Starting phenix.real_space_refine on Tue Mar 11 16:22:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zap_39883/03_2025/8zap_39883.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zap_39883/03_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_39883/03_2025/8zap_39883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zap_39883/03_2025/8zap_39883.map" model { file = "/net/cci-nas-00/data/ceres_data/8zap_39883/03_2025/8zap_39883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zap_39883/03_2025/8zap_39883.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 8.96, per 1000 atoms: 1.39 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: 1.70 Conformation dependent library (CDL) restraints added in 955.7 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: 0.58 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: 1.77 Time building geometry restraints manager: 2.00 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 260 or resid 301 throug \ h 309)) selection = (chain 'C' and (resid 2 through 126 or resid 128 through 260 or resid 301 throug \ h 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: 10.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.550 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.650 ------------------------------------------------------------------------------- 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 6633 Z= 0.213 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (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 TRP 0.010 0.001 TRP A 42 HIS 0.003 0.001 HIS A 225 PHE 0.011 0.001 PHE C 134 TYR 0.012 0.001 TYR B 81 ARG 0.002 0.000 ARG A 151 *********************** 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 : 0.781 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: 0.7610 (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: 0.7695 (mtpt) REVERT: B 183 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.6830 (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: 0.7663 (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: 0.9313 time to fit residues: 91.4804 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 : 0.673 ------------------------------------------------------------------------------- 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 63 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.1980 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3449 r_free = 0.3449 target = 0.129723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.116150 restraints weight = 5975.138| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 0.87 r_work: 0.3226 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6633 Z= 0.210 Angle : 0.519 5.209 9040 Z= 0.264 Chirality : 0.039 0.144 928 Planarity : 0.005 0.042 1111 Dihedral : 10.823 79.645 924 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.89 % Allowed : 13.77 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.29), residues: 768 helix: 1.72 (0.20), residues: 525 sheet: None (None), residues: 0 loop : 0.92 (0.44), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 42 HIS 0.002 0.001 HIS A 215 PHE 0.015 0.001 PHE B 144 TYR 0.010 0.002 TYR B 180 ARG 0.001 0.000 ARG C 186 *********************** 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 107 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7394 (m-80) REVERT: A 183 LYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6688 (mptt) REVERT: A 227 PHE cc_start: 0.7708 (m-10) cc_final: 0.7405 (m-80) REVERT: B 3 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7513 (m-80) REVERT: B 70 SER cc_start: 0.8940 (OUTLIER) cc_final: 0.8697 (m) REVERT: B 183 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6676 (mptt) REVERT: C 3 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7523 (m-80) REVERT: C 70 SER cc_start: 0.8922 (OUTLIER) cc_final: 0.8683 (m) REVERT: C 183 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6584 (mptt) REVERT: C 227 PHE cc_start: 0.7667 (m-10) cc_final: 0.7373 (m-80) outliers start: 26 outliers final: 8 residues processed: 100 average time/residue: 1.0803 time to fit residues: 114.7165 Evaluate side-chains 92 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 6 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3350 r_free = 0.3350 target = 0.123832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.109410 restraints weight = 6204.666| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 0.89 r_work: 0.3184 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6633 Z= 0.214 Angle : 0.511 5.248 9040 Z= 0.257 Chirality : 0.039 0.152 928 Planarity : 0.005 0.039 1111 Dihedral : 9.789 78.340 904 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.19 % Allowed : 14.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.29), residues: 768 helix: 1.92 (0.21), residues: 525 sheet: None (None), residues: 0 loop : 0.91 (0.44), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 42 HIS 0.003 0.001 HIS A 225 PHE 0.017 0.001 PHE B 144 TYR 0.009 0.001 TYR B 150 ARG 0.001 0.000 ARG C 186 *********************** 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 108 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7262 (m-80) REVERT: A 70 SER cc_start: 0.8938 (OUTLIER) cc_final: 0.8709 (m) REVERT: A 183 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.6694 (mptt) REVERT: A 227 PHE cc_start: 0.7683 (m-10) cc_final: 0.7400 (m-80) REVERT: B 3 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7267 (m-80) REVERT: B 70 SER cc_start: 0.8912 (OUTLIER) cc_final: 0.8710 (m) REVERT: B 183 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.6639 (mptt) REVERT: C 3 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7330 (m-80) REVERT: C 70 SER cc_start: 0.8901 (OUTLIER) cc_final: 0.8682 (m) REVERT: C 183 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.6609 (mptt) REVERT: C 227 PHE cc_start: 0.7651 (m-10) cc_final: 0.7402 (m-80) outliers start: 28 outliers final: 10 residues processed: 100 average time/residue: 1.0188 time to fit residues: 108.2474 Evaluate side-chains 91 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 1 optimal weight: 0.0570 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.1504 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.130376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.116882 restraints weight = 5994.890| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 0.87 r_work: 0.3180 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6633 Z= 0.259 Angle : 0.538 5.269 9040 Z= 0.270 Chirality : 0.040 0.157 928 Planarity : 0.005 0.040 1111 Dihedral : 9.563 82.301 904 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.79 % Allowed : 14.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.29), residues: 768 helix: 1.89 (0.20), residues: 520 sheet: None (None), residues: 0 loop : 0.89 (0.44), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 42 HIS 0.003 0.001 HIS B 225 PHE 0.019 0.002 PHE B 144 TYR 0.010 0.002 TYR B 180 ARG 0.001 0.000 ARG C 186 *********************** 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 103 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 71 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 SER cc_start: 0.8945 (OUTLIER) cc_final: 0.8722 (m) REVERT: A 183 LYS cc_start: 0.7423 (OUTLIER) cc_final: 0.6787 (mptt) REVERT: B 70 SER cc_start: 0.8927 (OUTLIER) cc_final: 0.8706 (m) REVERT: B 183 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.6710 (mptt) REVERT: B 230 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7265 (tp) REVERT: C 70 SER cc_start: 0.8917 (OUTLIER) cc_final: 0.8706 (m) REVERT: C 183 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.6690 (mptt) REVERT: C 227 PHE cc_start: 0.7725 (m-10) cc_final: 0.7493 (m-80) REVERT: C 230 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7293 (tp) outliers start: 32 outliers final: 18 residues processed: 98 average time/residue: 1.0697 time to fit residues: 111.2941 Evaluate side-chains 96 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 70 optimal weight: 0.0470 chunk 32 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- 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 = 0.3359 r_free = 0.3359 target = 0.123921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.109793 restraints weight = 5985.782| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 0.88 r_work: 0.3282 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6633 Z= 0.219 Angle : 0.508 5.253 9040 Z= 0.255 Chirality : 0.039 0.153 928 Planarity : 0.005 0.039 1111 Dihedral : 9.264 80.343 904 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.34 % Allowed : 14.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.29), residues: 768 helix: 1.95 (0.20), residues: 522 sheet: None (None), residues: 0 loop : 1.01 (0.44), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 42 HIS 0.002 0.001 HIS A 225 PHE 0.018 0.001 PHE B 144 TYR 0.008 0.001 TYR A 150 ARG 0.001 0.000 ARG A 186 *********************** 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 104 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.685 Fit side-chains REVERT: A 70 SER cc_start: 0.8945 (OUTLIER) cc_final: 0.8725 (m) REVERT: A 183 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.6715 (mptt) REVERT: A 230 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7410 (tp) REVERT: B 70 SER cc_start: 0.8921 (OUTLIER) cc_final: 0.8720 (m) REVERT: B 183 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.6652 (mptt) REVERT: B 230 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7222 (tp) REVERT: C 183 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.6637 (mptt) REVERT: C 227 PHE cc_start: 0.7694 (m-10) cc_final: 0.7442 (m-80) REVERT: C 230 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7359 (tp) outliers start: 29 outliers final: 18 residues processed: 95 average time/residue: 0.9419 time to fit residues: 95.2691 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 : 0.655 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.127531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.113921 restraints weight = 5700.691| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 0.86 r_work: 0.3249 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6633 Z= 0.336 Angle : 0.578 5.296 9040 Z= 0.291 Chirality : 0.043 0.161 928 Planarity : 0.005 0.039 1111 Dihedral : 9.661 89.340 904 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.34 % Allowed : 14.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.29), residues: 768 helix: 1.74 (0.20), residues: 515 sheet: None (None), residues: 0 loop : 0.91 (0.43), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 42 HIS 0.003 0.001 HIS A 225 PHE 0.022 0.002 PHE B 144 TYR 0.011 0.002 TYR A 180 ARG 0.002 0.000 ARG A 186 *********************** 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: 29 poor density : 68 time to evaluate : 0.807 Fit side-chains REVERT: A 70 SER cc_start: 0.8932 (OUTLIER) cc_final: 0.8695 (m) REVERT: A 183 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.6716 (mptt) REVERT: A 230 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7462 (tp) REVERT: B 70 SER cc_start: 0.8925 (OUTLIER) cc_final: 0.8681 (m) REVERT: B 183 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6636 (mptt) REVERT: B 230 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7259 (tp) REVERT: C 183 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.6609 (mptt) REVERT: C 230 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7341 (tp) outliers start: 29 outliers final: 16 residues processed: 92 average time/residue: 1.1626 time to fit residues: 113.3694 Evaluate side-chains 92 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 28 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 68 optimal weight: 0.0770 chunk 50 optimal weight: 0.0570 chunk 6 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 0.3856 ------------------------------------------------------------------------------- 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 = 0.3384 r_free = 0.3384 target = 0.126139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.111909 restraints weight = 6044.246| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 0.90 r_work: 0.3119 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6633 Z= 0.159 Angle : 0.477 5.169 9040 Z= 0.239 Chirality : 0.037 0.145 928 Planarity : 0.005 0.039 1111 Dihedral : 8.977 77.696 904 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.84 % Allowed : 16.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.30), residues: 768 helix: 2.08 (0.21), residues: 524 sheet: None (None), residues: 0 loop : 1.01 (0.45), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 190 HIS 0.001 0.000 HIS C 225 PHE 0.013 0.001 PHE B 144 TYR 0.011 0.001 TYR C 45 ARG 0.001 0.000 ARG B 244 *********************** 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 103 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.820 Fit side-chains REVERT: A 70 SER cc_start: 0.8918 (OUTLIER) cc_final: 0.8688 (m) REVERT: A 183 LYS cc_start: 0.7230 (OUTLIER) cc_final: 0.6586 (mptt) REVERT: A 227 PHE cc_start: 0.7637 (m-10) cc_final: 0.7349 (m-80) REVERT: B 183 LYS cc_start: 0.7231 (OUTLIER) cc_final: 0.6553 (mptt) REVERT: C 183 LYS cc_start: 0.7208 (OUTLIER) cc_final: 0.6478 (mptt) REVERT: C 227 PHE cc_start: 0.7637 (m-10) cc_final: 0.7396 (m-80) outliers start: 19 outliers final: 12 residues processed: 98 average time/residue: 1.0001 time to fit residues: 104.4956 Evaluate side-chains 98 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 183 LYS 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.132467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.118679 restraints weight = 5839.667| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 0.89 r_work: 0.3121 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6633 Z= 0.207 Angle : 0.499 5.218 9040 Z= 0.250 Chirality : 0.039 0.144 928 Planarity : 0.005 0.038 1111 Dihedral : 8.684 77.793 896 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.99 % Allowed : 15.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.29), residues: 768 helix: 2.08 (0.21), residues: 524 sheet: None (None), residues: 0 loop : 1.03 (0.45), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 42 HIS 0.002 0.001 HIS A 225 PHE 0.016 0.001 PHE B 144 TYR 0.008 0.001 TYR A 150 ARG 0.001 0.000 ARG C 186 *********************** 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 93 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.754 Fit side-chains REVERT: A 70 SER cc_start: 0.8912 (OUTLIER) cc_final: 0.8697 (m) REVERT: A 183 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6658 (mptt) REVERT: A 227 PHE cc_start: 0.7639 (m-10) cc_final: 0.7347 (m-80) REVERT: B 183 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.6624 (mptt) REVERT: C 183 LYS cc_start: 0.7228 (OUTLIER) cc_final: 0.6561 (mptt) REVERT: C 227 PHE cc_start: 0.7649 (m-10) cc_final: 0.7405 (m-80) outliers start: 20 outliers final: 15 residues processed: 91 average time/residue: 1.0511 time to fit residues: 101.5869 Evaluate side-chains 90 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 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 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 234 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.131699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.117891 restraints weight = 5854.088| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 0.89 r_work: 0.3267 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6633 Z= 0.228 Angle : 0.511 5.213 9040 Z= 0.257 Chirality : 0.039 0.151 928 Planarity : 0.005 0.038 1111 Dihedral : 8.605 79.214 894 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.59 % Allowed : 15.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.29), residues: 768 helix: 2.01 (0.20), residues: 524 sheet: None (None), residues: 0 loop : 1.03 (0.45), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 42 HIS 0.002 0.001 HIS C 225 PHE 0.019 0.001 PHE B 144 TYR 0.009 0.002 TYR C 103 ARG 0.001 0.000 ARG C 186 *********************** 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 96 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.822 Fit side-chains REVERT: A 70 SER cc_start: 0.8933 (OUTLIER) cc_final: 0.8723 (m) REVERT: A 183 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.6732 (mptt) REVERT: B 183 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.6690 (mptt) REVERT: C 183 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6626 (mptt) REVERT: C 227 PHE cc_start: 0.7690 (m-10) cc_final: 0.7455 (m-80) outliers start: 24 outliers final: 15 residues processed: 92 average time/residue: 1.0373 time to fit residues: 101.3037 Evaluate side-chains 91 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 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 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 234 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 7 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3232 r_free = 0.3232 target = 0.116490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.101385 restraints weight = 6113.521| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 0.91 r_work: 0.3243 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6633 Z= 0.277 Angle : 0.544 5.218 9040 Z= 0.274 Chirality : 0.041 0.154 928 Planarity : 0.005 0.038 1111 Dihedral : 8.803 84.177 894 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.99 % Allowed : 15.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.29), residues: 768 helix: 1.95 (0.21), residues: 515 sheet: None (None), residues: 0 loop : 0.93 (0.43), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 190 HIS 0.003 0.001 HIS A 225 PHE 0.025 0.002 PHE B 144 TYR 0.011 0.002 TYR C 103 ARG 0.001 0.000 ARG A 186 ********************** 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 90 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.770 Fit side-chains REVERT: A 70 SER cc_start: 0.8966 (OUTLIER) cc_final: 0.8744 (m) REVERT: A 183 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.6835 (mptt) REVERT: B 183 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.6794 (mptt) REVERT: C 183 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.6730 (mptt) outliers start: 20 outliers final: 15 residues processed: 89 average time/residue: 1.0986 time to fit residues: 103.5070 Evaluate side-chains 89 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 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 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 234 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 5 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3370 r_free = 0.3370 target = 0.124992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.110563 restraints weight = 6140.841| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 0.90 r_work: 0.3290 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6633 Z= 0.191 Angle : 0.489 5.206 9040 Z= 0.246 Chirality : 0.038 0.144 928 Planarity : 0.005 0.039 1111 Dihedral : 8.432 77.828 894 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.69 % Allowed : 15.87 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.29), residues: 768 helix: 2.08 (0.21), residues: 524 sheet: None (None), residues: 0 loop : 1.02 (0.44), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 190 HIS 0.002 0.000 HIS C 225 PHE 0.017 0.001 PHE B 144 TYR 0.009 0.001 TYR C 45 ARG 0.001 0.000 ARG C 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5262.40 seconds wall clock time: 90 minutes 35.43 seconds (5435.43 seconds total)