Starting phenix.real_space_refine on Fri Aug 22 17:09:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zap_39883/08_2025/8zap_39883.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zap_39883/08_2025/8zap_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_39883/08_2025/8zap_39883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zap_39883/08_2025/8zap_39883.map" model { file = "/net/cci-nas-00/data/ceres_data/8zap_39883/08_2025/8zap_39883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zap_39883/08_2025/8zap_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-2.0-5787/lib/python3.9/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, 28 Unusual residues: {' K': 8, 'RET': 1} Classifications: {'undetermined': 9} Link IDs: {None: 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, 28 Unusual residues: {' K': 8, 'RET': 1} Classifications: {'undetermined': 9} Link IDs: {None: 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, 28 Unusual residues: {' K': 8, 'RET': 1} Classifications: {'undetermined': 9} Link IDs: {None: 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: 1.84, per 1000 atoms: 0.29 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: 0.62 Conformation dependent library (CDL) restraints added in 326.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.17 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: 1.06 Time building geometry restraints manager: 0.81 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 2.850 nonbonded pdb=" K K B 305 " pdb=" O HOH B 406 " model vdw 1.492 2.850 nonbonded pdb=" K K C 305 " pdb=" O HOH C 406 " model vdw 1.495 2.850 nonbonded pdb=" K K B 305 " pdb=" O HOH B 410 " model vdw 1.574 2.850 nonbonded pdb=" K K C 305 " pdb=" O HOH C 410 " model vdw 1.584 2.850 ... (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: 21.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.240 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 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 aren 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 covalent geometry : bond 0.00327 ( 6633) covalent geometry : angle 0.59653 ( 9040) hydrogen bonds : bond 0.13624 ( 417) hydrogen bonds : angle 6.63489 ( 1242) Misc. bond : bond 0.00089 ( 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 : 0.224 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: 0.8047 (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: 0.7477 (m-80) outliers start: 28 outliers final: 12 residues processed: 92 average time/residue: 0.4843 time to fit residues: 47.3653 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 : 0.174 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.7980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3367 r_free = 0.3367 target = 0.125214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.110873 restraints weight = 6135.792| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 0.88 r_work: 0.3202 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.0760 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= 0.138 Angle : 0.512 5.294 9040 Z= 0.261 Chirality : 0.039 0.142 928 Planarity : 0.005 0.041 1111 Dihedral : 10.786 78.349 924 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.74 % Allowed : 13.62 % 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 aren not related in a simple way. whole: 2.15 (0.29), residues: 768 helix: 1.75 (0.21), residues: 525 sheet: None (None), residues: 0 loop : 0.93 (0.44), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 186 TYR 0.009 0.001 TYR B 180 PHE 0.014 0.001 PHE B 144 TRP 0.009 0.001 TRP C 42 HIS 0.003 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 6633) covalent geometry : angle 0.51235 ( 9040) hydrogen bonds : bond 0.04707 ( 417) hydrogen bonds : angle 4.47885 ( 1242) Misc. bond : bond 0.00047 ( 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: 25 poor density : 83 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7444 (m-80) REVERT: A 183 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6637 (mptt) REVERT: A 227 PHE cc_start: 0.7664 (m-10) cc_final: 0.7368 (m-80) REVERT: B 3 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7553 (m-80) REVERT: B 70 SER cc_start: 0.8936 (OUTLIER) cc_final: 0.8695 (m) REVERT: B 183 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6585 (mptt) REVERT: C 3 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7569 (m-80) REVERT: C 70 SER cc_start: 0.8908 (OUTLIER) cc_final: 0.8676 (m) REVERT: C 183 LYS cc_start: 0.7166 (OUTLIER) cc_final: 0.6523 (mptt) REVERT: C 227 PHE cc_start: 0.7627 (m-10) cc_final: 0.7367 (m-80) outliers start: 25 outliers final: 8 residues processed: 99 average time/residue: 0.5242 time to fit residues: 54.7731 Evaluate side-chains 95 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 70 SER 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 70 SER 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: 0.0870 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.126019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.111743 restraints weight = 6161.112| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 0.88 r_work: 0.3239 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6636 Z= 0.124 Angle : 0.487 5.274 9040 Z= 0.245 Chirality : 0.038 0.147 928 Planarity : 0.005 0.039 1111 Dihedral : 9.556 73.928 904 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.89 % Allowed : 15.12 % 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 aren not related in a simple way. whole: 2.52 (0.30), residues: 768 helix: 2.09 (0.21), residues: 525 sheet: None (None), residues: 0 loop : 0.91 (0.44), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 186 TYR 0.009 0.001 TYR A 150 PHE 0.014 0.001 PHE B 144 TRP 0.009 0.001 TRP C 42 HIS 0.002 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 6633) covalent geometry : angle 0.48738 ( 9040) hydrogen bonds : bond 0.04273 ( 417) hydrogen bonds : angle 4.29355 ( 1242) Misc. bond : bond 0.00036 ( 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 118 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 3 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7339 (m-80) REVERT: A 70 SER cc_start: 0.8921 (OUTLIER) cc_final: 0.8682 (m) REVERT: A 183 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6590 (mptt) REVERT: A 227 PHE cc_start: 0.7648 (m-10) cc_final: 0.7368 (m-80) REVERT: B 3 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7382 (m-80) REVERT: B 183 LYS cc_start: 0.7137 (OUTLIER) cc_final: 0.6504 (mptt) REVERT: C 3 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7437 (m-80) REVERT: C 70 SER cc_start: 0.8893 (OUTLIER) cc_final: 0.8685 (m) REVERT: C 183 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6513 (mptt) REVERT: C 227 PHE cc_start: 0.7598 (m-10) cc_final: 0.7334 (m-80) outliers start: 26 outliers final: 9 residues processed: 108 average time/residue: 0.4627 time to fit residues: 53.1358 Evaluate side-chains 94 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 70 SER 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 33 CYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 70 SER 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: 1.9990 chunk 4 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 1 optimal weight: 0.0570 chunk 47 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.127981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.113802 restraints weight = 6170.008| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 0.91 r_work: 0.3218 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6636 Z= 0.131 Angle : 0.489 5.267 9040 Z= 0.245 Chirality : 0.038 0.145 928 Planarity : 0.005 0.038 1111 Dihedral : 9.438 74.010 902 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.89 % Allowed : 16.32 % Favored : 79.79 % 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 aren not related in a simple way. whole: 2.56 (0.29), residues: 768 helix: 2.12 (0.21), residues: 524 sheet: None (None), residues: 0 loop : 0.92 (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 0.013 0.001 PHE B 144 TRP 0.009 0.001 TRP C 42 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 6633) covalent geometry : angle 0.48894 ( 9040) hydrogen bonds : bond 0.04279 ( 417) hydrogen bonds : angle 4.25732 ( 1242) Misc. bond : bond 0.00033 ( 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 107 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 0.257 Fit side-chains REVERT: A 3 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.7241 (m-80) REVERT: A 70 SER cc_start: 0.8921 (OUTLIER) cc_final: 0.8693 (m) REVERT: A 183 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6630 (mptt) REVERT: A 227 PHE cc_start: 0.7638 (m-10) cc_final: 0.7360 (m-80) REVERT: B 3 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7241 (m-80) REVERT: B 183 LYS cc_start: 0.7195 (OUTLIER) cc_final: 0.6541 (mptt) REVERT: C 3 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7357 (m-80) REVERT: C 183 LYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6601 (mptt) REVERT: C 227 PHE cc_start: 0.7644 (m-10) cc_final: 0.7383 (m-80) REVERT: C 230 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7427 (tt) outliers start: 26 outliers final: 10 residues processed: 98 average time/residue: 0.5078 time to fit residues: 52.7738 Evaluate side-chains 98 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 70 SER 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 183 LYS Chi-restraints excluded: chain B residue 184 CYS 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 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: 3.9990 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 59 optimal weight: 0.0770 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.124372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.109753 restraints weight = 6089.852| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 0.95 r_work: 0.2964 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1163 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= 0.147 Angle : 0.505 5.240 9040 Z= 0.254 Chirality : 0.039 0.149 928 Planarity : 0.005 0.038 1111 Dihedral : 9.318 76.764 902 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.89 % Allowed : 15.72 % Favored : 80.39 % 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 aren not related in a simple way. whole: 2.59 (0.29), residues: 768 helix: 2.11 (0.21), residues: 522 sheet: None (None), residues: 0 loop : 1.01 (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 A 150 PHE 0.016 0.001 PHE B 144 TRP 0.009 0.001 TRP C 42 HIS 0.003 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 6633) covalent geometry : angle 0.50510 ( 9040) hydrogen bonds : bond 0.04440 ( 417) hydrogen bonds : angle 4.26497 ( 1242) Misc. bond : bond 0.00042 ( 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 99 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 3 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.6604 (m-80) REVERT: A 70 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8678 (m) REVERT: A 183 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6507 (mptt) REVERT: A 227 PHE cc_start: 0.7533 (m-10) cc_final: 0.7212 (m-80) REVERT: B 3 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.6563 (m-80) REVERT: B 183 LYS cc_start: 0.7137 (OUTLIER) cc_final: 0.6396 (mptt) REVERT: B 230 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7163 (tp) REVERT: C 3 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.6869 (m-80) REVERT: C 183 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6450 (mptt) REVERT: C 227 PHE cc_start: 0.7549 (m-10) cc_final: 0.7250 (m-80) REVERT: C 230 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7335 (tt) outliers start: 26 outliers final: 13 residues processed: 94 average time/residue: 0.5298 time to fit residues: 52.7053 Evaluate side-chains 94 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 70 SER 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 107 VAL Chi-restraints excluded: chain B residue 110 THR 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 70 SER 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: 3.9990 chunk 36 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.115318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.100561 restraints weight = 6152.779| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 0.87 r_work: 0.3213 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1253 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= 0.205 Angle : 0.567 5.266 9040 Z= 0.286 Chirality : 0.042 0.163 928 Planarity : 0.005 0.039 1111 Dihedral : 9.512 87.149 902 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.89 % Allowed : 15.12 % 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 aren not related in a simple way. whole: 2.25 (0.29), residues: 768 helix: 1.87 (0.20), residues: 515 sheet: None (None), residues: 0 loop : 0.87 (0.43), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 186 TYR 0.011 0.002 TYR B 180 PHE 0.021 0.002 PHE B 144 TRP 0.010 0.002 TRP C 42 HIS 0.003 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 6633) covalent geometry : angle 0.56728 ( 9040) hydrogen bonds : bond 0.04991 ( 417) hydrogen bonds : angle 4.43337 ( 1242) Misc. bond : bond 0.00075 ( 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 97 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 SER cc_start: 0.8939 (OUTLIER) cc_final: 0.8714 (m) REVERT: A 183 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.6760 (mptt) REVERT: A 230 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7487 (tp) REVERT: B 183 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.6647 (mptt) REVERT: B 230 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7277 (tp) REVERT: C 183 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.6674 (mptt) REVERT: C 230 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7444 (tt) outliers start: 26 outliers final: 16 residues processed: 93 average time/residue: 0.5496 time to fit residues: 54.0232 Evaluate side-chains 94 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 70 SER 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 33 CYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 THR 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 70 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 74 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 0.0970 chunk 46 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.118048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.103354 restraints weight = 6108.349| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 0.87 r_work: 0.3080 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 2.16 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1231 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= 0.145 Angle : 0.507 5.226 9040 Z= 0.255 Chirality : 0.039 0.149 928 Planarity : 0.005 0.039 1111 Dihedral : 9.181 82.771 902 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.74 % Allowed : 14.97 % 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 aren not related in a simple way. whole: 2.38 (0.29), residues: 768 helix: 1.95 (0.21), residues: 524 sheet: None (None), residues: 0 loop : 0.96 (0.45), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 186 TYR 0.008 0.001 TYR C 45 PHE 0.021 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 covalent geometry : bond 0.00331 ( 6633) covalent geometry : angle 0.50673 ( 9040) hydrogen bonds : bond 0.04472 ( 417) hydrogen bonds : angle 4.34260 ( 1242) Misc. bond : bond 0.00042 ( 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 97 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.266 Fit side-chains REVERT: A 70 SER cc_start: 0.8932 (OUTLIER) cc_final: 0.8727 (m) REVERT: A 183 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.6731 (mptt) REVERT: A 227 PHE cc_start: 0.7669 (m-10) cc_final: 0.7380 (m-80) REVERT: B 183 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6594 (mptt) REVERT: B 230 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7333 (tp) REVERT: C 183 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.6661 (mptt) REVERT: C 227 PHE cc_start: 0.7680 (m-10) cc_final: 0.7439 (m-80) REVERT: C 230 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7438 (tt) outliers start: 25 outliers final: 17 residues processed: 92 average time/residue: 0.5207 time to fit residues: 50.6976 Evaluate side-chains 96 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 70 SER 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 107 VAL Chi-restraints excluded: chain B residue 110 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 26 optimal weight: 0.0870 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.126949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.112425 restraints weight = 5994.605| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 0.94 r_work: 0.3141 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1253 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= 0.134 Angle : 0.494 5.192 9040 Z= 0.248 Chirality : 0.038 0.144 928 Planarity : 0.005 0.039 1111 Dihedral : 8.974 78.601 902 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.44 % Allowed : 15.27 % 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 aren not related in a simple way. whole: 2.53 (0.29), residues: 768 helix: 2.07 (0.21), residues: 524 sheet: None (None), residues: 0 loop : 0.99 (0.45), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 186 TYR 0.008 0.001 TYR C 103 PHE 0.018 0.001 PHE B 144 TRP 0.010 0.001 TRP C 42 HIS 0.002 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 6633) covalent geometry : angle 0.49419 ( 9040) hydrogen bonds : bond 0.04349 ( 417) hydrogen bonds : angle 4.29320 ( 1242) Misc. bond : bond 0.00042 ( 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 98 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.267 Fit side-chains REVERT: A 70 SER cc_start: 0.8935 (OUTLIER) cc_final: 0.8721 (m) REVERT: A 183 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6695 (mptt) REVERT: A 227 PHE cc_start: 0.7655 (m-10) cc_final: 0.7366 (m-80) REVERT: A 230 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7438 (tp) REVERT: B 183 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6530 (mptt) REVERT: B 230 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7199 (tp) REVERT: C 183 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6640 (mptt) REVERT: C 227 PHE cc_start: 0.7643 (m-10) cc_final: 0.7387 (m-80) REVERT: C 230 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7426 (tt) outliers start: 23 outliers final: 15 residues processed: 92 average time/residue: 0.5142 time to fit residues: 50.0802 Evaluate side-chains 96 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 70 SER 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 107 VAL Chi-restraints excluded: chain B residue 110 THR 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 33 CYS Chi-restraints excluded: chain C residue 70 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 22 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.122538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.108111 restraints weight = 6175.623| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 0.90 r_work: 0.3088 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6636 Z= 0.175 Angle : 0.532 5.205 9040 Z= 0.268 Chirality : 0.041 0.153 928 Planarity : 0.005 0.038 1111 Dihedral : 8.844 82.827 896 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.59 % Allowed : 15.27 % Favored : 81.14 % 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 aren not related in a simple way. whole: 2.42 (0.29), residues: 768 helix: 2.00 (0.20), residues: 518 sheet: None (None), residues: 0 loop : 0.95 (0.44), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 186 TYR 0.010 0.002 TYR B 81 PHE 0.023 0.002 PHE B 144 TRP 0.010 0.002 TRP C 42 HIS 0.003 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 6633) covalent geometry : angle 0.53179 ( 9040) hydrogen bonds : bond 0.04679 ( 417) hydrogen bonds : angle 4.36400 ( 1242) Misc. bond : bond 0.00059 ( 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 93 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.322 Fit side-chains REVERT: A 70 SER cc_start: 0.8940 (OUTLIER) cc_final: 0.8725 (m) REVERT: A 183 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.6798 (mptt) REVERT: A 230 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7499 (tp) REVERT: B 183 LYS cc_start: 0.7268 (OUTLIER) cc_final: 0.6612 (mptt) REVERT: B 230 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7289 (tp) REVERT: C 183 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.6730 (mptt) REVERT: C 227 PHE cc_start: 0.7694 (m-10) cc_final: 0.7452 (m-80) REVERT: C 230 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7451 (tt) outliers start: 24 outliers final: 15 residues processed: 90 average time/residue: 0.5270 time to fit residues: 50.3081 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 : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 70 SER 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 107 VAL Chi-restraints excluded: chain B residue 110 THR 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 33 CYS Chi-restraints excluded: chain C residue 70 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 24 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.126825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.112342 restraints weight = 5950.438| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 0.93 r_work: 0.3191 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1273 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= 0.138 Angle : 0.498 5.189 9040 Z= 0.250 Chirality : 0.039 0.145 928 Planarity : 0.005 0.039 1111 Dihedral : 8.631 79.568 896 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.44 % Allowed : 15.27 % 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 aren not related in a simple way. whole: 2.53 (0.29), residues: 768 helix: 2.07 (0.21), residues: 524 sheet: None (None), residues: 0 loop : 0.97 (0.44), residues: 244 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 0.011 0.001 TRP C 42 HIS 0.002 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 6633) covalent geometry : angle 0.49832 ( 9040) hydrogen bonds : bond 0.04372 ( 417) hydrogen bonds : angle 4.30719 ( 1242) Misc. bond : bond 0.00033 ( 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 96 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.260 Fit side-chains REVERT: A 70 SER cc_start: 0.8935 (OUTLIER) cc_final: 0.8716 (m) REVERT: A 183 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6694 (mptt) REVERT: A 227 PHE cc_start: 0.7666 (m-10) cc_final: 0.7369 (m-80) REVERT: A 230 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7442 (tp) REVERT: B 183 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6538 (mptt) REVERT: B 230 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7298 (tp) REVERT: C 183 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.6655 (mptt) REVERT: C 227 PHE cc_start: 0.7660 (m-10) cc_final: 0.7406 (m-80) REVERT: C 230 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7393 (tt) outliers start: 23 outliers final: 15 residues processed: 90 average time/residue: 0.5215 time to fit residues: 49.6312 Evaluate side-chains 95 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 70 SER 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 107 VAL Chi-restraints excluded: chain B residue 110 THR 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 33 CYS Chi-restraints excluded: chain C residue 70 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 60 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 64 optimal weight: 0.0570 chunk 68 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.118946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.104005 restraints weight = 6066.168| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 0.88 r_work: 0.3179 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6636 Z= 0.132 Angle : 0.492 5.203 9040 Z= 0.247 Chirality : 0.039 0.142 928 Planarity : 0.005 0.039 1111 Dihedral : 8.524 76.700 896 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.14 % Allowed : 15.57 % 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 aren not related in a simple way. whole: 2.61 (0.30), residues: 768 helix: 2.14 (0.21), residues: 524 sheet: None (None), residues: 0 loop : 0.99 (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 C 45 PHE 0.018 0.001 PHE B 144 TRP 0.010 0.001 TRP C 42 HIS 0.002 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6633) covalent geometry : angle 0.49190 ( 9040) hydrogen bonds : bond 0.04313 ( 417) hydrogen bonds : angle 4.27659 ( 1242) Misc. bond : bond 0.00032 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2963.17 seconds wall clock time: 51 minutes 32.71 seconds (3092.71 seconds total)