Starting phenix.real_space_refine on Thu Jul 2 03:22:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zap_39883/07_2026/8zap_39883.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zap_39883/07_2026/8zap_39883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zap_39883/07_2026/8zap_39883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zap_39883/07_2026/8zap_39883.map" model { file = "/net/cci-nas-00/data/ceres_data/8zap_39883/07_2026/8zap_39883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zap_39883/07_2026/8zap_39883.cif" } resolution = 2.6 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= -0.000 sd= 0.014 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 K 24 8.98 5 S 57 5.16 5 C 4323 2.51 5 N 965 2.21 5 O 1073 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6442 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2102 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 16, 'TRANS': 241} Chain breaks: 1 Chain: "B" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2110 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 16, 'TRANS': 242} Chain: "C" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2110 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 16, 'TRANS': 242} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 20 Ad-hoc single atom residues: {' K': 8} Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Chain breaks: 8 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 20 Ad-hoc single atom residues: {' K': 8} Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Chain breaks: 8 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 20 Ad-hoc single atom residues: {' K': 8} Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Chain breaks: 8 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 1.49, per 1000 atoms: 0.23 Number of scatterers: 6442 At special positions: 0 Unit cell: (74.2, 73.85, 79.1, 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) K 24 19.00 S 57 16.00 O 1073 8.00 N 965 7.00 C 4323 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 419.4 milliseconds 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 74.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 21 through 50 removed outlier: 3.689A pdb=" N GLY A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 Processing helix chain 'A' and resid 68 through 90 Processing helix chain 'A' and resid 105 through 122 removed outlier: 3.585A pdb=" N THR A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 125 through 126 No H-bonds generated for 'chain 'A' and resid 125 through 126' Processing helix chain 'A' and resid 128 through 128 No H-bonds generated for 'chain 'A' and resid 128 through 128' Processing helix chain 'A' and resid 129 through 146 Processing helix chain 'A' and resid 149 through 178 removed outlier: 3.722A pdb=" N ALA A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Proline residue: A 164 - end of helix removed outlier: 3.585A pdb=" N LEU A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 199 Processing helix chain 'A' and resid 200 through 209 removed outlier: 3.539A pdb=" N ILE A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 233 through 252 Processing helix chain 'B' and resid 21 through 50 removed outlier: 3.688A pdb=" N GLY B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 67 Processing helix chain 'B' and resid 68 through 90 Processing helix chain 'B' and resid 105 through 121 removed outlier: 3.564A pdb=" N THR B 109 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 125 through 146 Processing helix chain 'B' and resid 149 through 178 removed outlier: 3.747A pdb=" N ALA B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Proline residue: B 164 - end of helix removed outlier: 3.583A pdb=" N LEU B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 199 Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.572A pdb=" N ILE B 204 " --> pdb=" O PRO B 200 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 207 " --> pdb=" O PRO B 203 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 233 through 252 Processing helix chain 'C' and resid 21 through 50 removed outlier: 3.671A pdb=" N GLY C 50 " --> pdb=" O ARG C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 67 Processing helix chain 'C' and resid 68 through 90 Processing helix chain 'C' and resid 105 through 121 removed outlier: 3.541A pdb=" N THR C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'C' and resid 149 through 178 removed outlier: 3.747A pdb=" N ALA C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) Proline residue: C 164 - end of helix removed outlier: 3.580A pdb=" N LEU C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 199 Processing helix chain 'C' and resid 200 through 209 removed outlier: 3.546A pdb=" N ILE C 204 " --> pdb=" O PRO C 200 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C 208 " --> pdb=" O ILE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 233 Processing helix chain 'C' and resid 233 through 252 417 hydrogen bonds defined for protein. 1242 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: 1.11 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1814 1.34 - 1.46: 1947 1.46 - 1.58: 2794 1.58 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 6633 Sorted by residual: bond pdb=" CA PHE B 202 " pdb=" C PHE B 202 " ideal model delta sigma weight residual 1.520 1.531 -0.011 1.23e-02 6.61e+03 7.98e-01 bond pdb=" CA PHE C 202 " pdb=" C PHE C 202 " ideal model delta sigma weight residual 1.520 1.531 -0.011 1.23e-02 6.61e+03 7.90e-01 bond pdb=" CA PHE A 202 " pdb=" C PHE A 202 " ideal model delta sigma weight residual 1.520 1.531 -0.010 1.23e-02 6.61e+03 7.21e-01 bond pdb=" CA GLY A 158 " pdb=" C GLY A 158 " ideal model delta sigma weight residual 1.516 1.507 0.009 1.12e-02 7.97e+03 6.88e-01 bond pdb=" C PHE B 3 " pdb=" N TYR B 4 " ideal model delta sigma weight residual 1.329 1.314 0.014 1.79e-02 3.12e+03 6.44e-01 ... (remaining 6628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 8869 1.89 - 3.78: 143 3.78 - 5.67: 25 5.67 - 7.56: 0 7.56 - 9.46: 3 Bond angle restraints: 9040 Sorted by residual: angle pdb=" C GLY A 93 " pdb=" N THR A 94 " pdb=" CA THR A 94 " ideal model delta sigma weight residual 120.49 129.95 -9.46 1.42e+00 4.96e-01 4.43e+01 angle pdb=" C GLY B 93 " pdb=" N THR B 94 " pdb=" CA THR B 94 " ideal model delta sigma weight residual 120.49 129.57 -9.08 1.42e+00 4.96e-01 4.09e+01 angle pdb=" C GLY C 93 " pdb=" N THR C 94 " pdb=" CA THR C 94 " ideal model delta sigma weight residual 120.49 129.53 -9.04 1.42e+00 4.96e-01 4.05e+01 angle pdb=" N VAL A 107 " pdb=" CA VAL A 107 " pdb=" C VAL A 107 " ideal model delta sigma weight residual 113.00 109.03 3.97 1.30e+00 5.92e-01 9.34e+00 angle pdb=" N VAL C 107 " pdb=" CA VAL C 107 " pdb=" C VAL C 107 " ideal model delta sigma weight residual 113.00 109.18 3.82 1.30e+00 5.92e-01 8.64e+00 ... (remaining 9035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 3140 15.94 - 31.87: 412 31.87 - 47.80: 109 47.80 - 63.73: 34 63.73 - 79.67: 4 Dihedral angle restraints: 3699 sinusoidal: 1447 harmonic: 2252 Sorted by residual: dihedral pdb=" CA ASP A 5 " pdb=" CB ASP A 5 " pdb=" CG ASP A 5 " pdb=" OD1 ASP A 5 " ideal model delta sinusoidal sigma weight residual -30.00 -85.00 55.00 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA ASP C 5 " pdb=" CB ASP C 5 " pdb=" CG ASP C 5 " pdb=" OD1 ASP C 5 " ideal model delta sinusoidal sigma weight residual -30.00 -84.10 54.10 1 2.00e+01 2.50e-03 9.93e+00 dihedral pdb=" CA THR C 109 " pdb=" C THR C 109 " pdb=" N THR C 110 " pdb=" CA THR C 110 " ideal model delta harmonic sigma weight residual -180.00 -164.55 -15.45 0 5.00e+00 4.00e-02 9.55e+00 ... (remaining 3696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 488 0.026 - 0.052: 274 0.052 - 0.079: 116 0.079 - 0.105: 32 0.105 - 0.131: 18 Chirality restraints: 928 Sorted by residual: chirality pdb=" CA THR C 110 " pdb=" N THR C 110 " pdb=" C THR C 110 " pdb=" CB THR C 110 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA PHE C 144 " pdb=" N PHE C 144 " pdb=" C PHE C 144 " pdb=" CB PHE C 144 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA PRO A 182 " pdb=" N PRO A 182 " pdb=" C PRO A 182 " pdb=" CB PRO A 182 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 925 not shown) Planarity restraints: 1111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 132 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" C ALA A 132 " -0.030 2.00e-02 2.50e+03 pdb=" O ALA A 132 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL A 133 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 94 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO C 95 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 94 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO B 95 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " -0.023 5.00e-02 4.00e+02 ... (remaining 1108 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.22: 18 2.22 - 2.95: 2986 2.95 - 3.68: 12339 3.68 - 4.41: 21831 4.41 - 5.14: 34117 Nonbonded interactions: 71291 Sorted by model distance: nonbonded pdb=" K K A 305 " pdb=" O HOH A 405 " model vdw 1.487 3.590 nonbonded pdb=" K K B 305 " pdb=" O HOH B 406 " model vdw 1.492 3.590 nonbonded pdb=" K K C 305 " pdb=" O HOH C 406 " model vdw 1.495 3.590 nonbonded pdb=" K K B 305 " pdb=" O HOH B 410 " model vdw 1.574 3.590 nonbonded pdb=" K K C 305 " pdb=" O HOH C 410 " model vdw 1.584 3.590 ... (remaining 71286 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 'B' and (resid 2 through 126 or resid 128 through 309)) selection = (chain 'C' and (resid 2 through 126 or resid 128 through 309)) } 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: 25.120 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: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.720 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 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 : 0.003 0.032 6636 Z= 0.157 Angle : 0.597 9.456 9040 Z= 0.347 Chirality : 0.040 0.131 928 Planarity : 0.006 0.043 1111 Dihedral : 16.029 79.666 2267 Min Nonbonded Distance : 1.487 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.19 % Allowed : 14.52 % Favored : 81.29 % 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: 1.24 (0.30), residues: 768 helix: 0.86 (0.22), residues: 520 sheet: None (None), residues: 0 loop : 1.10 (0.43), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 151 TYR 0.012 0.001 TYR B 81 PHE 0.011 0.001 PHE C 134 TRP 0.010 0.001 TRP A 42 HIS 0.003 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 ( 6633) covalent geometry : angle 0.59653 / 0.35 ( 9040) hydrogen bonds : bond 0.13624 / 9.27 ( 417) hydrogen bonds : angle 6.63489 / 4.66 ( 1242) Misc. bond : bond 0.00089 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7669 (m-80) REVERT: A 174 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7611 (mtpt) REVERT: A 183 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.6778 (mptt) REVERT: A 227 PHE cc_start: 0.7707 (m-10) cc_final: 0.7436 (m-80) REVERT: B 3 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7713 (m-80) REVERT: B 174 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7692 (mtpt) REVERT: B 183 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.6755 (mptt) REVERT: C 3 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.7698 (m-80) REVERT: C 174 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7662 (mtpt) REVERT: C 227 PHE cc_start: 0.7695 (m-10) cc_final: 0.7478 (m-80) outliers start: 28 outliers final: 12 residues processed: 92 average time/residue: 0.4176 time to fit residues: 40.9260 Evaluate side-chains 91 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0870 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS B 215 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.126120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.111075 restraints weight = 5904.509| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 0.83 r_work: 0.3055 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6636 Z= 0.146 Angle : 0.529 5.260 9040 Z= 0.267 Chirality : 0.039 0.145 928 Planarity : 0.005 0.042 1111 Dihedral : 10.825 79.207 924 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.89 % Allowed : 13.47 % Favored : 82.63 % 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: 2.11 (0.29), residues: 768 helix: 1.72 (0.21), residues: 525 sheet: None (None), residues: 0 loop : 0.90 (0.44), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 186 TYR 0.009 0.002 TYR B 180 PHE 0.015 0.001 PHE B 144 TRP 0.010 0.001 TRP A 138 HIS 0.003 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 6633) covalent geometry : angle 0.52876 / 0.27 ( 9040) hydrogen bonds : bond 0.04682 / 3.17 ( 417) hydrogen bonds : angle 4.48185 / 3.16 ( 1242) Misc. bond : bond 0.00050 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7471 (m-80) REVERT: A 183 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6584 (mptt) REVERT: A 227 PHE cc_start: 0.7604 (m-10) cc_final: 0.7303 (m-80) REVERT: B 3 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7498 (m-80) REVERT: B 183 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6486 (mptt) REVERT: C 3 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7527 (m-80) REVERT: C 183 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6469 (mptt) REVERT: C 227 PHE cc_start: 0.7602 (m-10) cc_final: 0.7334 (m-80) outliers start: 26 outliers final: 8 residues processed: 100 average time/residue: 0.4013 time to fit residues: 42.5060 Evaluate side-chains 92 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.124704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.109747 restraints weight = 5881.235| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 0.82 r_work: 0.3035 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6636 Z= 0.158 Angle : 0.533 5.264 9040 Z= 0.267 Chirality : 0.040 0.154 928 Planarity : 0.005 0.039 1111 Dihedral : 9.817 80.245 904 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.94 % Allowed : 13.77 % Favored : 81.29 % 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: 2.33 (0.29), residues: 768 helix: 1.91 (0.21), residues: 525 sheet: None (None), residues: 0 loop : 0.90 (0.44), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 186 TYR 0.010 0.002 TYR A 150 PHE 0.017 0.002 PHE B 144 TRP 0.010 0.001 TRP C 42 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 6633) covalent geometry : angle 0.53331 / 0.27 ( 9040) hydrogen bonds : bond 0.04609 / 3.12 ( 417) hydrogen bonds : angle 4.38760 / 3.09 ( 1242) Misc. bond : bond 0.00056 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 81 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7155 (m-80) REVERT: A 183 LYS cc_start: 0.7322 (OUTLIER) cc_final: 0.6655 (mptt) REVERT: A 227 PHE cc_start: 0.7668 (m-10) cc_final: 0.7358 (m-80) REVERT: B 3 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7124 (m-80) REVERT: B 183 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6519 (mptt) REVERT: C 3 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7178 (m-80) REVERT: C 183 LYS cc_start: 0.7277 (OUTLIER) cc_final: 0.6588 (mptt) REVERT: C 227 PHE cc_start: 0.7648 (m-10) cc_final: 0.7348 (m-80) outliers start: 33 outliers final: 10 residues processed: 106 average time/residue: 0.4152 time to fit residues: 46.9264 Evaluate side-chains 87 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 62 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.121511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.105583 restraints weight = 5946.466| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 0.89 r_work: 0.3200 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6636 Z= 0.147 Angle : 0.519 5.241 9040 Z= 0.258 Chirality : 0.039 0.155 928 Planarity : 0.005 0.039 1111 Dihedral : 9.433 78.512 904 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.04 % Allowed : 15.42 % Favored : 80.54 % 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: 2.38 (0.29), residues: 768 helix: 1.94 (0.21), residues: 524 sheet: None (None), residues: 0 loop : 0.96 (0.44), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 186 TYR 0.008 0.001 TYR A 150 PHE 0.017 0.001 PHE B 144 TRP 0.011 0.001 TRP C 42 HIS 0.002 0.001 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 6633) covalent geometry : angle 0.51907 / 0.26 ( 9040) hydrogen bonds : bond 0.04441 / 3.00 ( 417) hydrogen bonds : angle 4.35130 / 3.06 ( 1242) Misc. bond : bond 0.00047 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.196 Fit side-chains REVERT: A 183 LYS cc_start: 0.7297 (OUTLIER) cc_final: 0.6654 (mptt) REVERT: A 227 PHE cc_start: 0.7655 (m-10) cc_final: 0.7351 (m-80) REVERT: B 183 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6530 (mptt) REVERT: B 230 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7221 (tp) REVERT: C 183 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.6606 (mptt) REVERT: C 227 PHE cc_start: 0.7645 (m-10) cc_final: 0.7359 (m-80) REVERT: C 230 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7234 (tp) outliers start: 27 outliers final: 19 residues processed: 97 average time/residue: 0.4178 time to fit residues: 43.1360 Evaluate side-chains 93 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 230 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 2 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.118029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.102128 restraints weight = 5979.361| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 0.89 r_work: 0.3153 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6636 Z= 0.212 Angle : 0.580 5.251 9040 Z= 0.290 Chirality : 0.042 0.166 928 Planarity : 0.005 0.039 1111 Dihedral : 9.684 86.894 904 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.04 % Allowed : 15.12 % Favored : 80.84 % 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: 2.16 (0.29), residues: 768 helix: 1.77 (0.20), residues: 515 sheet: None (None), residues: 0 loop : 0.93 (0.43), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 186 TYR 0.011 0.002 TYR B 180 PHE 0.023 0.002 PHE B 144 TRP 0.011 0.002 TRP C 42 HIS 0.003 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 ( 6633) covalent geometry : angle 0.57988 / 0.29 ( 9040) hydrogen bonds : bond 0.04974 / 3.37 ( 417) hydrogen bonds : angle 4.47967 / 3.16 ( 1242) Misc. bond : bond 0.00086 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 183 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.6766 (mptt) REVERT: A 230 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7501 (tp) REVERT: B 183 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6645 (mptt) REVERT: B 230 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7322 (tp) REVERT: C 183 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.6719 (mptt) REVERT: C 230 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7448 (tp) outliers start: 27 outliers final: 15 residues processed: 92 average time/residue: 0.4582 time to fit residues: 44.6596 Evaluate side-chains 90 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 230 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 0.0030 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 54 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.128257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.113436 restraints weight = 5814.541| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 0.89 r_work: 0.2983 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6636 Z= 0.129 Angle : 0.501 5.292 9040 Z= 0.249 Chirality : 0.038 0.152 928 Planarity : 0.005 0.039 1111 Dihedral : 9.173 79.396 904 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.89 % Allowed : 15.57 % Favored : 80.54 % 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: 2.43 (0.29), residues: 768 helix: 1.95 (0.20), residues: 522 sheet: None (None), residues: 0 loop : 1.06 (0.45), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 186 TYR 0.010 0.001 TYR C 45 PHE 0.016 0.001 PHE B 144 TRP 0.012 0.001 TRP C 42 HIS 0.002 0.000 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 6633) covalent geometry : angle 0.50114 / 0.25 ( 9040) hydrogen bonds : bond 0.04285 / 2.89 ( 417) hydrogen bonds : angle 4.36454 / 3.07 ( 1242) Misc. bond : bond 0.00035 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.248 Fit side-chains REVERT: A 183 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6446 (mptt) REVERT: A 227 PHE cc_start: 0.7533 (m-10) cc_final: 0.7202 (m-80) REVERT: B 183 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6354 (mptt) REVERT: C 183 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6417 (mptt) REVERT: C 227 PHE cc_start: 0.7544 (m-10) cc_final: 0.7239 (m-80) REVERT: C 230 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7226 (tp) outliers start: 26 outliers final: 20 residues processed: 100 average time/residue: 0.4083 time to fit residues: 43.4247 Evaluate side-chains 101 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 234 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.118416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.102849 restraints weight = 5959.361| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 0.87 r_work: 0.2925 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6636 Z= 0.222 Angle : 0.584 5.373 9040 Z= 0.291 Chirality : 0.043 0.165 928 Planarity : 0.005 0.039 1111 Dihedral : 9.620 88.439 904 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.74 % Allowed : 15.42 % Favored : 80.84 % 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: 2.16 (0.29), residues: 768 helix: 1.74 (0.20), residues: 515 sheet: None (None), residues: 0 loop : 0.99 (0.44), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 186 TYR 0.012 0.002 TYR A 81 PHE 0.022 0.002 PHE B 144 TRP 0.011 0.002 TRP C 42 HIS 0.003 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.22 ( 6633) covalent geometry : angle 0.58420 / 0.29 ( 9040) hydrogen bonds : bond 0.05000 / 3.39 ( 417) hydrogen bonds : angle 4.49355 / 3.17 ( 1242) Misc. bond : bond 0.00079 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.166 Fit side-chains REVERT: A 183 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.6745 (mptt) REVERT: A 230 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7547 (tp) REVERT: B 183 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6628 (mptt) REVERT: B 230 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7308 (tp) REVERT: C 183 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.6684 (mptt) REVERT: C 230 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7421 (tp) outliers start: 25 outliers final: 16 residues processed: 92 average time/residue: 0.4104 time to fit residues: 40.0766 Evaluate side-chains 91 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 230 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.127806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.112894 restraints weight = 5757.169| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 0.90 r_work: 0.2981 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6636 Z= 0.134 Angle : 0.502 5.243 9040 Z= 0.249 Chirality : 0.039 0.154 928 Planarity : 0.005 0.039 1111 Dihedral : 9.114 80.386 904 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.44 % Allowed : 15.57 % Favored : 80.99 % 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: 2.43 (0.29), residues: 768 helix: 1.94 (0.20), residues: 522 sheet: None (None), residues: 0 loop : 1.10 (0.44), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 186 TYR 0.010 0.001 TYR C 45 PHE 0.016 0.001 PHE B 144 TRP 0.012 0.001 TRP A 190 HIS 0.002 0.000 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 6633) covalent geometry : angle 0.50213 / 0.25 ( 9040) hydrogen bonds : bond 0.04279 / 2.89 ( 417) hydrogen bonds : angle 4.37017 / 3.07 ( 1242) Misc. bond : bond 0.00046 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.302 Fit side-chains REVERT: A 183 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6434 (mptt) REVERT: A 227 PHE cc_start: 0.7541 (m-10) cc_final: 0.7202 (m-80) REVERT: A 230 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7343 (tp) REVERT: B 183 LYS cc_start: 0.7082 (OUTLIER) cc_final: 0.6300 (mptt) REVERT: C 183 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6418 (mptt) REVERT: C 227 PHE cc_start: 0.7546 (m-10) cc_final: 0.7298 (m-80) REVERT: C 230 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7207 (tp) outliers start: 23 outliers final: 16 residues processed: 96 average time/residue: 0.3910 time to fit residues: 39.8904 Evaluate side-chains 99 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 234 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 22 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.126619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.111535 restraints weight = 5907.986| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 0.92 r_work: 0.3129 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6636 Z= 0.149 Angle : 0.518 5.240 9040 Z= 0.257 Chirality : 0.039 0.151 928 Planarity : 0.005 0.039 1111 Dihedral : 8.814 80.032 898 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.44 % Allowed : 15.87 % Favored : 80.69 % 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: 2.40 (0.29), residues: 768 helix: 1.92 (0.20), residues: 524 sheet: None (None), residues: 0 loop : 1.07 (0.45), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 186 TYR 0.009 0.001 TYR C 103 PHE 0.019 0.001 PHE B 144 TRP 0.011 0.001 TRP C 42 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 6633) covalent geometry : angle 0.51798 / 0.26 ( 9040) hydrogen bonds : bond 0.04443 / 3.01 ( 417) hydrogen bonds : angle 4.35589 / 3.06 ( 1242) Misc. bond : bond 0.00044 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.159 Fit side-chains REVERT: A 183 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6663 (mptt) REVERT: A 227 PHE cc_start: 0.7665 (m-10) cc_final: 0.7374 (m-80) REVERT: A 230 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7435 (tp) REVERT: B 183 LYS cc_start: 0.7168 (OUTLIER) cc_final: 0.6504 (mptt) REVERT: C 183 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.6645 (mptt) REVERT: C 227 PHE cc_start: 0.7638 (m-10) cc_final: 0.7342 (m-80) REVERT: C 230 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7333 (tp) outliers start: 23 outliers final: 17 residues processed: 99 average time/residue: 0.3606 time to fit residues: 38.0208 Evaluate side-chains 100 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 234 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 24 optimal weight: 0.7980 chunk 54 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.132806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.118075 restraints weight = 5723.933| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 0.89 r_work: 0.3240 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6636 Z= 0.124 Angle : 0.492 5.292 9040 Z= 0.244 Chirality : 0.038 0.150 928 Planarity : 0.005 0.039 1111 Dihedral : 8.566 74.671 898 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.29 % Allowed : 16.02 % Favored : 80.69 % 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: 2.61 (0.29), residues: 768 helix: 2.09 (0.20), residues: 522 sheet: None (None), residues: 0 loop : 1.12 (0.44), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 186 TYR 0.009 0.001 TYR C 45 PHE 0.016 0.001 PHE B 144 TRP 0.011 0.001 TRP C 42 HIS 0.002 0.000 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 6633) covalent geometry : angle 0.49151 / 0.24 ( 9040) hydrogen bonds : bond 0.04181 / 2.83 ( 417) hydrogen bonds : angle 4.30019 / 3.02 ( 1242) Misc. bond : bond 0.00027 / 0.02 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.273 Fit side-chains REVERT: A 183 LYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6594 (mptt) REVERT: A 227 PHE cc_start: 0.7667 (m-10) cc_final: 0.7388 (m-80) REVERT: A 230 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7392 (tp) REVERT: B 183 LYS cc_start: 0.7084 (OUTLIER) cc_final: 0.6465 (mptt) REVERT: C 183 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6627 (mptt) REVERT: C 227 PHE cc_start: 0.7633 (m-10) cc_final: 0.7403 (m-80) REVERT: C 230 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7318 (tp) outliers start: 22 outliers final: 16 residues processed: 102 average time/residue: 0.3597 time to fit residues: 39.2678 Evaluate side-chains 101 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 234 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 60 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.131613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.116824 restraints weight = 5803.556| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 0.90 r_work: 0.2976 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6636 Z= 0.144 Angle : 0.508 5.243 9040 Z= 0.253 Chirality : 0.039 0.150 928 Planarity : 0.005 0.038 1111 Dihedral : 8.554 75.919 896 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.44 % Allowed : 15.87 % Favored : 80.69 % 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: 2.55 (0.29), residues: 768 helix: 2.05 (0.20), residues: 522 sheet: None (None), residues: 0 loop : 1.11 (0.44), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 186 TYR 0.009 0.001 TYR C 103 PHE 0.019 0.001 PHE B 144 TRP 0.010 0.001 TRP B 42 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 6633) covalent geometry : angle 0.50835 / 0.25 ( 9040) hydrogen bonds : bond 0.04344 / 2.95 ( 417) hydrogen bonds : angle 4.30948 / 3.03 ( 1242) Misc. bond : bond 0.00040 / 0.03 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2429.80 seconds wall clock time: 42 minutes 24.68 seconds (2544.68 seconds total)