Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:32:47 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y97_10733/11_2022/6y97_10733.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y97_10733/11_2022/6y97_10733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y97_10733/11_2022/6y97_10733.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y97_10733/11_2022/6y97_10733.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y97_10733/11_2022/6y97_10733.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y97_10733/11_2022/6y97_10733.pdb" } resolution = 4.33 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= 0.026 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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 4366 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1310 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "B" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1310 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "H" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 906 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "L" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 840 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Time building chain proxies: 2.94, per 1000 atoms: 0.67 Number of scatterers: 4366 At special positions: 0 Unit cell: (61.05, 65.934, 118.03, 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 36 16.00 O 790 8.00 N 700 7.00 C 2840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 167 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 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 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 644.6 milliseconds 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1032 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 4 sheets defined 47.3% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 50 through 70 removed outlier: 4.157A pdb=" N ALA A 54 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 55 " --> pdb=" O THR A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.626A pdb=" N VAL A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 100 removed outlier: 3.955A pdb=" N TRP A 89 " --> pdb=" O TRP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 143 Processing helix chain 'A' and resid 152 through 156 Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 177 through 213 removed outlier: 4.121A pdb=" N GLU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 51 removed outlier: 3.880A pdb=" N SER B 49 " --> pdb=" O MET B 46 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LYS B 50 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR B 51 " --> pdb=" O GLU B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 71 Processing helix chain 'B' and resid 79 through 84 Processing helix chain 'B' and resid 85 through 102 removed outlier: 3.855A pdb=" N TRP B 89 " --> pdb=" O TRP B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 143 removed outlier: 4.301A pdb=" N MET B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.521A pdb=" N LYS B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN B 176 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 213 removed outlier: 3.617A pdb=" N GLN B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.980A pdb=" N SER H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.510A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS H 22 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU H 82 " --> pdb=" O THR H 69 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR H 69 " --> pdb=" O GLU H 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.177A pdb=" N GLU H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.646A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER L 22 " --> pdb=" O THR L 7 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR L 77 " --> pdb=" O SER L 70 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER L 70 " --> pdb=" O THR L 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 58 through 59 removed outlier: 4.056A pdb=" N ASN L 58 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR L 54 " --> pdb=" O ASN L 58 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLN L 50 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU L 42 " --> pdb=" O GLN L 50 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR L 39 " --> pdb=" O ALA L 94 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN L 95 " --> pdb=" O THR L 102 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N THR L 102 " --> pdb=" O GLN L 95 " (cutoff:3.500A) 216 hydrogen bonds defined for protein. 609 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1335 1.35 - 1.46: 1057 1.46 - 1.58: 2016 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 4468 Sorted by residual: bond pdb=" N GLN L 55 " pdb=" CA GLN L 55 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.78e+00 bond pdb=" CB PRO B 79 " pdb=" CG PRO B 79 " ideal model delta sigma weight residual 1.492 1.547 -0.055 5.00e-02 4.00e+02 1.23e+00 bond pdb=" CB LYS B 175 " pdb=" CG LYS B 175 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.07e+00 bond pdb=" CB LYS B 50 " pdb=" CG LYS B 50 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.07e-01 bond pdb=" CG LYS B 175 " pdb=" CD LYS B 175 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.05e-01 ... (remaining 4463 not shown) Histogram of bond angle deviations from ideal: 100.38 - 107.10: 137 107.10 - 113.82: 2492 113.82 - 120.54: 1722 120.54 - 127.26: 1658 127.26 - 133.98: 46 Bond angle restraints: 6055 Sorted by residual: angle pdb=" CB LYS B 175 " pdb=" CG LYS B 175 " pdb=" CD LYS B 175 " ideal model delta sigma weight residual 111.30 118.60 -7.30 2.30e+00 1.89e-01 1.01e+01 angle pdb=" C GLN L 43 " pdb=" N LYS L 44 " pdb=" CA LYS L 44 " ideal model delta sigma weight residual 121.95 111.42 10.53 3.74e+00 7.15e-02 7.93e+00 angle pdb=" CA GLN L 55 " pdb=" CB GLN L 55 " pdb=" CG GLN L 55 " ideal model delta sigma weight residual 114.10 118.84 -4.74 2.00e+00 2.50e-01 5.61e+00 angle pdb=" CA LYS B 50 " pdb=" CB LYS B 50 " pdb=" CG LYS B 50 " ideal model delta sigma weight residual 114.10 118.74 -4.64 2.00e+00 2.50e-01 5.38e+00 angle pdb=" C GLN L 55 " pdb=" N MET L 56 " pdb=" CA MET L 56 " ideal model delta sigma weight residual 121.54 125.86 -4.32 1.91e+00 2.74e-01 5.12e+00 ... (remaining 6050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 2369 17.99 - 35.98: 227 35.98 - 53.97: 46 53.97 - 71.96: 5 71.96 - 89.95: 5 Dihedral angle restraints: 2652 sinusoidal: 1031 harmonic: 1621 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 93 " pdb=" CB CYS L 93 " ideal model delta sinusoidal sigma weight residual 93.00 55.10 37.90 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" CB MET A 93 " pdb=" CG MET A 93 " pdb=" SD MET A 93 " pdb=" CE MET A 93 " ideal model delta sinusoidal sigma weight residual -60.00 -113.09 53.09 3 1.50e+01 4.44e-03 9.17e+00 dihedral pdb=" CB MET A 136 " pdb=" CG MET A 136 " pdb=" SD MET A 136 " pdb=" CE MET A 136 " ideal model delta sinusoidal sigma weight residual 180.00 127.86 52.14 3 1.50e+01 4.44e-03 9.09e+00 ... (remaining 2649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 461 0.034 - 0.069: 154 0.069 - 0.103: 60 0.103 - 0.137: 12 0.137 - 0.172: 1 Chirality restraints: 688 Sorted by residual: chirality pdb=" CA GLN L 55 " pdb=" N GLN L 55 " pdb=" C GLN L 55 " pdb=" CB GLN L 55 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA ILE B 143 " pdb=" N ILE B 143 " pdb=" C ILE B 143 " pdb=" CB ILE B 143 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE L 53 " pdb=" N ILE L 53 " pdb=" C ILE L 53 " pdb=" CB ILE L 53 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.61e-01 ... (remaining 685 not shown) Planarity restraints: 748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 78 " 0.065 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO B 79 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO B 79 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 79 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 63 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO L 64 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO L 64 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO L 64 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 94 " -0.007 2.00e-02 2.50e+03 9.89e-03 1.96e+00 pdb=" CG TYR A 94 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 94 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 94 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 94 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 94 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 94 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 94 " 0.000 2.00e-02 2.50e+03 ... (remaining 745 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 80 2.70 - 3.25: 4316 3.25 - 3.80: 6674 3.80 - 4.35: 7774 4.35 - 4.90: 13128 Nonbonded interactions: 31972 Sorted by model distance: nonbonded pdb=" OH TYR B 161 " pdb=" OG SER H 30 " model vdw 2.147 2.440 nonbonded pdb=" OH TYR A 86 " pdb=" O ALA A 126 " model vdw 2.176 2.440 nonbonded pdb=" OH TYR A 182 " pdb=" O ASN B 163 " model vdw 2.213 2.440 nonbonded pdb=" OG1 THR H 69 " pdb=" O GLU H 82 " model vdw 2.230 2.440 nonbonded pdb=" OD1 ASN A 171 " pdb=" OG SER A 173 " model vdw 2.271 2.440 ... (remaining 31967 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 2840 2.51 5 N 700 2.21 5 O 790 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 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: 1.980 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: 8.900 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.040 Process input model: 16.850 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6193 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.055 4468 Z= 0.163 Angle : 0.578 10.533 6055 Z= 0.293 Chirality : 0.040 0.172 688 Planarity : 0.005 0.098 748 Dihedral : 14.610 89.950 1608 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.38), residues: 556 helix: 2.81 (0.36), residues: 210 sheet: 0.41 (0.53), residues: 92 loop : -1.00 (0.43), residues: 254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1330 time to fit residues: 27.8329 Evaluate side-chains 134 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.525 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN B 145 HIS ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 4468 Z= 0.224 Angle : 0.585 6.767 6055 Z= 0.299 Chirality : 0.041 0.141 688 Planarity : 0.005 0.063 748 Dihedral : 3.952 16.761 603 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.38), residues: 556 helix: 2.52 (0.35), residues: 225 sheet: 0.79 (0.53), residues: 88 loop : -1.10 (0.43), residues: 243 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.1317 time to fit residues: 26.6290 Evaluate side-chains 129 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.489 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 43 optimal weight: 0.0970 chunk 48 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN A 187 GLN B 140 ASN ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN L 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 4468 Z= 0.163 Angle : 0.572 6.568 6055 Z= 0.289 Chirality : 0.041 0.135 688 Planarity : 0.005 0.069 748 Dihedral : 3.857 15.403 603 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.38), residues: 556 helix: 2.83 (0.35), residues: 225 sheet: 0.73 (0.52), residues: 92 loop : -1.21 (0.43), residues: 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.1386 time to fit residues: 27.5987 Evaluate side-chains 130 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.418 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 4468 Z= 0.194 Angle : 0.581 6.390 6055 Z= 0.298 Chirality : 0.041 0.137 688 Planarity : 0.005 0.046 748 Dihedral : 4.029 15.853 603 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.38), residues: 556 helix: 2.69 (0.36), residues: 225 sheet: 0.61 (0.51), residues: 88 loop : -1.26 (0.42), residues: 243 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1238 time to fit residues: 23.5561 Evaluate side-chains 129 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.396 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 38 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 46 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN B 56 GLN B 140 ASN ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 4468 Z= 0.177 Angle : 0.592 6.436 6055 Z= 0.295 Chirality : 0.041 0.133 688 Planarity : 0.005 0.050 748 Dihedral : 4.086 15.173 603 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.38), residues: 556 helix: 2.65 (0.35), residues: 225 sheet: 0.81 (0.52), residues: 88 loop : -1.25 (0.43), residues: 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1358 time to fit residues: 27.0769 Evaluate side-chains 130 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.511 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 0.0980 chunk 52 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN B 140 ASN ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 4468 Z= 0.189 Angle : 0.612 7.012 6055 Z= 0.305 Chirality : 0.042 0.134 688 Planarity : 0.004 0.045 748 Dihedral : 4.174 15.524 603 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.38), residues: 556 helix: 2.55 (0.35), residues: 224 sheet: 0.89 (0.51), residues: 93 loop : -1.27 (0.43), residues: 239 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1293 time to fit residues: 25.6366 Evaluate side-chains 126 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.512 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 4.9990 chunk 38 optimal weight: 0.0270 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 0.0670 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 HIS ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 4468 Z= 0.216 Angle : 0.649 7.688 6055 Z= 0.326 Chirality : 0.043 0.145 688 Planarity : 0.004 0.047 748 Dihedral : 4.446 17.123 603 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.97 (0.38), residues: 556 helix: 2.37 (0.35), residues: 224 sheet: 0.90 (0.52), residues: 83 loop : -1.13 (0.43), residues: 249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1372 time to fit residues: 28.2048 Evaluate side-chains 135 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.526 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 0.0980 chunk 45 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 HIS ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 4468 Z= 0.198 Angle : 0.650 8.549 6055 Z= 0.326 Chirality : 0.043 0.148 688 Planarity : 0.005 0.051 748 Dihedral : 4.434 16.600 603 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.89 (0.38), residues: 556 helix: 2.37 (0.35), residues: 224 sheet: 0.53 (0.53), residues: 88 loop : -1.15 (0.44), residues: 244 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1328 time to fit residues: 27.6567 Evaluate side-chains 132 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.523 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 HIS ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4468 Z= 0.209 Angle : 0.667 8.563 6055 Z= 0.330 Chirality : 0.043 0.157 688 Planarity : 0.005 0.049 748 Dihedral : 4.517 16.981 603 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.91 (0.38), residues: 556 helix: 2.35 (0.35), residues: 224 sheet: 0.85 (0.54), residues: 83 loop : -1.20 (0.43), residues: 249 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1261 time to fit residues: 26.1782 Evaluate side-chains 129 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.533 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 0.0070 chunk 34 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 0.0980 chunk 39 optimal weight: 0.9980 chunk 6 optimal weight: 0.0370 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 HIS ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 4468 Z= 0.176 Angle : 0.658 9.636 6055 Z= 0.320 Chirality : 0.043 0.163 688 Planarity : 0.005 0.050 748 Dihedral : 4.377 14.343 603 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.39), residues: 556 helix: 2.39 (0.36), residues: 223 sheet: 0.69 (0.50), residues: 103 loop : -1.10 (0.47), residues: 230 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1194 time to fit residues: 25.1377 Evaluate side-chains 131 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.521 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 2 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 HIS B 158 HIS ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.128612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.108578 restraints weight = 11621.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.112351 restraints weight = 7294.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.114975 restraints weight = 4964.402| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4468 Z= 0.194 Angle : 0.671 9.000 6055 Z= 0.331 Chirality : 0.044 0.177 688 Planarity : 0.005 0.048 748 Dihedral : 4.389 14.366 603 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.68 (0.38), residues: 556 helix: 2.07 (0.35), residues: 230 sheet: 0.67 (0.51), residues: 103 loop : -1.47 (0.45), residues: 223 =============================================================================== Job complete usr+sys time: 1357.14 seconds wall clock time: 26 minutes 4.45 seconds (1564.45 seconds total)