Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:57:57 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxx_23578/11_2022/7lxx_23578.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxx_23578/11_2022/7lxx_23578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxx_23578/11_2022/7lxx_23578.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxx_23578/11_2022/7lxx_23578.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxx_23578/11_2022/7lxx_23578.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxx_23578/11_2022/7lxx_23578.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.029 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 2740 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 971 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 123} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 777 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 940 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain breaks: 5 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.22, per 1000 atoms: 0.81 Number of scatterers: 2740 At special positions: 0 Unit cell: (71.4, 86.1, 71.4, 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 10 16.00 O 540 8.00 N 466 7.00 C 1724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.07 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 " BETA1-6 " NAG B 1 " - " FUC B 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 149 " " NAG B 1 " - " ASN A 17 " Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 791.7 milliseconds 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 642 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 9 sheets defined 4.3% alpha, 50.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.847A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.669A pdb=" N TYR H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.530A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA7, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA8, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.464A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 83 through 84 removed outlier: 12.962A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.148A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.535A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) 120 hydrogen bonds defined for protein. 276 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: 0.83 Time building geometry restraints manager: 1.33 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: 719 1.33 - 1.45: 607 1.45 - 1.57: 1465 1.57 - 1.69: 0 1.69 - 1.81: 13 Bond restraints: 2804 Sorted by residual: bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.435 1.464 -0.029 1.10e-02 8.26e+03 7.13e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.435 1.463 -0.028 1.10e-02 8.26e+03 6.38e+00 bond pdb=" CD GLU A 154 " pdb=" OE2 GLU A 154 " ideal model delta sigma weight residual 1.249 1.204 0.045 1.90e-02 2.77e+03 5.54e+00 bond pdb=" CG ASP H 114 " pdb=" OD2 ASP H 114 " ideal model delta sigma weight residual 1.249 1.204 0.045 1.90e-02 2.77e+03 5.51e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.435 1.461 -0.026 1.10e-02 8.26e+03 5.49e+00 ... (remaining 2799 not shown) Histogram of bond angle deviations from ideal: 101.16 - 107.70: 91 107.70 - 114.24: 1561 114.24 - 120.78: 1166 120.78 - 127.32: 962 127.32 - 133.86: 30 Bond angle restraints: 3810 Sorted by residual: angle pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 120.03 127.05 -7.02 9.90e-01 1.02e+00 5.03e+01 angle pdb=" C ALA L 45 " pdb=" N PRO L 46 " pdb=" CA PRO L 46 " ideal model delta sigma weight residual 119.85 126.55 -6.70 1.01e+00 9.80e-01 4.40e+01 angle pdb=" C ARG L 56 " pdb=" N PRO L 57 " pdb=" CA PRO L 57 " ideal model delta sigma weight residual 119.78 126.60 -6.82 1.03e+00 9.43e-01 4.38e+01 angle pdb=" C ASP A 138 " pdb=" N PRO A 139 " pdb=" CA PRO A 139 " ideal model delta sigma weight residual 120.14 126.93 -6.79 1.06e+00 8.90e-01 4.10e+01 angle pdb=" C THR A 250 " pdb=" N PRO A 251 " pdb=" CA PRO A 251 " ideal model delta sigma weight residual 119.85 126.28 -6.43 1.01e+00 9.80e-01 4.05e+01 ... (remaining 3805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.98: 1540 14.98 - 29.95: 55 29.95 - 44.93: 9 44.93 - 59.90: 5 59.90 - 74.87: 4 Dihedral angle restraints: 1613 sinusoidal: 607 harmonic: 1006 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 120.22 -27.22 1 1.00e+01 1.00e-02 1.06e+01 dihedral pdb=" CG ARG H 67 " pdb=" CD ARG H 67 " pdb=" NE ARG H 67 " pdb=" CZ ARG H 67 " ideal model delta sinusoidal sigma weight residual 180.00 141.04 38.96 2 1.50e+01 4.44e-03 8.43e+00 dihedral pdb=" CB GLU A 154 " pdb=" CG GLU A 154 " pdb=" CD GLU A 154 " pdb=" OE1 GLU A 154 " ideal model delta sinusoidal sigma weight residual 0.00 74.87 -74.87 1 3.00e+01 1.11e-03 7.88e+00 ... (remaining 1610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 310 0.061 - 0.121: 100 0.121 - 0.181: 10 0.181 - 0.242: 4 0.242 - 0.302: 3 Chirality restraints: 427 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 -2.48 0.08 2.00e-02 2.50e+03 1.72e+01 chirality pdb=" C1 FUC B 3 " pdb=" O6 NAG B 1 " pdb=" C2 FUC B 3 " pdb=" O5 FUC B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.06e+01 chirality pdb=" C2 NAG A1301 " pdb=" C1 NAG A1301 " pdb=" C3 NAG A1301 " pdb=" N2 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.49 -2.79 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 424 not shown) Planarity restraints: 481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.353 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG B 1 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.123 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.544 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR H 95 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.17e+00 pdb=" C TYR H 95 " -0.049 2.00e-02 2.50e+03 pdb=" O TYR H 95 " 0.019 2.00e-02 2.50e+03 pdb=" N CYS H 96 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 29 " 0.025 2.00e-02 2.50e+03 1.52e-02 4.05e+00 pdb=" CG PHE H 29 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE H 29 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE H 29 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE H 29 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE H 29 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE H 29 " 0.014 2.00e-02 2.50e+03 ... (remaining 478 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 1519 3.00 - 3.47: 2371 3.47 - 3.95: 4484 3.95 - 4.42: 5187 4.42 - 4.90: 8533 Nonbonded interactions: 22094 Sorted by model distance: nonbonded pdb=" OD2 ASP H 73 " pdb=" NZ LYS H 76 " model vdw 2.519 2.520 nonbonded pdb=" N ASP H 62 " pdb=" OD1 ASP H 62 " model vdw 2.529 2.520 nonbonded pdb=" O THR A 250 " pdb=" OG1 THR A 250 " model vdw 2.573 2.440 nonbonded pdb=" N ASN L 33 " pdb=" OD1 ASN L 33 " model vdw 2.579 2.520 nonbonded pdb=" N LYS H 104 " pdb=" N TRP H 105 " model vdw 2.582 2.560 ... (remaining 22089 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 1724 2.51 5 N 466 2.21 5 O 540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 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: 0.000 Extract box with map and model: 12.120 Check model and map are aligned: 0.030 Convert atoms to be neutral: 0.020 Process input model: 14.850 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:11.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 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 : 0.012 0.052 2804 Z= 0.795 Angle : 1.183 7.023 3810 Z= 0.810 Chirality : 0.061 0.302 427 Planarity : 0.015 0.306 479 Dihedral : 10.067 74.874 962 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.46), residues: 336 helix: None (None), residues: 0 sheet: 0.72 (0.40), residues: 154 loop : 0.35 (0.48), residues: 182 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.234 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.6326 time to fit residues: 56.7065 Evaluate side-chains 61 residues out of total 298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.321 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.0470 chunk 25 optimal weight: 0.0980 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.1980 chunk 10 optimal weight: 0.0870 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.0970 overall best weight: 0.1054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN L 33 ASN A 99 ASN A 137 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 2804 Z= 0.173 Angle : 0.564 6.466 3810 Z= 0.309 Chirality : 0.044 0.211 427 Planarity : 0.004 0.026 479 Dihedral : 4.323 15.748 406 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer Outliers : 3.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.46), residues: 336 helix: None (None), residues: 0 sheet: 0.89 (0.40), residues: 152 loop : 0.04 (0.48), residues: 184 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 0.324 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 72 average time/residue: 0.6711 time to fit residues: 50.4307 Evaluate side-chains 69 residues out of total 298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.338 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 1 residues processed: 5 average time/residue: 0.5469 time to fit residues: 3.2872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 20 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.1980 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 29 optimal weight: 0.0270 chunk 10 optimal weight: 0.1980 chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 0.0980 chunk 15 optimal weight: 0.0570 chunk 3 optimal weight: 0.5980 overall best weight: 0.1156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN L 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 2804 Z= 0.157 Angle : 0.497 6.950 3810 Z= 0.267 Chirality : 0.041 0.160 427 Planarity : 0.004 0.026 479 Dihedral : 4.126 16.022 406 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 2.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.46), residues: 336 helix: None (None), residues: 0 sheet: 0.86 (0.41), residues: 142 loop : 0.10 (0.47), residues: 194 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.311 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 72 average time/residue: 0.6182 time to fit residues: 46.6536 Evaluate side-chains 68 residues out of total 298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 0.312 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.5482 time to fit residues: 2.1274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 15 optimal weight: 0.0870 chunk 28 optimal weight: 0.0980 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN H 77 ASN H 118 GLN L 41 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.066 2804 Z= 0.370 Angle : 0.636 7.632 3810 Z= 0.335 Chirality : 0.047 0.266 427 Planarity : 0.005 0.030 479 Dihedral : 4.747 17.657 406 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 5.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.46), residues: 336 helix: None (None), residues: 0 sheet: 0.48 (0.41), residues: 154 loop : -0.15 (0.48), residues: 182 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 0.320 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 78 average time/residue: 0.6063 time to fit residues: 49.5140 Evaluate side-chains 74 residues out of total 298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.295 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 4 residues processed: 5 average time/residue: 0.6551 time to fit residues: 3.8000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 28 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 0.0470 chunk 6 optimal weight: 0.2980 chunk 18 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 overall best weight: 0.3078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN H 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 2804 Z= 0.272 Angle : 0.563 7.754 3810 Z= 0.298 Chirality : 0.044 0.260 427 Planarity : 0.004 0.024 479 Dihedral : 4.499 16.828 406 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 4.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.46), residues: 336 helix: None (None), residues: 0 sheet: 0.40 (0.41), residues: 154 loop : -0.25 (0.47), residues: 182 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.327 Fit side-chains outliers start: 12 outliers final: 11 residues processed: 75 average time/residue: 0.6190 time to fit residues: 48.5802 Evaluate side-chains 73 residues out of total 298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.329 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.4644 time to fit residues: 2.3929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 0.0970 chunk 10 optimal weight: 0.0970 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 3 optimal weight: 0.0970 chunk 18 optimal weight: 0.3980 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 overall best weight: 0.1774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN H 84 ASN H 118 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 2804 Z= 0.188 Angle : 0.535 7.408 3810 Z= 0.283 Chirality : 0.043 0.250 427 Planarity : 0.003 0.025 479 Dihedral : 4.298 17.260 406 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 5.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.46), residues: 336 helix: None (None), residues: 0 sheet: 0.36 (0.41), residues: 154 loop : -0.21 (0.47), residues: 182 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 0.313 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 75 average time/residue: 0.5975 time to fit residues: 46.9254 Evaluate side-chains 74 residues out of total 298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.321 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 4 average time/residue: 0.4693 time to fit residues: 2.4143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 18 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN H 84 ASN H 118 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.074 2804 Z= 0.399 Angle : 0.642 7.974 3810 Z= 0.340 Chirality : 0.048 0.359 427 Planarity : 0.004 0.031 479 Dihedral : 4.795 18.120 406 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 6.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.45), residues: 336 helix: None (None), residues: 0 sheet: 0.15 (0.42), residues: 153 loop : -0.45 (0.45), residues: 183 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 69 time to evaluate : 0.317 Fit side-chains outliers start: 19 outliers final: 13 residues processed: 80 average time/residue: 0.6179 time to fit residues: 51.6456 Evaluate side-chains 83 residues out of total 298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 0.330 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 5 average time/residue: 0.3434 time to fit residues: 2.2413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 25 optimal weight: 0.4980 chunk 28 optimal weight: 0.0970 chunk 30 optimal weight: 0.4980 chunk 27 optimal weight: 0.0980 chunk 29 optimal weight: 0.2980 chunk 17 optimal weight: 0.4980 chunk 12 optimal weight: 0.0980 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 0.0970 overall best weight: 0.1376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN H 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 2804 Z= 0.206 Angle : 0.565 7.709 3810 Z= 0.301 Chirality : 0.045 0.295 427 Planarity : 0.003 0.026 479 Dihedral : 4.432 17.391 406 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 3.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.46), residues: 336 helix: None (None), residues: 0 sheet: 0.12 (0.42), residues: 154 loop : -0.37 (0.46), residues: 182 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.296 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 76 average time/residue: 0.6245 time to fit residues: 49.5887 Evaluate side-chains 74 residues out of total 298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 0.321 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.8260 time to fit residues: 2.1446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.1980 chunk 32 optimal weight: 0.5980 chunk 30 optimal weight: 0.2980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.0980 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 0.0770 overall best weight: 0.2538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN H 118 GLN A 121 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 2804 Z= 0.247 Angle : 0.583 7.771 3810 Z= 0.307 Chirality : 0.045 0.311 427 Planarity : 0.004 0.040 479 Dihedral : 4.408 17.069 406 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 3.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.46), residues: 336 helix: None (None), residues: 0 sheet: 0.12 (0.42), residues: 154 loop : -0.40 (0.46), residues: 182 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.323 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 75 average time/residue: 0.6642 time to fit residues: 51.9760 Evaluate side-chains 76 residues out of total 298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.309 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.0336 time to fit residues: 0.5358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 0.0980 chunk 1 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN H 118 GLN A 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.073 2804 Z= 0.410 Angle : 0.668 7.859 3810 Z= 0.355 Chirality : 0.049 0.360 427 Planarity : 0.005 0.039 479 Dihedral : 4.782 17.767 406 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 4.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.45), residues: 336 helix: None (None), residues: 0 sheet: 0.00 (0.42), residues: 153 loop : -0.53 (0.45), residues: 183 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 0.326 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 78 average time/residue: 0.5792 time to fit residues: 47.3959 Evaluate side-chains 77 residues out of total 298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 0.317 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.8055 time to fit residues: 2.0855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 17 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 20 optimal weight: 0.1980 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 0.0980 chunk 32 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 0.2980 chunk 6 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.138845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.129172 restraints weight = 3499.240| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.37 r_work: 0.3492 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 1.24 restraints_weight: 0.2500 r_work: 0.3468 rms_B_bonded: 1.33 restraints_weight: 0.1250 r_work: 0.3455 rms_B_bonded: 1.50 restraints_weight: 0.0625 r_work: 0.3437 rms_B_bonded: 1.73 restraints_weight: 0.0312 r_work: 0.3416 rms_B_bonded: 2.06 restraints_weight: 0.0156 r_work: 0.3388 rms_B_bonded: 2.54 restraints_weight: 0.0078 r_work: 0.3356 rms_B_bonded: 3.11 restraints_weight: 0.0039 r_work: 0.3320 rms_B_bonded: 3.80 restraints_weight: 0.0020 r_work: 0.3279 rms_B_bonded: 4.62 restraints_weight: 0.0010 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 2804 Z= 0.264 Angle : 0.611 7.870 3810 Z= 0.319 Chirality : 0.046 0.315 427 Planarity : 0.004 0.039 479 Dihedral : 4.577 17.358 406 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 4.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.46), residues: 336 helix: None (None), residues: 0 sheet: 0.03 (0.42), residues: 154 loop : -0.50 (0.46), residues: 182 =============================================================================== Job complete usr+sys time: 1636.97 seconds wall clock time: 30 minutes 1.25 seconds (1801.25 seconds total)