Starting phenix.real_space_refine on Fri Sep 11 21:38:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t93_10408/09_2026/6t93_10408.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t93_10408/09_2026/6t93_10408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6t93_10408/09_2026/6t93_10408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t93_10408/09_2026/6t93_10408.map" model { file = "/net/cci-nas-00/data/ceres_data/6t93_10408/09_2026/6t93_10408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t93_10408/09_2026/6t93_10408.cif" } resolution = 3.49 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= 0.003 sd= 0.051 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: 5 Type Number sf(0) Gaussians P 300 5.49 5 S 14 5.16 5 C 6730 2.51 5 N 2287 2.21 5 O 2868 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12199 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3072 Classifications: {'DNA': 151} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 150} Chain: "J" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3113 Classifications: {'DNA': 151} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 150} Time building chain proxies: 2.62, per 1000 atoms: 0.21 Number of scatterers: 12199 At special positions: 0 Unit cell: (73.96, 121.26, 117.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 300 15.00 O 2868 8.00 N 2287 7.00 C 6730 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: 1.02 Conformation dependent library (CDL) restraints added in 448.7 milliseconds 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1412 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 70.7% alpha, 2.9% beta 151 base pairs and 279 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 86 through 115 Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.502A pdb=" N ILE A 125 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 23 removed outlier: 3.717A pdb=" N ARG C 21 " --> pdb=" O THR C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 37 Processing helix chain 'C' and resid 47 through 74 Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 125 Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.530A pdb=" N ARG E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.699A pdb=" N PHE E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 132 Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 removed outlier: 3.598A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.519A pdb=" N ARG F 93 " --> pdb=" O TYR F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 removed outlier: 3.571A pdb=" N ARG G 21 " --> pdb=" O THR G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 37 Processing helix chain 'G' and resid 47 through 73 Processing helix chain 'G' and resid 80 through 91 Processing helix chain 'G' and resid 93 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 125 removed outlier: 3.535A pdb=" N HIS H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.007A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.190A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.887A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.000A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 398 hydrogen bonds defined for protein. 1176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 380 hydrogen bonds 760 hydrogen bond angles 0 basepair planarities 151 basepair parallelities 279 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1888 1.32 - 1.44: 4716 1.44 - 1.57: 5804 1.57 - 1.69: 600 1.69 - 1.81: 24 Bond restraints: 13032 Sorted by residual: bond pdb=" CD ARG E 129 " pdb=" NE ARG E 129 " ideal model delta sigma weight residual 1.458 1.395 0.063 1.40e-02 5.10e+03 2.05e+01 bond pdb=" CD ARG D 100 " pdb=" NE ARG D 100 " ideal model delta sigma weight residual 1.458 1.395 0.063 1.40e-02 5.10e+03 2.03e+01 bond pdb=" CD ARG B 93 " pdb=" NE ARG B 93 " ideal model delta sigma weight residual 1.458 1.395 0.063 1.40e-02 5.10e+03 2.00e+01 bond pdb=" CD ARG A 129 " pdb=" NE ARG A 129 " ideal model delta sigma weight residual 1.458 1.396 0.062 1.40e-02 5.10e+03 1.96e+01 bond pdb=" CD ARG F 93 " pdb=" NE ARG F 93 " ideal model delta sigma weight residual 1.458 1.398 0.060 1.40e-02 5.10e+03 1.86e+01 ... (remaining 13027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 17041 1.88 - 3.76: 1638 3.76 - 5.64: 177 5.64 - 7.51: 30 7.51 - 9.39: 7 Bond angle restraints: 18893 Sorted by residual: angle pdb=" C HIS D 50 " pdb=" N PRO D 51 " pdb=" CA PRO D 51 " ideal model delta sigma weight residual 119.56 127.54 -7.98 1.02e+00 9.61e-01 6.12e+01 angle pdb=" C HIS H 50 " pdb=" N PRO H 51 " pdb=" CA PRO H 51 " ideal model delta sigma weight residual 119.56 127.23 -7.67 1.02e+00 9.61e-01 5.66e+01 angle pdb=" C3' DT J 89 " pdb=" O3' DT J 89 " pdb=" P DA J 90 " ideal model delta sigma weight residual 119.70 128.25 -8.55 1.20e+00 6.94e-01 5.07e+01 angle pdb=" C LEU D 103 " pdb=" N PRO D 104 " pdb=" CA PRO D 104 " ideal model delta sigma weight residual 119.78 126.98 -7.20 1.03e+00 9.43e-01 4.88e+01 angle pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sigma weight residual 119.70 127.55 -7.85 1.20e+00 6.94e-01 4.28e+01 ... (remaining 18888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.25: 5714 34.25 - 68.50: 1356 68.50 - 102.75: 12 102.75 - 137.00: 0 137.00 - 171.25: 4 Dihedral angle restraints: 7086 sinusoidal: 4894 harmonic: 2192 Sorted by residual: dihedral pdb=" C4' DT J 89 " pdb=" C3' DT J 89 " pdb=" O3' DT J 89 " pdb=" P DA J 90 " ideal model delta sinusoidal sigma weight residual 220.00 48.75 171.25 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual 220.00 56.09 163.91 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DG I 3 " pdb=" C3' DG I 3 " pdb=" O3' DG I 3 " pdb=" P DG I 4 " ideal model delta sinusoidal sigma weight residual 220.00 63.58 156.42 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 7083 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1474 0.063 - 0.127: 577 0.127 - 0.190: 83 0.190 - 0.253: 9 0.253 - 0.317: 3 Chirality restraints: 2146 Sorted by residual: chirality pdb=" CA LYS F 32 " pdb=" N LYS F 32 " pdb=" C LYS F 32 " pdb=" CB LYS F 32 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA LEU A 66 " pdb=" N LEU A 66 " pdb=" C LEU A 66 " pdb=" CB LEU A 66 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C3' DT J 15 " pdb=" C4' DT J 15 " pdb=" O3' DT J 15 " pdb=" C2' DT J 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.47 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 2143 not shown) Planarity restraints: 1346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS G 37 " -0.020 2.00e-02 2.50e+03 3.98e-02 1.59e+01 pdb=" C LYS G 37 " 0.069 2.00e-02 2.50e+03 pdb=" O LYS G 37 " -0.026 2.00e-02 2.50e+03 pdb=" N GLY G 38 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 52 " 0.055 2.00e-02 2.50e+03 2.79e-02 1.55e+01 pdb=" CG TYR F 52 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR F 52 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR F 52 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR F 52 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR F 52 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR F 52 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR F 52 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 103 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C GLY B 103 " 0.067 2.00e-02 2.50e+03 pdb=" O GLY B 103 " -0.024 2.00e-02 2.50e+03 pdb=" OXT GLY B 103 " -0.024 2.00e-02 2.50e+03 ... (remaining 1343 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 4776 2.93 - 3.42: 10638 3.42 - 3.91: 24618 3.91 - 4.41: 29004 4.41 - 4.90: 36678 Nonbonded interactions: 105714 Sorted by model distance: nonbonded pdb=" NZ LYS F 60 " pdb=" OE2 GLU F 64 " model vdw 2.435 3.120 nonbonded pdb=" O ARG A 43 " pdb=" OG1 THR A 46 " model vdw 2.481 3.040 nonbonded pdb=" N GLY C 38 " pdb=" N ASN C 39 " model vdw 2.491 2.560 nonbonded pdb=" N GLY G 38 " pdb=" N ASN G 39 " model vdw 2.493 2.560 nonbonded pdb=" N ASP D 52 " pdb=" OD1 ASP D 52 " model vdw 2.497 3.120 ... (remaining 105709 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 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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=0.00 max=1.00 mean=0.99 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.210 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 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 : 0.014 0.118 13032 Z= 0.814 Angle : 1.153 9.394 18893 Z= 0.875 Chirality : 0.064 0.317 2146 Planarity : 0.010 0.069 1346 Dihedral : 27.104 171.253 5674 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 0.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 0.78 (0.26), residues: 742 helix: 0.67 (0.19), residues: 528 sheet: None (None), residues: 0 loop : 0.50 (0.36), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG B 37 TYR 0.055 0.011 TYR F 52 PHE 0.032 0.007 PHE D 71 HIS 0.013 0.003 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.01415 / 0.81 (13032) covalent geometry : angle 1.15307 / 0.87 (18893) hydrogen bonds : bond 0.16604 / 11.05 ( 778) hydrogen bonds : angle 5.31406 / 3.80 ( 1936) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8263 (tt0) cc_final: 0.8062 (mt-10) REVERT: A 75 ILE cc_start: 0.9462 (mt) cc_final: 0.9124 (mm) REVERT: A 77 GLN cc_start: 0.8200 (pt0) cc_final: 0.7991 (pp30) REVERT: A 82 ASP cc_start: 0.8647 (m-30) cc_final: 0.8385 (m-30) REVERT: A 114 HIS cc_start: 0.8772 (t70) cc_final: 0.8462 (t-90) REVERT: B 24 ARG cc_start: 0.8295 (mtm110) cc_final: 0.8032 (ppt170) REVERT: B 97 THR cc_start: 0.8582 (m) cc_final: 0.8379 (p) REVERT: C 74 ASN cc_start: 0.8984 (m-40) cc_final: 0.8406 (t0) REVERT: C 102 THR cc_start: 0.8968 (m) cc_final: 0.8690 (p) REVERT: D 35 LYS cc_start: 0.8194 (mmtt) cc_final: 0.7540 (mmmm) REVERT: D 52 ASP cc_start: 0.8489 (p0) cc_final: 0.8131 (p0) REVERT: D 60 MET cc_start: 0.9081 (tpp) cc_final: 0.8869 (tpp) REVERT: D 72 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7934 (tp30) REVERT: D 80 ARG cc_start: 0.8635 (mtm-85) cc_final: 0.8274 (mtm-85) REVERT: E 104 LEU cc_start: 0.9483 (tp) cc_final: 0.9221 (tp) REVERT: E 121 MET cc_start: 0.8349 (mmm) cc_final: 0.8147 (mmm) REVERT: G 37 LYS cc_start: 0.7759 (mttm) cc_final: 0.7535 (mttp) REVERT: G 105 GLN cc_start: 0.8637 (mp10) cc_final: 0.8409 (mp10) REVERT: G 119 LYS cc_start: 0.8693 (pttt) cc_final: 0.8380 (tppt) REVERT: H 80 ARG cc_start: 0.8980 (mtm-85) cc_final: 0.8187 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.1203 time to fit residues: 51.6524 Evaluate side-chains 228 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN E 40 HIS E 77 GLN E 94 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.072351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.054437 restraints weight = 44219.213| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.44 r_work: 0.2817 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13032 Z= 0.206 Angle : 0.780 7.779 18893 Z= 0.448 Chirality : 0.049 0.294 2146 Planarity : 0.005 0.038 1346 Dihedral : 30.608 177.303 4172 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 4.29 % Allowed : 12.70 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 2.37 (0.29), residues: 742 helix: 2.08 (0.21), residues: 540 sheet: None (None), residues: 0 loop : 0.26 (0.39), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 36 TYR 0.018 0.002 TYR H 122 PHE 0.015 0.002 PHE A 68 HIS 0.008 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.21 (13032) covalent geometry : angle 0.77955 / 0.45 (18893) hydrogen bonds : bond 0.07116 / 4.83 ( 778) hydrogen bonds : angle 3.60005 / 2.60 ( 1936) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 275 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8454 (tt0) cc_final: 0.7942 (mt-10) REVERT: A 77 GLN cc_start: 0.8119 (pt0) cc_final: 0.7707 (pp30) REVERT: A 114 HIS cc_start: 0.8892 (t70) cc_final: 0.8516 (t-90) REVERT: B 74 THR cc_start: 0.9325 (OUTLIER) cc_final: 0.8973 (p) REVERT: B 97 THR cc_start: 0.8964 (m) cc_final: 0.8585 (p) REVERT: B 99 TYR cc_start: 0.9117 (m-10) cc_final: 0.8705 (m-80) REVERT: C 74 ASN cc_start: 0.8845 (m-40) cc_final: 0.8439 (t0) REVERT: C 93 GLU cc_start: 0.9333 (mp0) cc_final: 0.9072 (mp0) REVERT: C 102 THR cc_start: 0.9127 (m) cc_final: 0.8786 (p) REVERT: D 52 ASP cc_start: 0.8921 (p0) cc_final: 0.8671 (p0) REVERT: D 69 ASP cc_start: 0.8970 (t0) cc_final: 0.8722 (t0) REVERT: D 89 THR cc_start: 0.9182 (p) cc_final: 0.8892 (p) REVERT: D 94 GLU cc_start: 0.8959 (mp0) cc_final: 0.7948 (mp0) REVERT: D 120 THR cc_start: 0.8932 (p) cc_final: 0.8708 (t) REVERT: E 121 MET cc_start: 0.7683 (mmm) cc_final: 0.7348 (mmm) REVERT: G 93 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8709 (mp0) REVERT: G 105 GLN cc_start: 0.8868 (mp10) cc_final: 0.8386 (mp10) REVERT: G 119 LYS cc_start: 0.8907 (pttt) cc_final: 0.8606 (tppt) outliers start: 27 outliers final: 19 residues processed: 287 average time/residue: 0.1149 time to fit residues: 46.4392 Evaluate side-chains 259 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 239 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain H residue 90 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 98 optimal weight: 30.0000 chunk 59 optimal weight: 9.9990 chunk 74 optimal weight: 30.0000 chunk 14 optimal weight: 8.9990 chunk 73 optimal weight: 30.0000 chunk 19 optimal weight: 0.0970 chunk 84 optimal weight: 30.0000 chunk 56 optimal weight: 2.9990 chunk 20 optimal weight: 0.0770 overall best weight: 2.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 ASN H 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.071531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.053414 restraints weight = 44727.180| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.46 r_work: 0.2792 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13032 Z= 0.178 Angle : 0.687 7.309 18893 Z= 0.403 Chirality : 0.045 0.321 2146 Planarity : 0.005 0.039 1346 Dihedral : 30.753 179.409 4172 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 3.49 % Allowed : 14.76 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 2.79 (0.29), residues: 742 helix: 2.45 (0.21), residues: 540 sheet: None (None), residues: 0 loop : 0.24 (0.39), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 80 TYR 0.022 0.002 TYR C 58 PHE 0.015 0.002 PHE D 71 HIS 0.007 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.18 (13032) covalent geometry : angle 0.68733 / 0.40 (18893) hydrogen bonds : bond 0.06417 / 4.37 ( 778) hydrogen bonds : angle 3.31367 / 2.38 ( 1936) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 264 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8691 (tt0) cc_final: 0.8019 (mt-10) REVERT: A 77 GLN cc_start: 0.8232 (pt0) cc_final: 0.7801 (pp30) REVERT: A 114 HIS cc_start: 0.8950 (t70) cc_final: 0.8599 (t-90) REVERT: A 121 MET cc_start: 0.8676 (mpp) cc_final: 0.8419 (mpp) REVERT: B 74 THR cc_start: 0.9359 (OUTLIER) cc_final: 0.8992 (p) REVERT: B 97 THR cc_start: 0.9100 (m) cc_final: 0.8655 (p) REVERT: B 99 TYR cc_start: 0.9077 (m-10) cc_final: 0.8742 (m-80) REVERT: C 57 GLU cc_start: 0.9064 (tt0) cc_final: 0.8791 (tt0) REVERT: C 65 GLU cc_start: 0.9405 (tt0) cc_final: 0.9066 (tm-30) REVERT: C 74 ASN cc_start: 0.8854 (m-40) cc_final: 0.8423 (t0) REVERT: C 93 GLU cc_start: 0.9436 (mp0) cc_final: 0.8916 (mp0) REVERT: C 102 THR cc_start: 0.9193 (m) cc_final: 0.8747 (p) REVERT: C 103 ILE cc_start: 0.9411 (mm) cc_final: 0.9119 (mm) REVERT: D 52 ASP cc_start: 0.8899 (p0) cc_final: 0.8626 (p0) REVERT: D 69 ASP cc_start: 0.8975 (t0) cc_final: 0.8672 (t0) REVERT: D 81 LEU cc_start: 0.9509 (mm) cc_final: 0.9176 (mt) REVERT: D 89 THR cc_start: 0.9221 (p) cc_final: 0.8853 (p) REVERT: D 94 GLU cc_start: 0.8957 (mp0) cc_final: 0.8011 (mp0) REVERT: D 121 LYS cc_start: 0.9538 (ttmt) cc_final: 0.9156 (ttpp) REVERT: F 28 GLN cc_start: 0.8975 (pt0) cc_final: 0.8532 (pm20) REVERT: F 54 GLU cc_start: 0.9190 (tp30) cc_final: 0.8963 (tp30) REVERT: F 64 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8726 (mp0) REVERT: F 99 TYR cc_start: 0.9276 (m-10) cc_final: 0.8940 (m-10) REVERT: G 40 TYR cc_start: 0.8929 (m-80) cc_final: 0.8693 (m-80) REVERT: G 62 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8311 (mm-30) REVERT: G 92 GLU cc_start: 0.8413 (pm20) cc_final: 0.8142 (pm20) REVERT: G 93 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8788 (mp0) REVERT: G 119 LYS cc_start: 0.8951 (pttt) cc_final: 0.8626 (tppt) REVERT: H 102 LEU cc_start: 0.9128 (mt) cc_final: 0.8853 (mt) REVERT: H 114 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8733 (mm-30) REVERT: H 117 LYS cc_start: 0.8847 (mtmm) cc_final: 0.8274 (mttp) outliers start: 22 outliers final: 13 residues processed: 276 average time/residue: 0.1145 time to fit residues: 44.8095 Evaluate side-chains 256 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 242 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 46 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 98 optimal weight: 30.0000 chunk 26 optimal weight: 0.0010 chunk 6 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 86 optimal weight: 40.0000 chunk 71 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS H 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.071086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.053080 restraints weight = 44605.608| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.45 r_work: 0.2784 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13032 Z= 0.166 Angle : 0.662 8.044 18893 Z= 0.387 Chirality : 0.043 0.351 2146 Planarity : 0.004 0.046 1346 Dihedral : 30.702 174.691 4172 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 3.17 % Allowed : 17.14 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 2.96 (0.29), residues: 742 helix: 2.61 (0.21), residues: 540 sheet: None (None), residues: 0 loop : 0.16 (0.39), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 100 TYR 0.016 0.002 TYR G 51 PHE 0.011 0.001 PHE A 68 HIS 0.012 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.17 (13032) covalent geometry : angle 0.66239 / 0.39 (18893) hydrogen bonds : bond 0.05637 / 3.82 ( 778) hydrogen bonds : angle 3.22166 / 2.30 ( 1936) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 260 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8760 (tt0) cc_final: 0.8038 (mt-10) REVERT: A 77 GLN cc_start: 0.8313 (pt0) cc_final: 0.7877 (pp30) REVERT: A 114 HIS cc_start: 0.8912 (t70) cc_final: 0.8626 (t-90) REVERT: B 74 THR cc_start: 0.9340 (OUTLIER) cc_final: 0.8940 (p) REVERT: B 97 THR cc_start: 0.9219 (m) cc_final: 0.8762 (p) REVERT: B 99 TYR cc_start: 0.9075 (m-10) cc_final: 0.8773 (m-80) REVERT: C 57 GLU cc_start: 0.9078 (tt0) cc_final: 0.8798 (tt0) REVERT: C 65 GLU cc_start: 0.9387 (tt0) cc_final: 0.8988 (tm-30) REVERT: C 74 ASN cc_start: 0.8802 (m-40) cc_final: 0.8485 (t0) REVERT: C 93 GLU cc_start: 0.9497 (mp0) cc_final: 0.9012 (mp0) REVERT: C 102 THR cc_start: 0.9177 (m) cc_final: 0.8804 (p) REVERT: C 103 ILE cc_start: 0.9400 (mm) cc_final: 0.9164 (mm) REVERT: D 52 ASP cc_start: 0.8914 (p0) cc_final: 0.8633 (p0) REVERT: D 69 ASP cc_start: 0.9010 (t0) cc_final: 0.8675 (t0) REVERT: D 89 THR cc_start: 0.9197 (p) cc_final: 0.8792 (p) REVERT: D 94 GLU cc_start: 0.8984 (mp0) cc_final: 0.8157 (mp0) REVERT: E 121 MET cc_start: 0.7924 (mmm) cc_final: 0.7569 (mmm) REVERT: F 60 LYS cc_start: 0.8813 (tttm) cc_final: 0.8428 (tppt) REVERT: F 64 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8756 (mp0) REVERT: G 40 TYR cc_start: 0.8895 (m-80) cc_final: 0.8682 (m-80) REVERT: G 62 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8332 (mm-30) REVERT: G 93 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8825 (mp0) REVERT: G 105 GLN cc_start: 0.8986 (mp10) cc_final: 0.8715 (mp10) REVERT: G 119 LYS cc_start: 0.8967 (pttt) cc_final: 0.8654 (tppt) REVERT: H 102 LEU cc_start: 0.9139 (mt) cc_final: 0.8903 (mt) REVERT: H 117 LYS cc_start: 0.8903 (mtmm) cc_final: 0.8671 (mtmm) outliers start: 20 outliers final: 14 residues processed: 268 average time/residue: 0.1105 time to fit residues: 41.9718 Evaluate side-chains 255 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 240 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 99 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 89 optimal weight: 30.0000 chunk 74 optimal weight: 30.0000 chunk 79 optimal weight: 30.0000 chunk 3 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 34 optimal weight: 0.0040 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN H 110 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.071822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.053844 restraints weight = 44813.992| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.43 r_work: 0.2805 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 13032 Z= 0.146 Angle : 0.633 8.242 18893 Z= 0.373 Chirality : 0.042 0.347 2146 Planarity : 0.004 0.040 1346 Dihedral : 30.569 175.632 4172 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.54 % Allowed : 18.73 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 3.00 (0.29), residues: 742 helix: 2.66 (0.21), residues: 540 sheet: None (None), residues: 0 loop : 0.12 (0.38), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 100 TYR 0.020 0.002 TYR E 55 PHE 0.010 0.001 PHE D 71 HIS 0.007 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.15 (13032) covalent geometry : angle 0.63252 / 0.37 (18893) hydrogen bonds : bond 0.05232 / 3.56 ( 778) hydrogen bonds : angle 3.04699 / 2.19 ( 1936) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 259 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8743 (tt0) cc_final: 0.8045 (mt-10) REVERT: A 77 GLN cc_start: 0.8253 (pt0) cc_final: 0.7861 (pp30) REVERT: A 95 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8281 (mt-10) REVERT: B 74 THR cc_start: 0.9291 (m) cc_final: 0.8895 (p) REVERT: B 97 THR cc_start: 0.9183 (m) cc_final: 0.8684 (p) REVERT: B 99 TYR cc_start: 0.9034 (m-10) cc_final: 0.8825 (m-80) REVERT: C 57 GLU cc_start: 0.9096 (tt0) cc_final: 0.8810 (tt0) REVERT: C 65 GLU cc_start: 0.9311 (tt0) cc_final: 0.8942 (tm-30) REVERT: C 74 ASN cc_start: 0.8776 (m-40) cc_final: 0.8490 (t0) REVERT: C 93 GLU cc_start: 0.9476 (mp0) cc_final: 0.9019 (mp0) REVERT: C 102 THR cc_start: 0.9186 (m) cc_final: 0.8805 (p) REVERT: C 103 ILE cc_start: 0.9408 (mm) cc_final: 0.9175 (mm) REVERT: D 52 ASP cc_start: 0.8864 (p0) cc_final: 0.8584 (p0) REVERT: D 69 ASP cc_start: 0.9040 (t0) cc_final: 0.8683 (t0) REVERT: D 89 THR cc_start: 0.9198 (p) cc_final: 0.8782 (p) REVERT: D 94 GLU cc_start: 0.8944 (mp0) cc_final: 0.8158 (mp0) REVERT: D 121 LYS cc_start: 0.9465 (ttmt) cc_final: 0.9067 (ttpp) REVERT: E 82 ASP cc_start: 0.8967 (t0) cc_final: 0.8749 (t0) REVERT: F 54 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8939 (mm-30) REVERT: F 60 LYS cc_start: 0.8829 (tttm) cc_final: 0.8463 (tppt) REVERT: F 64 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8667 (mp0) REVERT: G 93 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8785 (pm20) REVERT: G 105 GLN cc_start: 0.9064 (mp10) cc_final: 0.8681 (mp10) REVERT: G 119 LYS cc_start: 0.8964 (pttt) cc_final: 0.8667 (tppt) REVERT: H 102 LEU cc_start: 0.9107 (mt) cc_final: 0.8872 (mt) REVERT: H 114 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8717 (mm-30) REVERT: H 117 LYS cc_start: 0.8921 (mtmm) cc_final: 0.8463 (mttp) outliers start: 16 outliers final: 12 residues processed: 265 average time/residue: 0.1147 time to fit residues: 42.5822 Evaluate side-chains 249 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 237 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 96 LYS Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 50 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 101 optimal weight: 30.0000 chunk 53 optimal weight: 0.0270 chunk 64 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 GLN H 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.072063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.053714 restraints weight = 44786.697| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.45 r_work: 0.2809 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 13032 Z= 0.146 Angle : 0.637 10.017 18893 Z= 0.372 Chirality : 0.041 0.291 2146 Planarity : 0.004 0.046 1346 Dihedral : 30.455 175.899 4172 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.38 % Allowed : 20.95 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.29), residues: 742 helix: 2.72 (0.21), residues: 540 sheet: None (None), residues: 0 loop : 0.13 (0.38), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 100 TYR 0.019 0.002 TYR A 100 PHE 0.009 0.001 PHE D 71 HIS 0.005 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.15 (13032) covalent geometry : angle 0.63703 / 0.37 (18893) hydrogen bonds : bond 0.05054 / 3.43 ( 778) hydrogen bonds : angle 3.00112 / 2.15 ( 1936) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 255 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8780 (tt0) cc_final: 0.8096 (mt-10) REVERT: A 77 GLN cc_start: 0.8291 (pt0) cc_final: 0.7837 (pp30) REVERT: B 24 ARG cc_start: 0.8356 (mtm110) cc_final: 0.7886 (mmt180) REVERT: B 97 THR cc_start: 0.9239 (m) cc_final: 0.8855 (p) REVERT: B 99 TYR cc_start: 0.9022 (m-10) cc_final: 0.8809 (m-80) REVERT: C 57 GLU cc_start: 0.9095 (tt0) cc_final: 0.8812 (tt0) REVERT: C 65 GLU cc_start: 0.9300 (tt0) cc_final: 0.8984 (tm-30) REVERT: C 74 ASN cc_start: 0.8801 (m-40) cc_final: 0.8532 (t0) REVERT: C 85 GLN cc_start: 0.8872 (tp40) cc_final: 0.8572 (tt0) REVERT: C 93 GLU cc_start: 0.9488 (mp0) cc_final: 0.9183 (mp0) REVERT: C 102 THR cc_start: 0.9186 (m) cc_final: 0.8818 (p) REVERT: C 103 ILE cc_start: 0.9393 (mm) cc_final: 0.9177 (mm) REVERT: D 52 ASP cc_start: 0.8873 (p0) cc_final: 0.8591 (p0) REVERT: D 69 ASP cc_start: 0.9065 (t0) cc_final: 0.8714 (t0) REVERT: D 89 THR cc_start: 0.9174 (p) cc_final: 0.8746 (p) REVERT: D 94 GLU cc_start: 0.8944 (mp0) cc_final: 0.8187 (mp0) REVERT: D 121 LYS cc_start: 0.9522 (ttmt) cc_final: 0.9059 (ttpp) REVERT: E 59 THR cc_start: 0.8716 (p) cc_final: 0.8382 (t) REVERT: E 82 ASP cc_start: 0.8998 (t0) cc_final: 0.8743 (t0) REVERT: E 121 MET cc_start: 0.7958 (mmm) cc_final: 0.7691 (mmm) REVERT: F 54 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8959 (mm-30) REVERT: F 60 LYS cc_start: 0.8815 (tttm) cc_final: 0.8436 (tppt) REVERT: F 64 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8632 (mp0) REVERT: F 85 MET cc_start: 0.8723 (mmm) cc_final: 0.8062 (mmm) REVERT: G 62 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8370 (mm-30) REVERT: G 65 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8427 (tm-30) REVERT: G 92 GLU cc_start: 0.8427 (pm20) cc_final: 0.8146 (pm20) REVERT: G 119 LYS cc_start: 0.8982 (pttt) cc_final: 0.8681 (tppt) REVERT: H 102 LEU cc_start: 0.9131 (mt) cc_final: 0.8908 (mt) REVERT: H 114 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8650 (mm-30) REVERT: H 117 LYS cc_start: 0.8893 (mtmm) cc_final: 0.8404 (mttp) outliers start: 15 outliers final: 10 residues processed: 261 average time/residue: 0.1195 time to fit residues: 43.6485 Evaluate side-chains 254 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 244 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 84 optimal weight: 30.0000 chunk 87 optimal weight: 50.0000 chunk 3 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 80 optimal weight: 30.0000 chunk 90 optimal weight: 30.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.070683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.052607 restraints weight = 44594.799| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.43 r_work: 0.2783 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 13032 Z= 0.165 Angle : 0.646 9.975 18893 Z= 0.375 Chirality : 0.041 0.249 2146 Planarity : 0.004 0.038 1346 Dihedral : 30.488 177.234 4172 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.17 % Allowed : 21.11 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 3.07 (0.29), residues: 742 helix: 2.71 (0.21), residues: 540 sheet: None (None), residues: 0 loop : 0.14 (0.38), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 100 TYR 0.022 0.002 TYR G 40 PHE 0.021 0.002 PHE H 66 HIS 0.005 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.17 (13032) covalent geometry : angle 0.64605 / 0.37 (18893) hydrogen bonds : bond 0.05177 / 3.49 ( 778) hydrogen bonds : angle 3.11246 / 2.22 ( 1936) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 250 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8828 (tt0) cc_final: 0.8121 (tt0) REVERT: A 77 GLN cc_start: 0.8385 (pt0) cc_final: 0.7881 (pp30) REVERT: A 121 MET cc_start: 0.8725 (mpp) cc_final: 0.8459 (mpp) REVERT: B 97 THR cc_start: 0.9349 (m) cc_final: 0.8939 (p) REVERT: B 99 TYR cc_start: 0.9131 (m-10) cc_final: 0.8841 (m-80) REVERT: C 57 GLU cc_start: 0.9121 (tt0) cc_final: 0.8831 (tt0) REVERT: C 65 GLU cc_start: 0.9277 (tt0) cc_final: 0.8961 (tm-30) REVERT: C 74 ASN cc_start: 0.8830 (m-40) cc_final: 0.8616 (t0) REVERT: C 85 GLN cc_start: 0.8937 (tp40) cc_final: 0.8530 (tt0) REVERT: C 93 GLU cc_start: 0.9511 (mp0) cc_final: 0.9159 (mp0) REVERT: C 102 THR cc_start: 0.9183 (m) cc_final: 0.8810 (p) REVERT: C 103 ILE cc_start: 0.9386 (mm) cc_final: 0.9153 (mm) REVERT: D 52 ASP cc_start: 0.8868 (p0) cc_final: 0.8587 (p0) REVERT: D 69 ASP cc_start: 0.9065 (t0) cc_final: 0.8695 (t0) REVERT: D 94 GLU cc_start: 0.8999 (mp0) cc_final: 0.8194 (mp0) REVERT: D 121 LYS cc_start: 0.9523 (ttmt) cc_final: 0.9100 (ttpp) REVERT: E 59 THR cc_start: 0.8973 (p) cc_final: 0.8709 (t) REVERT: E 82 ASP cc_start: 0.9068 (t0) cc_final: 0.8796 (t0) REVERT: F 28 GLN cc_start: 0.8778 (pm20) cc_final: 0.8555 (pm20) REVERT: F 54 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8948 (mm-30) REVERT: F 60 LYS cc_start: 0.8814 (tttm) cc_final: 0.8495 (ttmt) REVERT: F 64 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8659 (mp0) REVERT: F 85 MET cc_start: 0.8815 (mmm) cc_final: 0.7988 (mmm) REVERT: G 65 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8400 (tm-30) REVERT: G 69 ASN cc_start: 0.8273 (m110) cc_final: 0.8069 (m-40) REVERT: G 93 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7928 (pm20) REVERT: G 105 GLN cc_start: 0.8845 (mp10) cc_final: 0.8554 (mp10) REVERT: G 119 LYS cc_start: 0.9011 (pttt) cc_final: 0.8726 (tppt) REVERT: H 69 ASP cc_start: 0.8597 (t0) cc_final: 0.8346 (t0) REVERT: H 114 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8582 (mm-30) REVERT: H 117 LYS cc_start: 0.8887 (mtmm) cc_final: 0.8397 (mttp) outliers start: 20 outliers final: 12 residues processed: 256 average time/residue: 0.1172 time to fit residues: 41.6552 Evaluate side-chains 249 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 236 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 93 GLU Chi-restraints excluded: chain G residue 112 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 24 optimal weight: 1.9990 chunk 78 optimal weight: 30.0000 chunk 69 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 70 optimal weight: 30.0000 chunk 49 optimal weight: 0.6980 chunk 93 optimal weight: 30.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.071509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.053407 restraints weight = 44448.303| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.45 r_work: 0.2808 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13032 Z= 0.144 Angle : 0.648 11.087 18893 Z= 0.373 Chirality : 0.041 0.245 2146 Planarity : 0.004 0.039 1346 Dihedral : 30.397 178.267 4172 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.06 % Allowed : 22.86 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 3.02 (0.29), residues: 742 helix: 2.68 (0.21), residues: 540 sheet: None (None), residues: 0 loop : 0.09 (0.38), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 100 TYR 0.017 0.002 TYR F 89 PHE 0.013 0.001 PHE A 79 HIS 0.005 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (13032) covalent geometry : angle 0.64750 / 0.37 (18893) hydrogen bonds : bond 0.04862 / 3.28 ( 778) hydrogen bonds : angle 3.04226 / 2.18 ( 1936) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 246 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8814 (tt0) cc_final: 0.8182 (tt0) REVERT: A 77 GLN cc_start: 0.8419 (pt0) cc_final: 0.7878 (pp30) REVERT: A 78 ASP cc_start: 0.7914 (m-30) cc_final: 0.7074 (m-30) REVERT: A 121 MET cc_start: 0.8763 (mpp) cc_final: 0.8479 (mpp) REVERT: B 97 THR cc_start: 0.9312 (m) cc_final: 0.8947 (p) REVERT: B 99 TYR cc_start: 0.9105 (m-10) cc_final: 0.8873 (m-10) REVERT: C 57 GLU cc_start: 0.9101 (tt0) cc_final: 0.8810 (tt0) REVERT: C 85 GLN cc_start: 0.8845 (tp40) cc_final: 0.8535 (tt0) REVERT: C 93 GLU cc_start: 0.9445 (mp0) cc_final: 0.9052 (mp0) REVERT: C 102 THR cc_start: 0.9172 (m) cc_final: 0.8845 (p) REVERT: C 103 ILE cc_start: 0.9382 (mm) cc_final: 0.9152 (mm) REVERT: D 52 ASP cc_start: 0.8878 (p0) cc_final: 0.8594 (p0) REVERT: D 69 ASP cc_start: 0.9075 (t0) cc_final: 0.8743 (t0) REVERT: D 94 GLU cc_start: 0.8982 (mp0) cc_final: 0.8184 (mp0) REVERT: D 106 GLU cc_start: 0.7650 (pp20) cc_final: 0.7329 (tm-30) REVERT: E 59 THR cc_start: 0.8985 (p) cc_final: 0.8742 (t) REVERT: E 82 ASP cc_start: 0.9092 (t0) cc_final: 0.8861 (t0) REVERT: F 54 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8972 (mm-30) REVERT: F 60 LYS cc_start: 0.8841 (tttm) cc_final: 0.8450 (ttmt) REVERT: F 64 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8639 (mp0) REVERT: F 85 MET cc_start: 0.8804 (mmm) cc_final: 0.7999 (mmm) REVERT: G 65 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8400 (tm-30) REVERT: G 69 ASN cc_start: 0.8279 (m110) cc_final: 0.8019 (m-40) REVERT: G 105 GLN cc_start: 0.8832 (mp10) cc_final: 0.8477 (mp10) REVERT: G 119 LYS cc_start: 0.9027 (pttt) cc_final: 0.8741 (tppt) REVERT: H 69 ASP cc_start: 0.8467 (t0) cc_final: 0.8188 (t0) REVERT: H 114 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8525 (mm-30) REVERT: H 117 LYS cc_start: 0.8890 (mtmm) cc_final: 0.8363 (mttp) outliers start: 13 outliers final: 10 residues processed: 251 average time/residue: 0.1249 time to fit residues: 43.5712 Evaluate side-chains 242 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 232 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 112 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.9990 chunk 92 optimal weight: 30.0000 chunk 51 optimal weight: 7.9990 chunk 32 optimal weight: 0.0040 chunk 6 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 73 optimal weight: 40.0000 chunk 27 optimal weight: 6.9990 chunk 81 optimal weight: 30.0000 chunk 80 optimal weight: 20.0000 overall best weight: 3.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN D 110 HIS ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.069384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.051221 restraints weight = 44803.444| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.43 r_work: 0.2750 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13032 Z= 0.200 Angle : 0.702 10.669 18893 Z= 0.396 Chirality : 0.042 0.237 2146 Planarity : 0.005 0.038 1346 Dihedral : 30.498 179.258 4172 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.75 % Allowed : 24.13 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 2.93 (0.29), residues: 742 helix: 2.60 (0.21), residues: 540 sheet: None (None), residues: 0 loop : 0.10 (0.39), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 100 TYR 0.021 0.002 TYR G 40 PHE 0.010 0.001 PHE A 79 HIS 0.006 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.20 (13032) covalent geometry : angle 0.70214 / 0.40 (18893) hydrogen bonds : bond 0.05398 / 3.63 ( 778) hydrogen bonds : angle 3.24048 / 2.30 ( 1936) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 240 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8844 (tt0) cc_final: 0.8268 (tt0) REVERT: A 77 GLN cc_start: 0.8583 (pt0) cc_final: 0.7983 (pp30) REVERT: A 78 ASP cc_start: 0.7940 (m-30) cc_final: 0.7089 (m-30) REVERT: B 24 ARG cc_start: 0.8390 (mtm110) cc_final: 0.7903 (mmt180) REVERT: B 97 THR cc_start: 0.9425 (m) cc_final: 0.9103 (p) REVERT: B 99 TYR cc_start: 0.9135 (m-10) cc_final: 0.8867 (m-10) REVERT: C 57 GLU cc_start: 0.9124 (tt0) cc_final: 0.8819 (tt0) REVERT: C 85 GLN cc_start: 0.8862 (tp40) cc_final: 0.8525 (tt0) REVERT: C 93 GLU cc_start: 0.9508 (mp0) cc_final: 0.9162 (mp0) REVERT: C 102 THR cc_start: 0.9204 (m) cc_final: 0.8813 (p) REVERT: C 103 ILE cc_start: 0.9355 (mm) cc_final: 0.9134 (mm) REVERT: D 49 VAL cc_start: 0.8962 (t) cc_final: 0.8634 (p) REVERT: D 52 ASP cc_start: 0.8889 (p0) cc_final: 0.8595 (p0) REVERT: D 69 ASP cc_start: 0.9158 (t0) cc_final: 0.8761 (t0) REVERT: D 94 GLU cc_start: 0.9013 (mp0) cc_final: 0.8227 (mp0) REVERT: E 82 ASP cc_start: 0.9155 (t0) cc_final: 0.8860 (t0) REVERT: E 86 GLN cc_start: 0.8209 (mt0) cc_final: 0.7898 (mt0) REVERT: F 54 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8928 (mm-30) REVERT: F 60 LYS cc_start: 0.8917 (tttm) cc_final: 0.8512 (ttmt) REVERT: F 64 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8673 (mp0) REVERT: F 85 MET cc_start: 0.8913 (mmm) cc_final: 0.8145 (mmm) REVERT: G 62 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8298 (mm-30) REVERT: G 65 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8416 (tm-30) REVERT: G 69 ASN cc_start: 0.8278 (m110) cc_final: 0.8003 (m-40) REVERT: G 119 LYS cc_start: 0.9078 (pttt) cc_final: 0.8812 (tppt) REVERT: H 69 ASP cc_start: 0.8591 (t0) cc_final: 0.8354 (t0) REVERT: H 114 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8418 (mm-30) REVERT: H 117 LYS cc_start: 0.8937 (mtmm) cc_final: 0.8394 (mttp) outliers start: 11 outliers final: 9 residues processed: 246 average time/residue: 0.1210 time to fit residues: 41.5762 Evaluate side-chains 239 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 230 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 112 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 46 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 77 optimal weight: 30.0000 chunk 81 optimal weight: 30.0000 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.070142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.052245 restraints weight = 44584.371| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.40 r_work: 0.2776 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13032 Z= 0.159 Angle : 0.678 14.745 18893 Z= 0.385 Chirality : 0.041 0.236 2146 Planarity : 0.004 0.038 1346 Dihedral : 30.451 179.917 4172 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.06 % Allowed : 24.92 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 2.93 (0.29), residues: 742 helix: 2.62 (0.21), residues: 540 sheet: None (None), residues: 0 loop : 0.04 (0.39), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 72 TYR 0.019 0.002 TYR F 89 PHE 0.024 0.001 PHE H 66 HIS 0.006 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.16 (13032) covalent geometry : angle 0.67788 / 0.38 (18893) hydrogen bonds : bond 0.04900 / 3.30 ( 778) hydrogen bonds : angle 3.11083 / 2.22 ( 1936) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 232 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8809 (tt0) cc_final: 0.8169 (tt0) REVERT: A 77 GLN cc_start: 0.8589 (pt0) cc_final: 0.8016 (pp30) REVERT: A 78 ASP cc_start: 0.7917 (m-30) cc_final: 0.7026 (m-30) REVERT: B 24 ARG cc_start: 0.8371 (mtm110) cc_final: 0.7882 (mmt180) REVERT: B 97 THR cc_start: 0.9388 (m) cc_final: 0.9053 (p) REVERT: B 99 TYR cc_start: 0.9125 (m-10) cc_final: 0.8881 (m-10) REVERT: C 57 GLU cc_start: 0.9140 (tt0) cc_final: 0.8831 (tt0) REVERT: C 85 GLN cc_start: 0.8814 (tp40) cc_final: 0.8519 (tt0) REVERT: C 93 GLU cc_start: 0.9505 (mp0) cc_final: 0.9168 (mp0) REVERT: C 102 THR cc_start: 0.9160 (m) cc_final: 0.8791 (p) REVERT: C 103 ILE cc_start: 0.9376 (mm) cc_final: 0.9160 (mm) REVERT: D 48 GLN cc_start: 0.9161 (tp40) cc_final: 0.8929 (tm-30) REVERT: D 52 ASP cc_start: 0.8905 (p0) cc_final: 0.8620 (p0) REVERT: D 69 ASP cc_start: 0.9157 (t0) cc_final: 0.8775 (t0) REVERT: D 94 GLU cc_start: 0.9005 (mp0) cc_final: 0.8191 (mp0) REVERT: E 42 TYR cc_start: 0.8826 (m-10) cc_final: 0.8473 (m-10) REVERT: E 86 GLN cc_start: 0.8189 (mt0) cc_final: 0.7885 (mt0) REVERT: F 54 GLU cc_start: 0.9225 (mm-30) cc_final: 0.8877 (mm-30) REVERT: F 60 LYS cc_start: 0.8913 (tttm) cc_final: 0.8469 (ttmt) REVERT: F 64 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8614 (mp0) REVERT: F 85 MET cc_start: 0.8828 (mmm) cc_final: 0.8060 (mmm) REVERT: G 65 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8367 (tm-30) REVERT: G 69 ASN cc_start: 0.8168 (m110) cc_final: 0.7834 (m-40) REVERT: G 105 GLN cc_start: 0.8784 (mp10) cc_final: 0.8536 (mp10) REVERT: G 119 LYS cc_start: 0.9095 (pttt) cc_final: 0.8833 (tppt) REVERT: H 69 ASP cc_start: 0.8572 (t0) cc_final: 0.8348 (t0) REVERT: H 114 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8526 (mm-30) REVERT: H 117 LYS cc_start: 0.8935 (mtmm) cc_final: 0.8399 (mttp) outliers start: 13 outliers final: 10 residues processed: 239 average time/residue: 0.1222 time to fit residues: 40.5621 Evaluate side-chains 239 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 229 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 112 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 9 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 80 optimal weight: 30.0000 chunk 52 optimal weight: 0.8980 chunk 74 optimal weight: 30.0000 chunk 97 optimal weight: 30.0000 chunk 7 optimal weight: 2.9990 chunk 98 optimal weight: 30.0000 chunk 101 optimal weight: 30.0000 chunk 53 optimal weight: 0.8980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.071405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.052284 restraints weight = 43607.243| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.20 r_work: 0.2791 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13032 Z= 0.165 Angle : 0.688 17.481 18893 Z= 0.388 Chirality : 0.041 0.236 2146 Planarity : 0.004 0.039 1346 Dihedral : 30.426 179.230 4172 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.38 % Allowed : 24.13 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 2.93 (0.30), residues: 742 helix: 2.62 (0.22), residues: 540 sheet: None (None), residues: 0 loop : 0.04 (0.39), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 100 TYR 0.020 0.002 TYR F 89 PHE 0.012 0.001 PHE A 79 HIS 0.006 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (13032) covalent geometry : angle 0.68848 / 0.39 (18893) hydrogen bonds : bond 0.04913 / 3.31 ( 778) hydrogen bonds : angle 3.14354 / 2.23 ( 1936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2362.06 seconds wall clock time: 41 minutes 11.57 seconds (2471.57 seconds total)