Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 11:51:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk8_33890/08_2023/7yk8_33890.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk8_33890/08_2023/7yk8_33890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk8_33890/08_2023/7yk8_33890.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk8_33890/08_2023/7yk8_33890.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk8_33890/08_2023/7yk8_33890.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk8_33890/08_2023/7yk8_33890.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1938 2.51 5 N 546 2.21 5 O 624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L ASP 98": "OD1" <-> "OD2" Residue "B ASP 98": "OD1" <-> "OD2" Residue "J ASP 98": "OD1" <-> "OD2" Residue "E ASP 98": "OD1" <-> "OD2" Residue "K ASP 98": "OD1" <-> "OD2" Residue "F ASP 98": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 3108 Number of models: 1 Model: "" Number of chains: 12 Chain: "L" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "I" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 80 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "B" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "A" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 80 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "J" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "G" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 80 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "E" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 80 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "K" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "H" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 80 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "F" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "D" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 80 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Time building chain proxies: 1.91, per 1000 atoms: 0.61 Number of scatterers: 3108 At special positions: 0 Unit cell: (94.34, 117.66, 32.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 624 8.00 N 546 7.00 C 1938 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 1.00 Conformation dependent library (CDL) restraints added in 468.2 milliseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 49.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'J' and resid 46 through 57 removed outlier: 6.878A pdb=" N VAL J 48 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL L 49 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N HIS J 50 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY L 51 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N GLU L 46 " --> pdb=" O GLY K 47 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N VAL K 49 " --> pdb=" O GLU L 46 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N VAL L 48 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N GLY K 51 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N HIS L 50 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N ALA K 53 " --> pdb=" O HIS L 50 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL L 52 " --> pdb=" O ALA K 53 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N VAL K 55 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR L 54 " --> pdb=" O VAL K 55 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLU K 57 " --> pdb=" O THR L 54 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA L 56 " --> pdb=" O GLU K 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 61 through 66 removed outlier: 6.312A pdb=" N GLN L 62 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ASN J 65 " --> pdb=" O GLN L 62 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR L 64 " --> pdb=" O ASN J 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 69 through 82 removed outlier: 6.597A pdb=" N ALA L 69 " --> pdb=" O VAL J 70 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N THR J 72 " --> pdb=" O ALA L 69 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL L 71 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL J 74 " --> pdb=" O VAL L 71 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N GLY L 73 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 9.763A pdb=" N ALA J 76 " --> pdb=" O GLY L 73 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N THR L 75 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N ALA J 78 " --> pdb=" O THR L 75 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL L 77 " --> pdb=" O ALA J 78 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N LYS J 80 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLN L 79 " --> pdb=" O LYS J 80 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N VAL J 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR L 81 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL L 74 " --> pdb=" O GLY K 73 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR K 75 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA L 76 " --> pdb=" O THR K 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 86 through 92 removed outlier: 6.976A pdb=" N SER L 87 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE J 88 " --> pdb=" O SER L 87 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N GLY L 86 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 9.503A pdb=" N ALA K 89 " --> pdb=" O GLY L 86 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ILE L 88 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ALA K 91 " --> pdb=" O ILE L 88 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA L 90 " --> pdb=" O ALA K 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 16 through 18 removed outlier: 6.225A pdb=" N VAL I 16 " --> pdb=" O ALA H 17 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 46 through 57 removed outlier: 6.883A pdb=" N VAL E 48 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 49 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N HIS E 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLY B 51 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N GLU B 46 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N VAL F 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N VAL B 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 10.475A pdb=" N GLY F 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N HIS B 50 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N ALA F 53 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL B 52 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N VAL F 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR B 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLU F 57 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA B 56 " --> pdb=" O GLU F 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 61 through 66 removed outlier: 6.310A pdb=" N GLN B 62 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASN E 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR B 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 69 through 82 removed outlier: 6.598A pdb=" N ALA B 69 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N THR E 72 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL B 71 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL E 74 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N GLY B 73 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N ALA E 76 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N THR B 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N ALA E 78 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL B 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N LYS E 80 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLN B 79 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N VAL E 82 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR B 81 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL B 74 " --> pdb=" O GLY F 73 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR F 75 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA B 76 " --> pdb=" O THR F 75 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 86 through 92 removed outlier: 6.980A pdb=" N SER B 87 " --> pdb=" O GLY E 86 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE E 88 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N GLY B 86 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N ALA F 89 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ILE B 88 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA F 91 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA B 90 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 16 through 18 removed outlier: 6.220A pdb=" N VAL A 16 " --> pdb=" O ALA D 17 " (cutoff:3.500A) 56 hydrogen bonds defined for protein. 168 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: 0.64 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 552 1.29 - 1.35: 482 1.35 - 1.42: 106 1.42 - 1.48: 498 1.48 - 1.55: 1476 Bond restraints: 3114 Sorted by residual: bond pdb=" N LEU E 38 " pdb=" CA LEU E 38 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.25e-02 6.40e+03 6.53e+00 bond pdb=" N LEU F 38 " pdb=" CA LEU F 38 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.25e-02 6.40e+03 6.50e+00 bond pdb=" N LEU L 38 " pdb=" CA LEU L 38 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.25e-02 6.40e+03 6.49e+00 bond pdb=" N LEU J 38 " pdb=" CA LEU J 38 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.25e-02 6.40e+03 6.49e+00 bond pdb=" N LEU K 38 " pdb=" CA LEU K 38 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.25e-02 6.40e+03 6.26e+00 ... (remaining 3109 not shown) Histogram of bond angle deviations from ideal: 105.90 - 110.97: 1263 110.97 - 116.04: 970 116.04 - 121.10: 938 121.10 - 126.17: 1017 126.17 - 131.23: 6 Bond angle restraints: 4194 Sorted by residual: angle pdb=" N LEU L 38 " pdb=" CA LEU L 38 " pdb=" C LEU L 38 " ideal model delta sigma weight residual 112.93 108.91 4.02 1.33e+00 5.65e-01 9.12e+00 angle pdb=" N LEU E 38 " pdb=" CA LEU E 38 " pdb=" C LEU E 38 " ideal model delta sigma weight residual 112.93 108.92 4.01 1.33e+00 5.65e-01 9.08e+00 angle pdb=" N LEU F 38 " pdb=" CA LEU F 38 " pdb=" C LEU F 38 " ideal model delta sigma weight residual 112.93 108.93 4.00 1.33e+00 5.65e-01 9.04e+00 angle pdb=" N LEU K 38 " pdb=" CA LEU K 38 " pdb=" C LEU K 38 " ideal model delta sigma weight residual 112.93 108.94 3.99 1.33e+00 5.65e-01 9.01e+00 angle pdb=" N LEU B 38 " pdb=" CA LEU B 38 " pdb=" C LEU B 38 " ideal model delta sigma weight residual 112.93 108.96 3.97 1.33e+00 5.65e-01 8.92e+00 ... (remaining 4189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.91: 1572 10.91 - 21.82: 192 21.82 - 32.73: 48 32.73 - 43.63: 12 43.63 - 54.54: 12 Dihedral angle restraints: 1836 sinusoidal: 624 harmonic: 1212 Sorted by residual: dihedral pdb=" N LYS F 45 " pdb=" CA LYS F 45 " pdb=" CB LYS F 45 " pdb=" CG LYS F 45 " ideal model delta sinusoidal sigma weight residual -180.00 -125.46 -54.54 3 1.50e+01 4.44e-03 9.29e+00 dihedral pdb=" N LYS J 45 " pdb=" CA LYS J 45 " pdb=" CB LYS J 45 " pdb=" CG LYS J 45 " ideal model delta sinusoidal sigma weight residual -180.00 -125.46 -54.54 3 1.50e+01 4.44e-03 9.29e+00 dihedral pdb=" N LYS L 45 " pdb=" CA LYS L 45 " pdb=" CB LYS L 45 " pdb=" CG LYS L 45 " ideal model delta sinusoidal sigma weight residual -180.00 -125.47 -54.53 3 1.50e+01 4.44e-03 9.29e+00 ... (remaining 1833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 261 0.033 - 0.067: 150 0.067 - 0.100: 50 0.100 - 0.134: 61 0.134 - 0.167: 24 Chirality restraints: 546 Sorted by residual: chirality pdb=" CA VAL E 37 " pdb=" N VAL E 37 " pdb=" C VAL E 37 " pdb=" CB VAL E 37 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CA VAL F 37 " pdb=" N VAL F 37 " pdb=" C VAL F 37 " pdb=" CB VAL F 37 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CA VAL L 37 " pdb=" N VAL L 37 " pdb=" C VAL L 37 " pdb=" CB VAL L 37 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 543 not shown) Planarity restraints: 522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL L 95 " -0.004 2.00e-02 2.50e+03 7.83e-03 6.13e-01 pdb=" C VAL L 95 " 0.014 2.00e-02 2.50e+03 pdb=" O VAL L 95 " -0.005 2.00e-02 2.50e+03 pdb=" N LYS L 96 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL J 95 " -0.004 2.00e-02 2.50e+03 7.80e-03 6.09e-01 pdb=" C VAL J 95 " 0.013 2.00e-02 2.50e+03 pdb=" O VAL J 95 " -0.005 2.00e-02 2.50e+03 pdb=" N LYS J 96 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 95 " -0.004 2.00e-02 2.50e+03 7.73e-03 5.97e-01 pdb=" C VAL F 95 " 0.013 2.00e-02 2.50e+03 pdb=" O VAL F 95 " -0.005 2.00e-02 2.50e+03 pdb=" N LYS F 96 " -0.004 2.00e-02 2.50e+03 ... (remaining 519 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 1354 2.95 - 3.44: 2895 3.44 - 3.93: 4431 3.93 - 4.41: 4982 4.41 - 4.90: 10182 Nonbonded interactions: 23844 Sorted by model distance: nonbonded pdb=" N VAL B 37 " pdb=" O VAL F 37 " model vdw 2.465 2.520 nonbonded pdb=" N VAL L 37 " pdb=" O VAL K 37 " model vdw 2.480 2.520 nonbonded pdb=" O VAL L 37 " pdb=" N VAL J 37 " model vdw 2.488 2.520 nonbonded pdb=" O VAL B 37 " pdb=" N VAL E 37 " model vdw 2.495 2.520 nonbonded pdb=" O ILE B 88 " pdb=" N ALA F 89 " model vdw 2.650 2.520 ... (remaining 23839 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 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 4.950 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.410 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.005 0.036 3114 Z= 0.320 Angle : 0.661 4.016 4194 Z= 0.415 Chirality : 0.063 0.167 546 Planarity : 0.002 0.008 522 Dihedral : 11.560 54.540 1068 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % 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: -3.55 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.26), residues: 426 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.343 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.9806 time to fit residues: 88.9615 Evaluate side-chains 76 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.354 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 0.0670 chunk 10 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS B 65 ASN J 50 HIS E 50 HIS K 65 ASN F 65 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.034 3114 Z= 0.422 Angle : 0.690 4.392 4194 Z= 0.406 Chirality : 0.057 0.158 546 Planarity : 0.003 0.016 522 Dihedral : 4.950 11.774 444 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % Rotamer Outliers : 11.86 % 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: -3.46 (0.35), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.27), residues: 426 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 78 time to evaluate : 0.355 Fit side-chains outliers start: 37 outliers final: 25 residues processed: 86 average time/residue: 1.1630 time to fit residues: 102.8012 Evaluate side-chains 101 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 76 time to evaluate : 0.368 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 7 residues processed: 18 average time/residue: 0.2220 time to fit residues: 4.9110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 0.0970 chunk 41 optimal weight: 9.9990 chunk 34 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 0.3980 chunk 19 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN K 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.014 3114 Z= 0.131 Angle : 0.456 4.518 4194 Z= 0.257 Chirality : 0.050 0.129 546 Planarity : 0.001 0.008 522 Dihedral : 4.189 13.651 444 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer Outliers : 8.01 % 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: -2.99 (0.37), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.29), residues: 426 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 83 time to evaluate : 0.369 Fit side-chains outliers start: 25 outliers final: 12 residues processed: 86 average time/residue: 0.9008 time to fit residues: 80.0425 Evaluate side-chains 89 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.349 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 1 residues processed: 11 average time/residue: 0.0639 time to fit residues: 1.4131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.031 3114 Z= 0.400 Angle : 0.663 4.291 4194 Z= 0.392 Chirality : 0.056 0.154 546 Planarity : 0.003 0.017 522 Dihedral : 4.819 12.961 444 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer Outliers : 11.54 % 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: -3.21 (0.36), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.28), residues: 426 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 84 time to evaluate : 0.329 Fit side-chains outliers start: 36 outliers final: 23 residues processed: 90 average time/residue: 1.1137 time to fit residues: 103.0209 Evaluate side-chains 102 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 79 time to evaluate : 0.364 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 5 residues processed: 18 average time/residue: 0.0527 time to fit residues: 1.8469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.0020 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 3114 Z= 0.221 Angle : 0.529 4.362 4194 Z= 0.310 Chirality : 0.052 0.140 546 Planarity : 0.002 0.010 522 Dihedral : 4.573 16.786 444 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer Outliers : 9.94 % 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: -3.03 (0.37), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.28), residues: 426 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 80 time to evaluate : 0.383 Fit side-chains outliers start: 31 outliers final: 16 residues processed: 89 average time/residue: 1.0139 time to fit residues: 93.0469 Evaluate side-chains 91 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 0.333 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 4 residues processed: 12 average time/residue: 0.0645 time to fit residues: 1.5180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 0.0980 chunk 29 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 3114 Z= 0.155 Angle : 0.545 9.826 4194 Z= 0.291 Chirality : 0.051 0.131 546 Planarity : 0.002 0.012 522 Dihedral : 4.345 16.714 444 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer Outliers : 6.41 % 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: -2.88 (0.38), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.29), residues: 426 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 76 time to evaluate : 0.347 Fit side-chains outliers start: 20 outliers final: 13 residues processed: 81 average time/residue: 0.9553 time to fit residues: 79.8123 Evaluate side-chains 85 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.320 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 3 residues processed: 10 average time/residue: 0.1980 time to fit residues: 2.6147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 0.0020 chunk 40 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.023 3114 Z= 0.270 Angle : 0.636 9.050 4194 Z= 0.350 Chirality : 0.053 0.142 546 Planarity : 0.002 0.013 522 Dihedral : 4.734 19.507 444 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer Outliers : 7.69 % 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: -3.00 (0.37), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.28), residues: 426 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 77 time to evaluate : 0.329 Fit side-chains outliers start: 24 outliers final: 19 residues processed: 82 average time/residue: 1.0328 time to fit residues: 87.1824 Evaluate side-chains 93 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 74 time to evaluate : 0.343 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 5 residues processed: 14 average time/residue: 0.0556 time to fit residues: 1.5541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 22 optimal weight: 0.3980 chunk 16 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN B 65 ASN E 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 3114 Z= 0.208 Angle : 0.584 8.833 4194 Z= 0.322 Chirality : 0.052 0.143 546 Planarity : 0.002 0.011 522 Dihedral : 4.511 15.196 444 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer Outliers : 5.45 % 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: -2.87 (0.37), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.28), residues: 426 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 76 time to evaluate : 0.361 Fit side-chains outliers start: 17 outliers final: 12 residues processed: 81 average time/residue: 1.0545 time to fit residues: 87.9240 Evaluate side-chains 86 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.340 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 3 residues processed: 9 average time/residue: 0.0613 time to fit residues: 1.2125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0060 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN E 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 3114 Z= 0.254 Angle : 0.660 10.847 4194 Z= 0.358 Chirality : 0.053 0.142 546 Planarity : 0.002 0.013 522 Dihedral : 4.749 20.103 444 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer Outliers : 5.77 % 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: -2.92 (0.37), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.28), residues: 426 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 0.343 Fit side-chains outliers start: 18 outliers final: 14 residues processed: 79 average time/residue: 1.0887 time to fit residues: 88.3712 Evaluate side-chains 87 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.342 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 4 residues processed: 10 average time/residue: 0.0563 time to fit residues: 1.2329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.2980 chunk 26 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.018 3114 Z= 0.197 Angle : 0.612 10.824 4194 Z= 0.329 Chirality : 0.052 0.149 546 Planarity : 0.002 0.010 522 Dihedral : 4.573 16.616 444 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer Outliers : 2.24 % 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: -2.81 (0.37), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.29), residues: 426 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.364 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 77 average time/residue: 1.0555 time to fit residues: 83.7418 Evaluate side-chains 79 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.342 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.1136 time to fit residues: 0.8714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 0.4980 chunk 41 optimal weight: 9.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.190913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.146693 restraints weight = 2989.257| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.28 r_work: 0.3887 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.025 3114 Z= 0.335 Angle : 0.704 10.552 4194 Z= 0.391 Chirality : 0.054 0.149 546 Planarity : 0.002 0.016 522 Dihedral : 4.925 19.325 444 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer Outliers : 4.81 % 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: -2.99 (0.37), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.28), residues: 426 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1943.55 seconds wall clock time: 34 minutes 51.89 seconds (2091.89 seconds total)