 97 TYR 0.004 0.001 TYR R 86 ARG 0.001 0.000 ARG R 289 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 245 GLN cc_start: 0.8590 (mp10) cc_final: 0.7245 (tt0) REVERT: R 277 MET cc_start: 0.9285 (ttp) cc_final: 0.8915 (ttp) REVERT: R 280 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7938 (tm-30) REVERT: D 43 THR cc_start: 0.9129 (m) cc_final: 0.8878 (t) REVERT: D 58 MET cc_start: 0.8519 (tpt) cc_final: 0.8240 (tpp) REVERT: E 44 LEU cc_start: 0.8841 (mp) cc_final: 0.8517 (mm) REVERT: E 53 ASN cc_start: 0.8363 (t0) cc_final: 0.8092 (t0) outliers start: 7 outliers final: 3 residues processed: 89 average time/residue: 0.1616 time to fit residues: 17.4090 Evaluate side-chains 87 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain D residue 30 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 18 optimal weight: 0.0770 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 27 optimal weight: 0.1980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.128623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.102009 restraints weight = 5245.742| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.30 r_work: 0.3145 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3352 Z= 0.161 Angle : 0.526 5.496 4561 Z= 0.276 Chirality : 0.039 0.119 567 Planarity : 0.003 0.020 556 Dihedral : 3.873 21.191 453 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.84 % Allowed : 16.16 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.42), residues: 421 helix: 2.31 (0.32), residues: 256 sheet: 1.03 (0.77), residues: 51 loop : -0.25 (0.61), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 207 HIS 0.003 0.001 HIS R 306 PHE 0.006 0.001 PHE R 97 TYR 0.005 0.001 TYR R 55 ARG 0.001 0.000 ARG R 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 245 GLN cc_start: 0.8557 (mp10) cc_final: 0.7178 (tt0) REVERT: R 277 MET cc_start: 0.9281 (ttp) cc_final: 0.8941 (ttp) REVERT: R 280 GLN cc_start: 0.8307 (tm-30) cc_final: 0.8052 (tm-30) REVERT: D 43 THR cc_start: 0.9106 (m) cc_final: 0.8869 (t) REVERT: D 58 MET cc_start: 0.8468 (tpt) cc_final: 0.8179 (tpp) REVERT: E 44 LEU cc_start: 0.8882 (mp) cc_final: 0.8514 (mm) REVERT: E 53 ASN cc_start: 0.8360 (t0) cc_final: 0.8105 (t0) outliers start: 3 outliers final: 2 residues processed: 85 average time/residue: 0.1581 time to fit residues: 16.4214 Evaluate side-chains 85 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 243 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 28 optimal weight: 0.0870 chunk 25 optimal weight: 4.9990 chunk 11 optimal weight: 0.0370 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.129587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.102941 restraints weight = 5359.469| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.22 r_work: 0.3167 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3352 Z= 0.166 Angle : 0.552 6.771 4561 Z= 0.287 Chirality : 0.040 0.144 567 Planarity : 0.003 0.021 556 Dihedral : 3.860 20.488 453 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.56 % Allowed : 17.55 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.42), residues: 421 helix: 2.30 (0.32), residues: 256 sheet: 0.94 (0.76), residues: 52 loop : -0.04 (0.62), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 207 HIS 0.003 0.001 HIS R 323 PHE 0.006 0.001 PHE R 97 TYR 0.004 0.001 TYR R 55 ARG 0.001 0.000 ARG R 251 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: R 245 GLN cc_start: 0.8529 (mp10) cc_final: 0.7191 (tt0) REVERT: R 277 MET cc_start: 0.9254 (ttp) cc_final: 0.8915 (ttp) REVERT: R 280 GLN cc_start: 0.8307 (tm-30) cc_final: 0.8052 (tm-30) REVERT: D 58 MET cc_start: 0.8413 (tpt) cc_final: 0.8169 (tpp) REVERT: E 44 LEU cc_start: 0.8980 (mp) cc_final: 0.8630 (mm) REVERT: E 48 GLN cc_start: 0.8432 (mp10) cc_final: 0.8109 (mp10) REVERT: E 53 ASN cc_start: 0.8334 (t0) cc_final: 0.8104 (t0) outliers start: 2 outliers final: 2 residues processed: 87 average time/residue: 0.1605 time to fit residues: 17.0162 Evaluate side-chains 85 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 243 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.0980 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.128891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.103435 restraints weight = 5398.940| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.33 r_work: 0.3162 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3352 Z= 0.198 Angle : 0.619 12.772 4561 Z= 0.322 Chirality : 0.041 0.191 567 Planarity : 0.003 0.021 556 Dihedral : 3.962 19.375 453 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.84 % Allowed : 18.11 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.42), residues: 421 helix: 2.14 (0.32), residues: 256 sheet: 1.02 (0.75), residues: 52 loop : -0.01 (0.61), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 112 HIS 0.007 0.001 HIS R 323 PHE 0.007 0.001 PHE R 97 TYR 0.004 0.001 TYR R 55 ARG 0.001 0.000 ARG R 322 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: R 245 GLN cc_start: 0.8547 (mp10) cc_final: 0.7204 (tt0) REVERT: R 277 MET cc_start: 0.9259 (ttp) cc_final: 0.9053 (ttp) REVERT: R 280 GLN cc_start: 0.8295 (tm-30) cc_final: 0.8071 (tm-30) REVERT: E 44 LEU cc_start: 0.8967 (mp) cc_final: 0.8616 (mm) REVERT: E 48 GLN cc_start: 0.8379 (mp10) cc_final: 0.8070 (mp10) REVERT: E 53 ASN cc_start: 0.8346 (t0) cc_final: 0.8121 (t0) outliers start: 3 outliers final: 3 residues processed: 86 average time/residue: 0.1581 time to fit residues: 16.5679 Evaluate side-chains 87 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain D residue 43 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.2980 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.128372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.103087 restraints weight = 5269.974| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.32 r_work: 0.3149 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3352 Z= 0.203 Angle : 0.645 12.756 4561 Z= 0.333 Chirality : 0.041 0.178 567 Planarity : 0.003 0.022 556 Dihedral : 3.958 19.136 453 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.11 % Allowed : 19.22 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.42), residues: 421 helix: 2.16 (0.32), residues: 256 sheet: 1.14 (0.74), residues: 52 loop : 0.04 (0.61), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 112 HIS 0.003 0.001 HIS R 150 PHE 0.008 0.001 PHE R 97 TYR 0.004 0.001 TYR R 55 ARG 0.001 0.000 ARG R 159 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: R 245 GLN cc_start: 0.8537 (mp10) cc_final: 0.7214 (tt0) REVERT: R 277 MET cc_start: 0.9268 (ttp) cc_final: 0.8870 (ttp) REVERT: E 44 LEU cc_start: 0.8981 (mp) cc_final: 0.8635 (mm) REVERT: E 48 GLN cc_start: 0.8404 (mp10) cc_final: 0.8082 (mp10) REVERT: E 53 ASN cc_start: 0.8366 (t0) cc_final: 0.8155 (t0) outliers start: 4 outliers final: 4 residues processed: 84 average time/residue: 0.1609 time to fit residues: 16.3446 Evaluate side-chains 85 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 27 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 11 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.130377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.105532 restraints weight = 5303.345| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.56 r_work: 0.3159 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3352 Z= 0.191 Angle : 0.665 12.669 4561 Z= 0.342 Chirality : 0.040 0.172 567 Planarity : 0.003 0.024 556 Dihedral : 3.884 18.719 453 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.39 % Allowed : 18.94 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.42), residues: 421 helix: 2.28 (0.32), residues: 256 sheet: 1.24 (0.74), residues: 52 loop : 0.14 (0.61), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 207 HIS 0.002 0.001 HIS R 306 PHE 0.006 0.001 PHE R 97 TYR 0.005 0.001 TYR R 55 ARG 0.001 0.000 ARG R 294 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2359.88 seconds wall clock time: 42 minutes 27.88 seconds (2547.88 seconds total)