Starting phenix.real_space_refine on Fri Dec 27 22:40:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqp_37751/12_2024/8wqp_37751.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqp_37751/12_2024/8wqp_37751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wqp_37751/12_2024/8wqp_37751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqp_37751/12_2024/8wqp_37751.map" model { file = "/net/cci-nas-00/data/ceres_data/8wqp_37751/12_2024/8wqp_37751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqp_37751/12_2024/8wqp_37751.cif" } resolution = 2.4 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= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 4 5.16 5 C 2210 2.51 5 N 622 2.21 5 O 676 1.98 5 H 3330 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6842 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 3421 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 215} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 3421 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 215} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 6.28, per 1000 atoms: 0.92 Number of scatterers: 6842 At special positions: 0 Unit cell: (72.8625, 68.5125, 100.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 4 16.00 O 676 8.00 N 622 7.00 C 2210 6.00 H 3330 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 710.2 milliseconds 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 840 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 4 sheets defined 8.0% alpha, 40.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 64 through 71 removed outlier: 3.752A pdb=" N UNK A 68 " --> pdb=" O UNK A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 180 Processing helix chain 'B' and resid 64 through 71 removed outlier: 3.610A pdb=" N ASN B 71 " --> pdb=" O UNK B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 180 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 77 removed outlier: 3.960A pdb=" N ASN A 136 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A 244 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ARG A 276 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL A 203 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA A 274 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE A 205 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL A 272 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU A 207 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA A 270 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 87 removed outlier: 4.065A pdb=" N HIS A 121 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU A 220 " --> pdb=" O LYS A 228 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL A 230 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE A 218 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLU A 232 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA A 216 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR A 234 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU A 214 " --> pdb=" O TYR A 234 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 75 through 77 removed outlier: 3.974A pdb=" N ASN B 136 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 246 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE B 244 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B 200 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL B 277 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER B 202 " --> pdb=" O TYR B 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 82 through 87 removed outlier: 4.234A pdb=" N HIS B 121 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU B 220 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL B 230 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE B 218 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLU B 232 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA B 216 " --> pdb=" O GLU B 232 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR B 234 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 214 " --> pdb=" O TYR B 234 " (cutoff:3.500A) 153 hydrogen bonds defined for protein. 405 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: 2.45 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3330 1.03 - 1.22: 0 1.22 - 1.42: 1486 1.42 - 1.61: 2094 1.61 - 1.80: 8 Bond restraints: 6918 Sorted by residual: bond pdb=" CB GLU A 93 " pdb=" CG GLU A 93 " ideal model delta sigma weight residual 1.520 1.540 -0.020 3.00e-02 1.11e+03 4.51e-01 bond pdb=" N PRO B 142 " pdb=" CA PRO B 142 " ideal model delta sigma weight residual 1.469 1.475 -0.007 1.28e-02 6.10e+03 2.71e-01 bond pdb=" CA ARG B 104 " pdb=" C ARG B 104 " ideal model delta sigma weight residual 1.522 1.528 -0.006 1.29e-02 6.01e+03 2.51e-01 bond pdb=" CA UNK A 62 " pdb=" CB UNK A 62 " ideal model delta sigma weight residual 1.530 1.520 0.010 2.00e-02 2.50e+03 2.41e-01 bond pdb=" CG PRO A 142 " pdb=" CD PRO A 142 " ideal model delta sigma weight residual 1.503 1.487 0.016 3.40e-02 8.65e+02 2.20e-01 ... (remaining 6913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 12381 1.79 - 3.59: 77 3.59 - 5.38: 9 5.38 - 7.18: 2 7.18 - 8.97: 1 Bond angle restraints: 12470 Sorted by residual: angle pdb=" CA PRO B 90 " pdb=" N PRO B 90 " pdb=" CD PRO B 90 " ideal model delta sigma weight residual 112.00 107.71 4.29 1.40e+00 5.10e-01 9.39e+00 angle pdb=" N PRO B 90 " pdb=" CD PRO B 90 " pdb=" CG PRO B 90 " ideal model delta sigma weight residual 103.20 98.95 4.25 1.50e+00 4.44e-01 8.01e+00 angle pdb=" CB PRO B 90 " pdb=" CG PRO B 90 " pdb=" CD PRO B 90 " ideal model delta sigma weight residual 106.10 97.13 8.97 3.20e+00 9.77e-02 7.86e+00 angle pdb=" CA PRO B 90 " pdb=" CB PRO B 90 " pdb=" CG PRO B 90 " ideal model delta sigma weight residual 104.50 100.17 4.33 1.90e+00 2.77e-01 5.19e+00 angle pdb=" CA PRO A 224 " pdb=" CB PRO A 224 " pdb=" CG PRO A 224 " ideal model delta sigma weight residual 104.50 100.75 3.75 1.90e+00 2.77e-01 3.90e+00 ... (remaining 12465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 2877 17.00 - 34.00: 260 34.00 - 51.00: 106 51.00 - 68.00: 32 68.00 - 85.00: 7 Dihedral angle restraints: 3282 sinusoidal: 1804 harmonic: 1478 Sorted by residual: dihedral pdb=" CA PRO B 142 " pdb=" C PRO B 142 " pdb=" N ARG B 143 " pdb=" CA ARG B 143 " ideal model delta harmonic sigma weight residual -180.00 -163.53 -16.47 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA PRO A 142 " pdb=" C PRO A 142 " pdb=" N ARG A 143 " pdb=" CA ARG A 143 " ideal model delta harmonic sigma weight residual 180.00 -164.28 -15.72 0 5.00e+00 4.00e-02 9.88e+00 dihedral pdb=" CB GLU A 232 " pdb=" CG GLU A 232 " pdb=" CD GLU A 232 " pdb=" OE1 GLU A 232 " ideal model delta sinusoidal sigma weight residual 0.00 85.00 -85.00 1 3.00e+01 1.11e-03 9.74e+00 ... (remaining 3279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 286 0.026 - 0.052: 167 0.052 - 0.078: 27 0.078 - 0.104: 28 0.104 - 0.131: 48 Chirality restraints: 556 Sorted by residual: chirality pdb=" CA ILE B 206 " pdb=" N ILE B 206 " pdb=" C ILE B 206 " pdb=" CB ILE B 206 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA ILE A 206 " pdb=" N ILE A 206 " pdb=" C ILE A 206 " pdb=" CB ILE A 206 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE B 150 " pdb=" N ILE B 150 " pdb=" C ILE B 150 " pdb=" CB ILE B 150 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 553 not shown) Planarity restraints: 1074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 89 " -0.026 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO B 90 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 90 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 90 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 104 " -0.016 5.00e-02 4.00e+02 2.50e-02 1.00e+00 pdb=" N PRO B 105 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO B 105 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 105 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 73 " 0.016 5.00e-02 4.00e+02 2.49e-02 9.90e-01 pdb=" N PRO A 74 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " 0.014 5.00e-02 4.00e+02 ... (remaining 1071 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 129 2.12 - 2.74: 11838 2.74 - 3.36: 18746 3.36 - 3.98: 25327 3.98 - 4.60: 37785 Nonbonded interactions: 93825 Sorted by model distance: nonbonded pdb=" OE1 GLU A 93 " pdb=" H GLU A 93 " model vdw 1.499 2.450 nonbonded pdb=" O ASP B 201 " pdb=" H THR B 249 " model vdw 1.609 2.450 nonbonded pdb=" HZ3 LYS B 100 " pdb=" OG1 THR B 134 " model vdw 1.636 2.450 nonbonded pdb=" OD1 ASN A 197 " pdb=" H THR A 199 " model vdw 1.641 2.450 nonbonded pdb=" H THR B 134 " pdb=" OE1 GLU B 248 " model vdw 1.646 2.450 ... (remaining 93820 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' } 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: 12.510 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: 0.130 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 21.450 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 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 : 0.002 0.020 3588 Z= 0.139 Angle : 0.532 8.970 4908 Z= 0.262 Chirality : 0.048 0.131 556 Planarity : 0.003 0.038 662 Dihedral : 15.801 84.999 1296 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.91 % Allowed : 18.85 % Favored : 79.23 % 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: -0.22 (0.38), residues: 448 helix: 0.05 (0.96), residues: 30 sheet: 0.46 (0.33), residues: 222 loop : -0.84 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 85 HIS 0.001 0.000 HIS B 121 PHE 0.008 0.001 PHE B 266 TYR 0.004 0.001 TYR A 194 ARG 0.002 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.432 Fit side-chains REVERT: B 107 ASP cc_start: 0.7597 (t0) cc_final: 0.7361 (t0) outliers start: 7 outliers final: 6 residues processed: 43 average time/residue: 1.6790 time to fit residues: 76.0936 Evaluate side-chains 40 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 179 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 chunk 13 optimal weight: 0.1980 chunk 21 optimal weight: 0.0970 chunk 26 optimal weight: 0.0970 chunk 41 optimal weight: 0.5980 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3588 Z= 0.229 Angle : 0.575 4.118 4908 Z= 0.302 Chirality : 0.051 0.146 556 Planarity : 0.005 0.033 662 Dihedral : 7.897 83.208 516 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.73 % Allowed : 17.49 % Favored : 79.78 % 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: -0.24 (0.39), residues: 448 helix: 0.17 (1.00), residues: 32 sheet: 0.62 (0.33), residues: 236 loop : -1.27 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 85 HIS 0.002 0.001 HIS A 121 PHE 0.013 0.002 PHE B 266 TYR 0.008 0.001 TYR A 126 ARG 0.002 0.000 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.533 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 45 average time/residue: 1.8723 time to fit residues: 87.9756 Evaluate side-chains 42 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 235 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 41 optimal weight: 0.0770 chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 0.1980 chunk 14 optimal weight: 0.1980 chunk 33 optimal weight: 0.3980 chunk 31 optimal weight: 0.0570 overall best weight: 0.1856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3588 Z= 0.180 Angle : 0.525 3.793 4908 Z= 0.273 Chirality : 0.050 0.146 556 Planarity : 0.004 0.036 662 Dihedral : 7.816 82.364 516 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.55 % Allowed : 16.12 % Favored : 80.33 % 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: -0.13 (0.39), residues: 448 helix: 0.49 (1.02), residues: 32 sheet: 0.73 (0.32), residues: 240 loop : -1.35 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 85 HIS 0.002 0.001 HIS A 121 PHE 0.010 0.001 PHE B 266 TYR 0.006 0.001 TYR A 126 ARG 0.002 0.000 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 285 ASP cc_start: 0.6449 (OUTLIER) cc_final: 0.6123 (m-30) REVERT: B 184 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7125 (pm20) outliers start: 13 outliers final: 9 residues processed: 45 average time/residue: 1.8659 time to fit residues: 87.6433 Evaluate side-chains 44 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 184 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 0.0770 chunk 41 optimal weight: 0.3980 chunk 44 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 37 optimal weight: 0.0870 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 0.8980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3588 Z= 0.280 Angle : 0.598 4.586 4908 Z= 0.316 Chirality : 0.052 0.169 556 Planarity : 0.005 0.044 662 Dihedral : 8.132 79.803 516 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.55 % Allowed : 17.21 % Favored : 79.23 % 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: -0.46 (0.39), residues: 448 helix: -0.02 (1.02), residues: 32 sheet: 0.46 (0.32), residues: 248 loop : -1.51 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 85 HIS 0.006 0.002 HIS A 121 PHE 0.015 0.002 PHE B 266 TYR 0.008 0.002 TYR A 126 ARG 0.003 0.000 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 70 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.6919 (t0) REVERT: B 155 GLN cc_start: 0.7437 (mm-40) cc_final: 0.7224 (pt0) REVERT: B 184 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7163 (pm20) outliers start: 13 outliers final: 9 residues processed: 44 average time/residue: 1.8155 time to fit residues: 83.5254 Evaluate side-chains 43 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 235 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 22 optimal weight: 0.0030 chunk 39 optimal weight: 0.1980 chunk 11 optimal weight: 0.3980 chunk 14 optimal weight: 0.0770 chunk 40 optimal weight: 0.0770 chunk 8 optimal weight: 0.5980 overall best weight: 0.1506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3588 Z= 0.155 Angle : 0.504 3.780 4908 Z= 0.261 Chirality : 0.050 0.143 556 Planarity : 0.004 0.042 662 Dihedral : 6.641 59.473 513 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.10 % Allowed : 16.39 % Favored : 79.51 % 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: -0.27 (0.39), residues: 448 helix: 0.26 (1.06), residues: 32 sheet: 0.52 (0.32), residues: 248 loop : -1.30 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 85 HIS 0.001 0.001 HIS A 121 PHE 0.007 0.001 PHE B 135 TYR 0.006 0.001 TYR A 194 ARG 0.001 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 70 ASP cc_start: 0.7208 (OUTLIER) cc_final: 0.6845 (t0) REVERT: A 285 ASP cc_start: 0.6227 (OUTLIER) cc_final: 0.5916 (m-30) outliers start: 15 outliers final: 10 residues processed: 46 average time/residue: 1.7546 time to fit residues: 84.5009 Evaluate side-chains 45 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 179 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 36 optimal weight: 0.1980 chunk 20 optimal weight: 0.0270 chunk 3 optimal weight: 0.1980 chunk 14 optimal weight: 0.1980 chunk 23 optimal weight: 0.0870 chunk 42 optimal weight: 0.1980 chunk 5 optimal weight: 0.0570 chunk 25 optimal weight: 0.3980 overall best weight: 0.1134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3588 Z= 0.134 Angle : 0.481 3.732 4908 Z= 0.248 Chirality : 0.049 0.143 556 Planarity : 0.004 0.042 662 Dihedral : 6.412 59.241 513 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.46 % Allowed : 17.49 % Favored : 80.05 % 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: -0.11 (0.40), residues: 448 helix: 0.47 (1.09), residues: 32 sheet: 0.58 (0.32), residues: 248 loop : -1.13 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 85 HIS 0.001 0.001 HIS A 121 PHE 0.006 0.001 PHE B 135 TYR 0.005 0.001 TYR A 194 ARG 0.001 0.000 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: B 107 ASP cc_start: 0.7489 (t0) cc_final: 0.7244 (t0) REVERT: B 277 VAL cc_start: 0.8448 (m) cc_final: 0.8200 (t) outliers start: 9 outliers final: 7 residues processed: 42 average time/residue: 1.9254 time to fit residues: 84.4335 Evaluate side-chains 39 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 179 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 0.4980 chunk 25 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 0.0970 chunk 44 optimal weight: 0.0170 chunk 27 optimal weight: 0.1980 chunk 20 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 0.0980 chunk 13 optimal weight: 0.0170 chunk 8 optimal weight: 0.4980 overall best weight: 0.0854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3588 Z= 0.120 Angle : 0.465 3.697 4908 Z= 0.239 Chirality : 0.049 0.143 556 Planarity : 0.004 0.042 662 Dihedral : 5.626 59.282 509 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.19 % Allowed : 17.49 % Favored : 80.33 % 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: 0.00 (0.40), residues: 448 helix: 0.59 (1.09), residues: 32 sheet: 0.80 (0.32), residues: 238 loop : -1.21 (0.46), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 85 HIS 0.001 0.001 HIS A 121 PHE 0.006 0.001 PHE B 244 TYR 0.005 0.001 TYR A 194 ARG 0.001 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: B 107 ASP cc_start: 0.7469 (t0) cc_final: 0.7065 (t70) REVERT: B 277 VAL cc_start: 0.8429 (m) cc_final: 0.8197 (t) outliers start: 8 outliers final: 8 residues processed: 42 average time/residue: 1.8525 time to fit residues: 81.3050 Evaluate side-chains 43 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 0.4980 chunk 28 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 0.2980 chunk 34 optimal weight: 0.4980 chunk 40 optimal weight: 0.1980 chunk 42 optimal weight: 0.6980 chunk 38 optimal weight: 0.0980 chunk 41 optimal weight: 0.0970 chunk 24 optimal weight: 0.4980 overall best weight: 0.1978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3588 Z= 0.179 Angle : 0.511 3.815 4908 Z= 0.266 Chirality : 0.050 0.145 556 Planarity : 0.004 0.044 662 Dihedral : 5.683 58.108 508 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.28 % Allowed : 16.12 % Favored : 80.60 % 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: -0.12 (0.39), residues: 448 helix: 0.58 (1.09), residues: 32 sheet: 0.55 (0.31), residues: 248 loop : -1.13 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 85 HIS 0.004 0.002 HIS A 121 PHE 0.009 0.001 PHE B 135 TYR 0.005 0.001 TYR A 194 ARG 0.002 0.000 ARG B 241 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 285 ASP cc_start: 0.6235 (OUTLIER) cc_final: 0.5889 (m-30) REVERT: B 107 ASP cc_start: 0.7509 (t0) cc_final: 0.7259 (t0) REVERT: B 277 VAL cc_start: 0.8454 (m) cc_final: 0.8204 (t) outliers start: 12 outliers final: 9 residues processed: 43 average time/residue: 1.8149 time to fit residues: 81.7504 Evaluate side-chains 44 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 39 optimal weight: 0.5980 chunk 41 optimal weight: 0.0970 chunk 27 optimal weight: 0.0980 chunk 43 optimal weight: 0.0270 chunk 26 optimal weight: 0.0270 chunk 20 optimal weight: 0.0770 chunk 30 optimal weight: 0.1980 overall best weight: 0.0652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3588 Z= 0.114 Angle : 0.457 3.701 4908 Z= 0.233 Chirality : 0.049 0.143 556 Planarity : 0.004 0.042 662 Dihedral : 5.427 57.932 508 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.19 % Allowed : 16.94 % Favored : 80.87 % 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: 0.12 (0.40), residues: 448 helix: 0.76 (1.10), residues: 32 sheet: 0.66 (0.32), residues: 244 loop : -0.86 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 85 HIS 0.002 0.001 HIS A 121 PHE 0.006 0.001 PHE B 244 TYR 0.004 0.001 TYR A 194 ARG 0.001 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: B 107 ASP cc_start: 0.7511 (t0) cc_final: 0.7104 (t70) REVERT: B 277 VAL cc_start: 0.8426 (m) cc_final: 0.8180 (t) outliers start: 8 outliers final: 7 residues processed: 43 average time/residue: 1.8926 time to fit residues: 85.2040 Evaluate side-chains 42 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 36 optimal weight: 0.0770 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 0.1980 chunk 22 optimal weight: 0.0040 chunk 38 optimal weight: 0.1980 chunk 11 optimal weight: 0.6980 chunk 33 optimal weight: 0.0970 chunk 5 optimal weight: 0.2980 chunk 10 optimal weight: 0.0970 overall best weight: 0.0946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3588 Z= 0.125 Angle : 0.465 3.698 4908 Z= 0.238 Chirality : 0.049 0.144 556 Planarity : 0.004 0.043 662 Dihedral : 5.409 58.315 508 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.73 % Allowed : 16.39 % Favored : 80.87 % 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: 0.15 (0.40), residues: 448 helix: 0.86 (1.11), residues: 32 sheet: 0.67 (0.32), residues: 244 loop : -0.83 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 85 HIS 0.001 0.001 HIS A 121 PHE 0.005 0.001 PHE B 244 TYR 0.005 0.001 TYR A 194 ARG 0.001 0.000 ARG B 104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: B 107 ASP cc_start: 0.7467 (t0) cc_final: 0.7055 (t70) REVERT: B 184 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6910 (pm20) REVERT: B 277 VAL cc_start: 0.8437 (m) cc_final: 0.8195 (t) outliers start: 10 outliers final: 9 residues processed: 43 average time/residue: 1.7980 time to fit residues: 81.1415 Evaluate side-chains 45 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 184 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 0.0770 chunk 15 optimal weight: 0.4980 chunk 37 optimal weight: 0.3980 chunk 4 optimal weight: 0.4980 chunk 6 optimal weight: 0.1980 chunk 32 optimal weight: 0.4980 chunk 2 optimal weight: 0.4980 chunk 26 optimal weight: 0.4980 chunk 41 optimal weight: 0.4980 chunk 24 optimal weight: 0.3980 chunk 31 optimal weight: 0.0980 overall best weight: 0.2338 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.133923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.117329 restraints weight = 10692.433| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.44 r_work: 0.3368 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3588 Z= 0.199 Angle : 0.528 3.856 4908 Z= 0.276 Chirality : 0.050 0.145 556 Planarity : 0.005 0.044 662 Dihedral : 5.705 56.683 508 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.28 % Allowed : 16.12 % Favored : 80.60 % 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: -0.07 (0.39), residues: 448 helix: 0.73 (1.09), residues: 32 sheet: 0.58 (0.31), residues: 248 loop : -1.10 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 85 HIS 0.005 0.002 HIS A 121 PHE 0.010 0.001 PHE B 135 TYR 0.005 0.001 TYR A 194 ARG 0.002 0.000 ARG B 241 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4074.28 seconds wall clock time: 73 minutes 28.66 seconds (4408.66 seconds total)