Starting phenix.real_space_refine on Wed Mar 5 14:17:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7us9_26729/03_2025/7us9_26729.cif Found real_map, /net/cci-nas-00/data/ceres_data/7us9_26729/03_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_26729/03_2025/7us9_26729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7us9_26729/03_2025/7us9_26729.map" model { file = "/net/cci-nas-00/data/ceres_data/7us9_26729/03_2025/7us9_26729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7us9_26729/03_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-5624/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: 2.81, per 1000 atoms: 2.49 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: 0.32 Conformation dependent library (CDL) restraints added in 128.5 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: 0.17 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: 0.27 Time building geometry restraints manager: 0.38 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: 5.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 10.100 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.250 ------------------------------------------------------------------------------- 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 : 0.106 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1176 time to fit residues: 4.3786 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 : 0.123 ------------------------------------------------------------------------------- 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: 0.1980 chunk 12 optimal weight: 0.2980 chunk 13 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 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 = 27)----------------| | 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 : 0.106 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: 0.0642 time to fit residues: 1.8162 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 : 0.110 ------------------------------------------------------------------------------- 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: 0.9990 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 = 0.3898 r_free = 0.3898 target = 0.166816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.145251 restraints weight = 1758.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.147480 restraints weight = 1250.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.149012 restraints weight = 991.560| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3761 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= 0.386 Angle : 0.805 8.829 1589 Z= 0.415 Chirality : 0.054 0.183 178 Planarity : 0.007 0.064 193 Dihedral : 7.459 41.101 235 Min Nonbonded Distance : 2.577 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: 0.10 (0.72), residues: 129 helix: 1.72 (1.33), residues: 12 sheet: 0.72 (0.58), residues: 77 loop : -1.77 (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 0.016 0.002 PHE A 197 TYR 0.013 0.002 TYR A 235 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 18 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.123 Fit side-chains REVERT: A 36 ILE cc_start: 0.9142 (mm) cc_final: 0.8902 (mt) REVERT: A 80 MET cc_start: 0.7537 (mmm) cc_final: 0.7062 (mmm) REVERT: A 199 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7922 (t0) outliers start: 3 outliers final: 2 residues processed: 17 average time/residue: 0.0980 time to fit residues: 2.0214 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 : 0.117 ------------------------------------------------------------------------------- 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: 0.0980 chunk 10 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 9 optimal weight: 0.0980 chunk 13 optimal weight: 0.0970 chunk 2 optimal weight: 0.1980 chunk 0 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.1778 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.167994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.146883 restraints weight = 1756.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.149245 restraints weight = 1213.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.150754 restraints weight = 932.532| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1162 Z= 0.217 Angle : 0.653 5.532 1589 Z= 0.337 Chirality : 0.054 0.214 178 Planarity : 0.005 0.044 193 Dihedral : 6.686 37.542 235 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.70 % Allowed : 11.11 % Favored : 85.19 % 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: 0.41 (0.73), residues: 129 helix: 2.48 (1.34), residues: 12 sheet: 0.76 (0.61), residues: 73 loop : -1.20 (0.85), 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 0.024 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 : 0.095 Fit side-chains REVERT: A 36 ILE cc_start: 0.9081 (mm) cc_final: 0.8828 (mt) REVERT: A 80 MET cc_start: 0.7556 (mmm) cc_final: 0.7123 (mmm) outliers start: 3 outliers final: 2 residues processed: 20 average time/residue: 0.0602 time to fit residues: 1.5596 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 : 0.120 ------------------------------------------------------------------------------- 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: 0.9980 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 8 optimal weight: 0.3980 chunk 0 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 13 optimal weight: 0.3980 chunk 4 optimal weight: 0.0980 chunk 1 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.166205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.144049 restraints weight = 1753.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.146686 restraints weight = 1190.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.148234 restraints weight = 918.807| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 1162 Z= 0.332 Angle : 0.772 9.557 1589 Z= 0.403 Chirality : 0.055 0.177 178 Planarity : 0.006 0.041 193 Dihedral : 7.439 38.757 235 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.23 % Allowed : 18.52 % Favored : 80.25 % 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: -0.07 (0.72), residues: 129 helix: 2.21 (1.37), residues: 12 sheet: 0.61 (0.60), residues: 77 loop : -2.09 (0.78), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 179 HIS 0.002 0.001 HIS A 157 PHE 0.027 0.003 PHE A 39 TYR 0.011 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 : 0.123 Fit side-chains REVERT: A 36 ILE cc_start: 0.9145 (mm) cc_final: 0.8916 (mt) REVERT: A 193 TYR cc_start: 0.7714 (m-80) cc_final: 0.7413 (m-80) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.1539 time to fit residues: 3.1448 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 : 0.120 ------------------------------------------------------------------------------- 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: 0.4980 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 0.0980 chunk 3 optimal weight: 0.0970 chunk 0 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.0870 chunk 1 optimal weight: 0.1980 overall best weight: 0.1956 ------------------------------------------------------------------------------- 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 = 0.169100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.147407 restraints weight = 1757.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.149925 restraints weight = 1176.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.151927 restraints weight = 896.585| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1162 Z= 0.241 Angle : 0.814 10.543 1589 Z= 0.392 Chirality : 0.087 0.910 178 Planarity : 0.005 0.039 193 Dihedral : 9.801 57.566 235 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % 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: -0.02 (0.72), residues: 129 helix: 3.15 (1.35), residues: 12 sheet: 0.53 (0.62), residues: 73 loop : -1.88 (0.71), 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 0.008 0.001 PHE A 202 TYR 0.008 0.001 TYR A 43 ARG 0.001 0.000 ARG A 237 *********************** 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 20 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.111 Fit side-chains REVERT: A 36 ILE cc_start: 0.9078 (mm) cc_final: 0.8777 (mt) REVERT: A 193 TYR cc_start: 0.7714 (m-80) cc_final: 0.7348 (m-80) outliers start: 1 outliers final: 1 residues processed: 20 average time/residue: 0.1461 time to fit residues: 3.3097 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 : 0.118 ------------------------------------------------------------------------------- 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: 0.5980 chunk 1 optimal weight: 0.1980 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 13 optimal weight: 0.0980 chunk 4 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 0.0970 chunk 10 optimal weight: 0.0670 chunk 6 optimal weight: 0.9990 overall best weight: 0.2116 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.166095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.146547 restraints weight = 1736.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.148983 restraints weight = 1093.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.150745 restraints weight = 816.512| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4762 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= 0.243 Angle : 0.733 8.916 1589 Z= 0.370 Chirality : 0.060 0.409 178 Planarity : 0.005 0.039 193 Dihedral : 7.296 34.683 235 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.47 % Allowed : 19.75 % Favored : 77.78 % 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: 0.20 (0.74), residues: 129 helix: 3.53 (1.31), residues: 12 sheet: 0.56 (0.63), residues: 73 loop : -1.59 (0.81), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 201 HIS 0.001 0.000 HIS A 157 PHE 0.008 0.001 PHE A 202 TYR 0.008 0.001 TYR A 43 ARG 0.001 0.000 ARG A 194 *********************** 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 20 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.124 Fit side-chains REVERT: A 36 ILE cc_start: 0.9028 (mm) cc_final: 0.8768 (mt) REVERT: A 39 PHE cc_start: 0.9186 (t80) cc_final: 0.8938 (t80) REVERT: A 193 TYR cc_start: 0.7677 (m-80) cc_final: 0.7346 (m-80) outliers start: 2 outliers final: 1 residues processed: 19 average time/residue: 0.1487 time to fit residues: 3.2206 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 : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 2 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 0.3980 chunk 5 optimal weight: 0.3980 chunk 8 optimal weight: 0.7980 chunk 3 optimal weight: 0.2980 chunk 11 optimal weight: 0.6980 chunk 1 optimal weight: 0.0270 chunk 9 optimal weight: 0.1980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.3980 overall best weight: 0.2638 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.168217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.146160 restraints weight = 1793.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.148767 restraints weight = 1253.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.150315 restraints weight = 975.403| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1162 Z= 0.274 Angle : 0.739 10.737 1589 Z= 0.367 Chirality : 0.076 0.732 178 Planarity : 0.005 0.039 193 Dihedral : 9.998 58.046 235 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.70 % Allowed : 20.99 % Favored : 75.31 % 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: 0.02 (0.74), residues: 129 helix: 3.42 (1.33), residues: 12 sheet: 0.40 (0.62), residues: 74 loop : -1.67 (0.83), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 179 HIS 0.001 0.001 HIS A 189 PHE 0.009 0.001 PHE A 202 TYR 0.010 0.001 TYR A 43 ARG 0.001 0.000 ARG A 237 *********************** 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 22 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: A 36 ILE cc_start: 0.9062 (mm) cc_final: 0.8819 (mt) REVERT: A 39 PHE cc_start: 0.9260 (t80) cc_final: 0.8956 (t80) REVERT: A 193 TYR cc_start: 0.7669 (m-80) cc_final: 0.7337 (m-80) outliers start: 3 outliers final: 3 residues processed: 21 average time/residue: 0.1401 time to fit residues: 3.3429 Evaluate side-chains 22 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 242 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 4 optimal weight: 0.3980 chunk 5 optimal weight: 0.2980 chunk 0 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 6 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 0.0870 chunk 8 optimal weight: 0.0970 chunk 11 optimal weight: 0.3980 chunk 1 optimal weight: 0.0270 overall best weight: 0.1214 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.171920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.150442 restraints weight = 1767.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.152595 restraints weight = 1292.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.154306 restraints weight = 1047.504| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1162 Z= 0.187 Angle : 0.621 8.070 1589 Z= 0.318 Chirality : 0.067 0.591 178 Planarity : 0.005 0.039 193 Dihedral : 7.945 54.393 235 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.47 % Allowed : 24.69 % Favored : 72.84 % 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: 0.49 (0.77), residues: 129 helix: 4.47 (1.24), residues: 12 sheet: 0.57 (0.63), residues: 74 loop : -1.33 (0.89), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 201 HIS 0.001 0.000 HIS A 157 PHE 0.008 0.001 PHE A 202 TYR 0.006 0.001 TYR A 43 ARG 0.001 0.001 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: 2 poor density : 18 time to evaluate : 0.109 Fit side-chains REVERT: A 36 ILE cc_start: 0.8959 (mm) cc_final: 0.8700 (mt) REVERT: A 39 PHE cc_start: 0.9249 (t80) cc_final: 0.9008 (t80) outliers start: 2 outliers final: 1 residues processed: 19 average time/residue: 0.1448 time to fit residues: 3.1060 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 : 0.121 ------------------------------------------------------------------------------- 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: 0.0010 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.0870 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 11 optimal weight: 0.2980 chunk 1 optimal weight: 0.0470 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.0060 overall best weight: 0.0878 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.170781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.150631 restraints weight = 1781.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.152807 restraints weight = 1243.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.154634 restraints weight = 974.595| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 1162 Z= 0.215 Angle : 0.628 5.861 1589 Z= 0.320 Chirality : 0.057 0.366 178 Planarity : 0.005 0.038 193 Dihedral : 7.755 59.799 235 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.23 % Allowed : 27.16 % Favored : 71.60 % 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: 0.42 (0.75), residues: 129 helix: 4.61 (1.23), residues: 12 sheet: 0.67 (0.61), residues: 79 loop : -2.06 (0.80), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 65 HIS 0.000 0.000 HIS A 157 PHE 0.005 0.001 PHE A 202 TYR 0.004 0.001 TYR A 43 ARG 0.007 0.001 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 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: 0.8940 (mm) cc_final: 0.8703 (mt) REVERT: A 39 PHE cc_start: 0.9229 (t80) cc_final: 0.9009 (t80) outliers start: 1 outliers final: 1 residues processed: 20 average time/residue: 0.1340 time to fit residues: 3.0553 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 : 0.116 ------------------------------------------------------------------------------- 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: 0.5980 chunk 13 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 chunk 1 optimal weight: 0.0970 chunk 6 optimal weight: 0.1980 chunk 10 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 0.0070 chunk 9 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 overall best weight: 0.1996 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.163797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.141249 restraints weight = 1801.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.144087 restraints weight = 1208.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.146168 restraints weight = 915.078| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 1162 Z= 0.245 Angle : 0.756 10.361 1589 Z= 0.428 Chirality : 0.109 1.247 178 Planarity : 0.008 0.078 193 Dihedral : 7.808 50.821 235 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.23 % Allowed : 24.69 % Favored : 74.07 % 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: 0.40 (0.74), residues: 129 helix: 4.40 (1.28), residues: 12 sheet: 0.66 (0.63), residues: 74 loop : -1.72 (0.77), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 65 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 0.008 0.002 ARG A 194 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1307.75 seconds wall clock time: 23 minutes 4.48 seconds (1384.48 seconds total)