Starting phenix.real_space_refine on Mon Feb 10 19:27:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7us9_26729/02_2025/7us9_26729.cif Found real_map, /net/cci-nas-00/data/ceres_data/7us9_26729/02_2025/7us9_26729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7us9_26729/02_2025/7us9_26729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7us9_26729/02_2025/7us9_26729.map" model { file = "/net/cci-nas-00/data/ceres_data/7us9_26729/02_2025/7us9_26729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7us9_26729/02_2025/7us9_26729.cif" } resolution = 3.8 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= 0.019 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: 4 Type Number sf(0) Gaussians S 4 5.16 5 C 744 2.51 5 N 185 2.21 5 O 194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 1127 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1071 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 137} Chain breaks: 7 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.09, per 1000 atoms: 3.63 Number of scatterers: 1127 At special positions: 0 Unit cell: (50.58, 48.894, 59.853, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 4 16.00 O 194 8.00 N 185 7.00 C 744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 153 " distance=2.09 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 301 " - " ASN A 42 " " NAG A 302 " - " ASN A 242 " " NAG B 1 " - " ASN A 249 " Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 114.0 milliseconds 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 274 Finding SS restraints... Secondary structure from input PDB file: 1 helices and 3 sheets defined 9.7% alpha, 43.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 32 through 45 removed outlier: 4.150A pdb=" N ILE A 36 " --> pdb=" O HIS A 32 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 57 Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81 removed outlier: 7.641A pdb=" N PHE A 202 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LYS A 110 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N THR A 204 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 109 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYR A 112 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A 130 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN A 156 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE A 132 " --> pdb=" O ARG A 154 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 196 removed outlier: 3.514A pdb=" N ALA A 85 " --> pdb=" O VAL A 230 " (cutoff:3.500A) 54 hydrogen bonds defined for protein. 141 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: 0.30 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 251 1.33 - 1.46: 358 1.46 - 1.58: 546 1.58 - 1.71: 1 1.71 - 1.84: 6 Bond restraints: 1162 Sorted by residual: bond pdb=" N PRO A 111 " pdb=" CD PRO A 111 " ideal model delta sigma weight residual 1.474 1.381 0.093 1.40e-02 5.10e+03 4.37e+01 bond pdb=" CZ2 TRP A 225 " pdb=" CH2 TRP A 225 " ideal model delta sigma weight residual 1.368 1.455 -0.087 1.90e-02 2.77e+03 2.10e+01 bond pdb=" CD2 TRP A 225 " pdb=" CE3 TRP A 225 " ideal model delta sigma weight residual 1.398 1.468 -0.070 1.60e-02 3.91e+03 1.90e+01 bond pdb=" CB LEU A 76 " pdb=" CG LEU A 76 " ideal model delta sigma weight residual 1.530 1.615 -0.085 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C LEU A 47 " pdb=" N PRO A 48 " ideal model delta sigma weight residual 1.329 1.371 -0.042 1.18e-02 7.18e+03 1.24e+01 ... (remaining 1157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 1429 2.34 - 4.69: 128 4.69 - 7.03: 27 7.03 - 9.38: 3 9.38 - 11.72: 2 Bond angle restraints: 1589 Sorted by residual: angle pdb=" N ILE A 195 " pdb=" CA ILE A 195 " pdb=" C ILE A 195 " ideal model delta sigma weight residual 108.11 117.48 -9.37 1.40e+00 5.10e-01 4.47e+01 angle pdb=" C PHE A 159 " pdb=" N PRO A 160 " pdb=" CA PRO A 160 " ideal model delta sigma weight residual 120.31 126.85 -6.54 9.80e-01 1.04e+00 4.45e+01 angle pdb=" C PRO A 48 " pdb=" N PRO A 49 " pdb=" CA PRO A 49 " ideal model delta sigma weight residual 119.84 127.79 -7.95 1.25e+00 6.40e-01 4.05e+01 angle pdb=" C LEU A 47 " pdb=" N PRO A 48 " pdb=" CA PRO A 48 " ideal model delta sigma weight residual 120.38 126.66 -6.28 1.03e+00 9.43e-01 3.72e+01 angle pdb=" N VAL A 78 " pdb=" CA VAL A 78 " pdb=" CB VAL A 78 " ideal model delta sigma weight residual 110.72 104.39 6.33 1.09e+00 8.42e-01 3.37e+01 ... (remaining 1584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.01: 623 8.01 - 16.02: 44 16.02 - 24.03: 10 24.03 - 32.04: 7 32.04 - 40.05: 4 Dihedral angle restraints: 688 sinusoidal: 266 harmonic: 422 Sorted by residual: dihedral pdb=" C GLN A 63 " pdb=" N GLN A 63 " pdb=" CA GLN A 63 " pdb=" CB GLN A 63 " ideal model delta harmonic sigma weight residual -122.60 -130.32 7.72 0 2.50e+00 1.60e-01 9.54e+00 dihedral pdb=" CA ILE A 195 " pdb=" CB ILE A 195 " pdb=" CG1 ILE A 195 " pdb=" CD1 ILE A 195 " ideal model delta sinusoidal sigma weight residual 60.00 100.05 -40.05 3 1.50e+01 4.44e-03 7.12e+00 dihedral pdb=" C LYS A 110 " pdb=" N LYS A 110 " pdb=" CA LYS A 110 " pdb=" CB LYS A 110 " ideal model delta harmonic sigma weight residual -122.60 -116.09 -6.51 0 2.50e+00 1.60e-01 6.77e+00 ... (remaining 685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 122 0.078 - 0.157: 30 0.157 - 0.235: 13 0.235 - 0.313: 9 0.313 - 0.392: 4 Chirality restraints: 178 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.42e+01 chirality pdb=" C2 NAG B 1 " pdb=" C1 NAG B 1 " pdb=" C3 NAG B 1 " pdb=" N2 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.88 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CG LEU A 76 " pdb=" CB LEU A 76 " pdb=" CD1 LEU A 76 " pdb=" CD2 LEU A 76 " both_signs ideal model delta sigma weight residual False -2.59 -2.97 0.38 2.00e-01 2.50e+01 3.59e+00 ... (remaining 175 not shown) Planarity restraints: 196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 42 " -0.046 2.00e-02 2.50e+03 4.80e-02 2.88e+01 pdb=" CG ASN A 42 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 42 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 42 " 0.075 2.00e-02 2.50e+03 pdb=" C1 NAG A 301 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 242 " -0.039 2.00e-02 2.50e+03 4.07e-02 2.07e+01 pdb=" CG ASN A 242 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 242 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 242 " 0.063 2.00e-02 2.50e+03 pdb=" C1 NAG A 302 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 64 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C PRO A 64 " 0.029 2.00e-02 2.50e+03 pdb=" O PRO A 64 " -0.011 2.00e-02 2.50e+03 pdb=" N TRP A 65 " -0.010 2.00e-02 2.50e+03 ... (remaining 193 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 519 2.97 - 3.45: 846 3.45 - 3.94: 1656 3.94 - 4.42: 1735 4.42 - 4.90: 3029 Nonbonded interactions: 7785 Sorted by model distance: nonbonded pdb=" O LYS A 110 " pdb=" CD PRO A 111 " model vdw 2.489 2.752 nonbonded pdb=" O GLN A 178 " pdb=" CA TRP A 179 " model vdw 2.627 2.776 nonbonded pdb=" N GLY A 109 " pdb=" O GLY A 109 " model vdw 2.636 2.496 nonbonded pdb=" N MET A 80 " pdb=" O MET A 80 " model vdw 2.641 2.496 nonbonded pdb=" O HIS A 189 " pdb=" ND1 HIS A 189 " model vdw 2.643 3.120 ... (remaining 7780 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 6.700 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: 0.020 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.880 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 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 : 0.015 0.093 1162 Z= 0.922 Angle : 1.582 11.720 1589 Z= 1.016 Chirality : 0.112 0.392 178 Planarity : 0.005 0.017 193 Dihedral : 7.489 40.047 411 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.07 (0.73), residues: 129 helix: 3.26 (1.42), residues: 12 sheet: 1.80 (0.75), residues: 47 loop : -0.57 (0.71), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP A 65 HIS 0.004 0.002 HIS A 189 PHE 0.011 0.003 PHE A 227 TYR 0.015 0.004 TYR A 43 ARG 0.002 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.119 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1203 time to fit residues: 4.4757 Evaluate side-chains 21 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 11 optimal weight: 0.0970 chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 0.0970 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 8 optimal weight: 0.2980 chunk 12 optimal weight: 0.2980 chunk 13 optimal weight: 0.1980 chunk 9 optimal weight: 0.1980 overall best weight: 0.1776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.172605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.152062 restraints weight = 1784.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.154742 restraints weight = 1166.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.156610 restraints weight = 862.846| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1162 Z= 0.210 Angle : 0.669 6.026 1589 Z= 0.353 Chirality : 0.052 0.186 178 Planarity : 0.005 0.029 193 Dihedral : 7.912 53.272 235 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 2.47 % Allowed : 11.11 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 (0.77), residues: 129 helix: 3.46 (1.30), residues: 12 sheet: 1.42 (0.58), residues: 76 loop : -1.25 (1.07), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 179 HIS 0.001 0.000 HIS A 189 PHE 0.012 0.002 PHE A 59 TYR 0.009 0.001 TYR A 235 ARG 0.001 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.124 Fit side-chains REVERT: A 199 ASN cc_start: 0.8245 (OUTLIER) cc_final: 0.7826 (t0) outliers start: 2 outliers final: 1 residues processed: 22 average time/residue: 0.0691 time to fit residues: 1.9344 Evaluate side-chains 15 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 199 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 4 optimal weight: 0.2980 chunk 9 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 13 optimal weight: 0.0870 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.167170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.145649 restraints weight = 1756.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.147797 restraints weight = 1255.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.149606 restraints weight = 986.842| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 1162 Z= 0.386 Angle : 0.815 9.570 1589 Z= 0.423 Chirality : 0.053 0.178 178 Planarity : 0.007 0.065 193 Dihedral : 7.543 40.974 235 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.70 % Allowed : 9.88 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 (0.72), residues: 129 helix: 1.74 (1.33), residues: 12 sheet: 0.72 (0.58), residues: 77 loop : -1.74 (0.89), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 179 HIS 0.002 0.001 HIS A 157 PHE 0.017 0.002 PHE A 197 TYR 0.012 0.002 TYR A 43 ARG 0.001 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.125 Fit side-chains REVERT: A 36 ILE cc_start: 0.9133 (mm) cc_final: 0.8892 (mt) REVERT: A 80 MET cc_start: 0.7522 (mmm) cc_final: 0.7068 (mmm) REVERT: A 199 ASN cc_start: 0.8256 (OUTLIER) cc_final: 0.7939 (t0) outliers start: 3 outliers final: 2 residues processed: 16 average time/residue: 0.0660 time to fit residues: 1.4101 Evaluate side-chains 16 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 13 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 199 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 4 optimal weight: 0.2980 chunk 10 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 9 optimal weight: 0.0870 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 0.0870 chunk 0 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.0980 overall best weight: 0.1936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.167840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.145944 restraints weight = 1749.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.148607 restraints weight = 1149.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.150358 restraints weight = 857.534| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1162 Z= 0.223 Angle : 0.654 4.894 1589 Z= 0.334 Chirality : 0.053 0.208 178 Planarity : 0.005 0.045 193 Dihedral : 6.842 37.751 235 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.70 % Allowed : 12.35 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.36 (0.73), residues: 129 helix: 2.38 (1.35), residues: 12 sheet: 0.74 (0.61), residues: 73 loop : -1.21 (0.86), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 179 HIS 0.001 0.000 HIS A 157 PHE 0.025 0.002 PHE A 39 TYR 0.008 0.001 TYR A 43 ARG 0.001 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.120 Fit side-chains REVERT: A 36 ILE cc_start: 0.9111 (mm) cc_final: 0.8858 (mt) REVERT: A 80 MET cc_start: 0.7508 (mmm) cc_final: 0.7097 (mmm) REVERT: A 199 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.8051 (t0) outliers start: 3 outliers final: 1 residues processed: 20 average time/residue: 0.0669 time to fit residues: 1.7281 Evaluate side-chains 16 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 199 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 8 optimal weight: 0.0770 chunk 0 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 13 optimal weight: 0.2980 chunk 4 optimal weight: 0.2980 chunk 1 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.0870 overall best weight: 0.1916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.168288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.146216 restraints weight = 1741.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.148720 restraints weight = 1187.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.150461 restraints weight = 917.573| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1162 Z= 0.233 Angle : 0.738 9.873 1589 Z= 0.388 Chirality : 0.054 0.172 178 Planarity : 0.006 0.039 193 Dihedral : 7.295 35.875 235 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.23 % Allowed : 17.28 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 (0.73), residues: 129 helix: 2.77 (1.31), residues: 12 sheet: 0.72 (0.60), residues: 78 loop : -1.95 (0.83), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 179 HIS 0.002 0.001 HIS A 189 PHE 0.022 0.002 PHE A 39 TYR 0.008 0.001 TYR A 43 ARG 0.001 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.122 Fit side-chains REVERT: A 33 TRP cc_start: 0.8492 (t-100) cc_final: 0.8102 (t-100) REVERT: A 36 ILE cc_start: 0.9125 (mm) cc_final: 0.8701 (mt) REVERT: A 193 TYR cc_start: 0.7633 (m-80) cc_final: 0.7353 (m-80) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.1006 time to fit residues: 2.1920 Evaluate side-chains 18 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 0.3980 chunk 3 optimal weight: 0.3980 chunk 0 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 0.2980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.3879 r_free = 0.3879 target = 0.165438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.143936 restraints weight = 1781.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.146136 restraints weight = 1269.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.147390 restraints weight = 1003.558| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 1162 Z= 0.389 Angle : 0.855 8.670 1589 Z= 0.428 Chirality : 0.067 0.531 178 Planarity : 0.006 0.040 193 Dihedral : 9.337 43.297 235 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.47 % Allowed : 18.52 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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 (0.70), residues: 129 helix: 1.98 (1.37), residues: 12 sheet: 0.45 (0.62), residues: 72 loop : -2.25 (0.68), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 179 HIS 0.002 0.001 HIS A 189 PHE 0.012 0.002 PHE A 59 TYR 0.014 0.002 TYR A 43 ARG 0.002 0.001 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.126 Fit side-chains REVERT: A 36 ILE cc_start: 0.9213 (mm) cc_final: 0.8999 (mt) REVERT: A 193 TYR cc_start: 0.7678 (m-80) cc_final: 0.7336 (m-80) outliers start: 2 outliers final: 1 residues processed: 18 average time/residue: 0.1477 time to fit residues: 3.0499 Evaluate side-chains 17 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 5 optimal weight: 0.2980 chunk 1 optimal weight: 0.0770 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 0.4980 chunk 13 optimal weight: 0.0470 chunk 4 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 0.3980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 overall best weight: 0.2636 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.167846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.146224 restraints weight = 1728.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.148564 restraints weight = 1259.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.150203 restraints weight = 1007.810| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1162 Z= 0.271 Angle : 0.761 7.723 1589 Z= 0.399 Chirality : 0.076 0.730 178 Planarity : 0.006 0.040 193 Dihedral : 8.619 52.950 235 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.47 % Allowed : 17.28 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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: -0.36 (0.71), residues: 129 helix: 3.62 (1.21), residues: 12 sheet: 0.38 (0.61), residues: 73 loop : -2.50 (0.66), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 179 HIS 0.001 0.000 HIS A 157 PHE 0.037 0.002 PHE A 39 TYR 0.010 0.001 TYR A 43 ARG 0.001 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.123 Fit side-chains REVERT: A 36 ILE cc_start: 0.9116 (mm) cc_final: 0.8880 (mt) REVERT: A 39 PHE cc_start: 0.8969 (t80) cc_final: 0.8703 (t80) REVERT: A 193 TYR cc_start: 0.7678 (m-80) cc_final: 0.7339 (m-80) outliers start: 2 outliers final: 2 residues processed: 23 average time/residue: 0.1309 time to fit residues: 3.4217 Evaluate side-chains 20 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 106 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 2 optimal weight: 0.0870 chunk 7 optimal weight: 3.9990 chunk 0 optimal weight: 0.1980 chunk 5 optimal weight: 0.0970 chunk 8 optimal weight: 0.5980 chunk 3 optimal weight: 0.0670 chunk 11 optimal weight: 0.0980 chunk 1 optimal weight: 0.0000 chunk 9 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 0.0970 overall best weight: 0.0696 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.168918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.148453 restraints weight = 1814.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.150992 restraints weight = 1206.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.152880 restraints weight = 910.426| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 1162 Z= 0.175 Angle : 0.643 5.754 1589 Z= 0.325 Chirality : 0.063 0.529 178 Planarity : 0.005 0.037 193 Dihedral : 7.550 35.850 235 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.23 % Allowed : 19.75 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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 (0.74), residues: 129 helix: 4.77 (1.23), residues: 12 sheet: 0.39 (0.63), residues: 74 loop : -2.16 (0.70), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 201 HIS 0.001 0.000 HIS A 157 PHE 0.024 0.002 PHE A 39 TYR 0.006 0.001 TYR A 43 ARG 0.001 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.116 Fit side-chains REVERT: A 36 ILE cc_start: 0.8994 (mm) cc_final: 0.8760 (mt) REVERT: A 193 TYR cc_start: 0.7595 (m-80) cc_final: 0.7288 (m-80) outliers start: 1 outliers final: 1 residues processed: 20 average time/residue: 0.1416 time to fit residues: 3.2063 Evaluate side-chains 19 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 4 optimal weight: 0.0870 chunk 5 optimal weight: 0.1980 chunk 0 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 6 optimal weight: 0.4980 chunk 10 optimal weight: 0.0060 chunk 9 optimal weight: 0.3980 chunk 8 optimal weight: 0.1980 chunk 11 optimal weight: 0.6980 chunk 1 optimal weight: 0.0870 overall best weight: 0.1152 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.168669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.149818 restraints weight = 1752.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.151997 restraints weight = 1209.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.153600 restraints weight = 938.645| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1162 Z= 0.186 Angle : 0.592 5.806 1589 Z= 0.302 Chirality : 0.056 0.378 178 Planarity : 0.005 0.037 193 Dihedral : 6.002 31.529 235 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.23 % Allowed : 19.75 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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 (0.74), residues: 129 helix: 4.85 (1.22), residues: 12 sheet: 0.47 (0.63), residues: 74 loop : -1.86 (0.72), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 201 HIS 0.001 0.000 HIS A 157 PHE 0.004 0.001 PHE A 180 TYR 0.005 0.001 TYR A 43 ARG 0.001 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.119 Fit side-chains REVERT: A 36 ILE cc_start: 0.8964 (mm) cc_final: 0.8751 (mt) outliers start: 1 outliers final: 1 residues processed: 20 average time/residue: 0.1689 time to fit residues: 3.7834 Evaluate side-chains 17 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 2 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.0770 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 chunk 11 optimal weight: 0.2980 chunk 1 optimal weight: 0.0870 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 overall best weight: 0.1716 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.168094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.148903 restraints weight = 1782.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.151356 restraints weight = 1220.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.153173 restraints weight = 921.649| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1162 Z= 0.210 Angle : 0.597 5.534 1589 Z= 0.311 Chirality : 0.061 0.479 178 Planarity : 0.005 0.036 193 Dihedral : 5.996 31.375 235 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.23 % Allowed : 22.22 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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: 0.28 (0.75), residues: 129 helix: 4.63 (1.19), residues: 12 sheet: 0.49 (0.63), residues: 74 loop : -1.69 (0.80), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 201 HIS 0.001 0.000 HIS A 189 PHE 0.007 0.001 PHE A 202 TYR 0.007 0.001 TYR A 43 ARG 0.000 0.000 ARG A 194 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.134 Fit side-chains REVERT: A 36 ILE cc_start: 0.8968 (mm) cc_final: 0.8757 (mt) REVERT: A 39 PHE cc_start: 0.9129 (t80) cc_final: 0.8761 (t80) outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.1517 time to fit residues: 3.2839 Evaluate side-chains 18 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 5 optimal weight: 0.3980 chunk 13 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 0.0970 chunk 6 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 chunk 9 optimal weight: 0.1980 chunk 3 optimal weight: 0.0980 overall best weight: 0.1778 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.162690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.139830 restraints weight = 1812.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.142732 restraints weight = 1197.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.144508 restraints weight = 907.649| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1162 Z= 0.226 Angle : 0.773 11.996 1589 Z= 0.363 Chirality : 0.109 1.247 178 Planarity : 0.005 0.036 193 Dihedral : 6.811 30.012 235 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.23 % Allowed : 23.46 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.19 (0.75), residues: 129 helix: 4.71 (1.19), residues: 12 sheet: 0.51 (0.63), residues: 74 loop : -1.96 (0.77), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 201 HIS 0.001 0.000 HIS A 157 PHE 0.007 0.001 PHE A 202 TYR 0.007 0.001 TYR A 43 ARG 0.003 0.001 ARG A 194 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1304.34 seconds wall clock time: 23 minutes 41.44 seconds (1421.44 seconds total)