Starting phenix.real_space_refine on Fri Dec 8 20:31:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsk_0499/12_2023/6nsk_0499_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsk_0499/12_2023/6nsk_0499.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsk_0499/12_2023/6nsk_0499_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsk_0499/12_2023/6nsk_0499_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsk_0499/12_2023/6nsk_0499_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsk_0499/12_2023/6nsk_0499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsk_0499/12_2023/6nsk_0499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsk_0499/12_2023/6nsk_0499_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsk_0499/12_2023/6nsk_0499_updated.pdb" } resolution = 2.7 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= 0.002 sd= 0.017 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 30 5.16 5 C 6234 2.51 5 N 1332 2.21 5 O 1494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9096 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1449 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "B" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1449 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "C" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1449 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "D" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1449 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "E" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1449 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "F" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1449 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'XP4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'XP4:plan-2': 1, 'XP4:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'XP4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'XP4:plan-2': 1, 'XP4:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 107 Unusual residues: {'XP4': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'XP4:plan-2': 1, 'XP4:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'XP4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'XP4:plan-2': 1, 'XP4:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'XP4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'XP4:plan-2': 1, 'XP4:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 107 Unusual residues: {'XP4': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'XP4:plan-2': 1, 'XP4:plan-1': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 5.15, per 1000 atoms: 0.57 Number of scatterers: 9096 At special positions: 0 Unit cell: (101.65, 97.37, 62.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 6 15.00 O 1494 8.00 N 1332 7.00 C 6234 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: 3.66 Conformation dependent library (CDL) restraints added in 1.9 seconds 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2004 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 0 sheets defined 72.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 2 through 22 removed outlier: 3.947A pdb=" N LEU A 7 " --> pdb=" O GLY A 3 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR A 8 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 21 " --> pdb=" O GLY A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 53 removed outlier: 3.732A pdb=" N VAL A 47 " --> pdb=" O CYS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 79 No H-bonds generated for 'chain 'A' and resid 76 through 79' Processing helix chain 'A' and resid 82 through 97 Processing helix chain 'A' and resid 102 through 123 Proline residue: A 117 - end of helix removed outlier: 3.665A pdb=" N ILE A 120 " --> pdb=" O VAL A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 160 Processing helix chain 'A' and resid 169 through 190 removed outlier: 4.614A pdb=" N ILE A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Proline residue: A 185 - end of helix Processing helix chain 'B' and resid 2 through 22 removed outlier: 3.904A pdb=" N LEU B 7 " --> pdb=" O GLY B 3 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 53 removed outlier: 4.339A pdb=" N VAL B 47 " --> pdb=" O CYS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 97 removed outlier: 3.983A pdb=" N LEU B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N PHE B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 123 Proline residue: B 117 - end of helix removed outlier: 3.577A pdb=" N ILE B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 160 Processing helix chain 'B' and resid 169 through 188 removed outlier: 4.669A pdb=" N ILE B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Proline residue: B 185 - end of helix Processing helix chain 'C' and resid 2 through 21 removed outlier: 3.876A pdb=" N LEU C 7 " --> pdb=" O GLY C 3 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR C 8 " --> pdb=" O LEU C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 53 removed outlier: 3.675A pdb=" N VAL C 47 " --> pdb=" O CYS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 97 removed outlier: 3.938A pdb=" N LEU C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N PHE C 84 " --> pdb=" O THR C 80 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY C 85 " --> pdb=" O GLY C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 123 Proline residue: C 117 - end of helix removed outlier: 3.644A pdb=" N ILE C 120 " --> pdb=" O VAL C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 160 Processing helix chain 'C' and resid 169 through 190 removed outlier: 4.659A pdb=" N ILE C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Proline residue: C 185 - end of helix Processing helix chain 'D' and resid 2 through 22 removed outlier: 3.947A pdb=" N LEU D 7 " --> pdb=" O GLY D 3 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR D 8 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 21 " --> pdb=" O GLY D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 53 removed outlier: 3.745A pdb=" N VAL D 47 " --> pdb=" O CYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 79 No H-bonds generated for 'chain 'D' and resid 76 through 79' Processing helix chain 'D' and resid 82 through 97 Processing helix chain 'D' and resid 102 through 123 Proline residue: D 117 - end of helix removed outlier: 3.665A pdb=" N ILE D 120 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 160 Processing helix chain 'D' and resid 169 through 190 removed outlier: 4.613A pdb=" N ILE D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) Proline residue: D 185 - end of helix Processing helix chain 'E' and resid 2 through 22 removed outlier: 3.904A pdb=" N LEU E 7 " --> pdb=" O GLY E 3 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR E 8 " --> pdb=" O LEU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 53 removed outlier: 4.339A pdb=" N VAL E 47 " --> pdb=" O CYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 97 removed outlier: 3.983A pdb=" N LEU E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N PHE E 84 " --> pdb=" O THR E 80 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY E 85 " --> pdb=" O GLY E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 123 Proline residue: E 117 - end of helix removed outlier: 3.577A pdb=" N ILE E 120 " --> pdb=" O VAL E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 160 Processing helix chain 'E' and resid 169 through 188 removed outlier: 4.669A pdb=" N ILE E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) Proline residue: E 185 - end of helix Processing helix chain 'F' and resid 2 through 21 removed outlier: 3.875A pdb=" N LEU F 7 " --> pdb=" O GLY F 3 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR F 8 " --> pdb=" O LEU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 53 removed outlier: 3.676A pdb=" N VAL F 47 " --> pdb=" O CYS F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 97 removed outlier: 3.938A pdb=" N LEU F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N PHE F 84 " --> pdb=" O THR F 80 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY F 85 " --> pdb=" O GLY F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 123 Proline residue: F 117 - end of helix removed outlier: 3.644A pdb=" N ILE F 120 " --> pdb=" O VAL F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 160 Processing helix chain 'F' and resid 169 through 190 removed outlier: 4.659A pdb=" N ILE F 184 " --> pdb=" O LEU F 180 " (cutoff:3.500A) Proline residue: F 185 - end of helix 562 hydrogen bonds defined for protein. 1686 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: 2.47 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1266 1.31 - 1.43: 2876 1.43 - 1.56: 5200 1.56 - 1.68: 6 1.68 - 1.81: 48 Bond restraints: 9396 Sorted by residual: bond pdb=" N TRP D 183 " pdb=" CA TRP D 183 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.20e-02 6.94e+03 7.72e+00 bond pdb=" N TRP A 183 " pdb=" CA TRP A 183 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.20e-02 6.94e+03 7.72e+00 bond pdb=" N TRP C 183 " pdb=" CA TRP C 183 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.23e-02 6.61e+03 7.36e+00 bond pdb=" N TRP F 183 " pdb=" CA TRP F 183 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.23e-02 6.61e+03 7.36e+00 bond pdb=" N TRP B 183 " pdb=" CA TRP B 183 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.23e-02 6.61e+03 7.13e+00 ... (remaining 9391 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.78: 328 106.78 - 113.72: 5407 113.72 - 120.66: 4052 120.66 - 127.60: 2805 127.60 - 134.54: 212 Bond angle restraints: 12804 Sorted by residual: angle pdb=" C PHE C 169 " pdb=" N THR C 170 " pdb=" CA THR C 170 " ideal model delta sigma weight residual 120.09 125.21 -5.12 1.25e+00 6.40e-01 1.67e+01 angle pdb=" C PHE F 169 " pdb=" N THR F 170 " pdb=" CA THR F 170 " ideal model delta sigma weight residual 120.09 125.21 -5.12 1.25e+00 6.40e-01 1.67e+01 angle pdb=" C THR D 181 " pdb=" N ALA D 182 " pdb=" CA ALA D 182 " ideal model delta sigma weight residual 122.15 112.59 9.56 2.83e+00 1.25e-01 1.14e+01 angle pdb=" C THR A 181 " pdb=" N ALA A 182 " pdb=" CA ALA A 182 " ideal model delta sigma weight residual 122.15 112.59 9.56 2.83e+00 1.25e-01 1.14e+01 angle pdb=" CA TYR F 90 " pdb=" CB TYR F 90 " pdb=" CG TYR F 90 " ideal model delta sigma weight residual 113.90 119.82 -5.92 1.80e+00 3.09e-01 1.08e+01 ... (remaining 12799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.94: 4421 11.94 - 23.88: 459 23.88 - 35.82: 166 35.82 - 47.76: 67 47.76 - 59.70: 77 Dihedral angle restraints: 5190 sinusoidal: 2058 harmonic: 3132 Sorted by residual: dihedral pdb=" CA LEU F 128 " pdb=" C LEU F 128 " pdb=" N ASP F 129 " pdb=" CA ASP F 129 " ideal model delta harmonic sigma weight residual -180.00 -156.63 -23.37 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA LEU C 128 " pdb=" C LEU C 128 " pdb=" N ASP C 129 " pdb=" CA ASP C 129 " ideal model delta harmonic sigma weight residual -180.00 -156.70 -23.30 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA LEU D 128 " pdb=" C LEU D 128 " pdb=" N ASP D 129 " pdb=" CA ASP D 129 " ideal model delta harmonic sigma weight residual 180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 5187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 604 0.034 - 0.068: 460 0.068 - 0.102: 241 0.102 - 0.136: 94 0.136 - 0.169: 41 Chirality restraints: 1440 Sorted by residual: chirality pdb=" CA TRP F 183 " pdb=" N TRP F 183 " pdb=" C TRP F 183 " pdb=" CB TRP F 183 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA ARG A 102 " pdb=" N ARG A 102 " pdb=" C ARG A 102 " pdb=" CB ARG A 102 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.04e-01 chirality pdb=" CA ARG D 102 " pdb=" N ARG D 102 " pdb=" C ARG D 102 " pdb=" CB ARG D 102 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.04e-01 ... (remaining 1437 not shown) Planarity restraints: 1470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 90 " 0.037 2.00e-02 2.50e+03 3.05e-02 1.86e+01 pdb=" CG TYR D 90 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR D 90 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR D 90 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR D 90 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR D 90 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR D 90 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR D 90 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 90 " 0.037 2.00e-02 2.50e+03 3.05e-02 1.86e+01 pdb=" CG TYR A 90 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR A 90 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 90 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 90 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 90 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 90 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 90 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 90 " 0.037 2.00e-02 2.50e+03 3.01e-02 1.82e+01 pdb=" CG TYR E 90 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR E 90 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR E 90 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR E 90 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR E 90 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR E 90 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 90 " 0.005 2.00e-02 2.50e+03 ... (remaining 1467 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1074 2.75 - 3.29: 8453 3.29 - 3.83: 14923 3.83 - 4.36: 18182 4.36 - 4.90: 32205 Nonbonded interactions: 74837 Sorted by model distance: nonbonded pdb=" O GLU B 177 " pdb=" OG1 THR B 181 " model vdw 2.213 2.440 nonbonded pdb=" O GLU E 177 " pdb=" OG1 THR E 181 " model vdw 2.213 2.440 nonbonded pdb=" O GLU F 177 " pdb=" OG1 THR F 181 " model vdw 2.219 2.440 nonbonded pdb=" O GLU C 177 " pdb=" OG1 THR C 181 " model vdw 2.219 2.440 nonbonded pdb=" O GLU D 177 " pdb=" OG1 THR D 181 " model vdw 2.230 2.440 ... (remaining 74832 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' and (resid 1 through 195 or resid 201)) selection = (chain 'B' and (resid 1 through 195 or (resid 201 and (name C18 or name C19 or n \ ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29 or name C30 or name C31 or name O \ 7 or name O8 )))) selection = (chain 'C' and (resid 1 through 195 or (resid 201 and (name C18 or name C19 or n \ ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29 or name C30 or name C31 or name O \ 7 or name O8 )))) selection = (chain 'D' and (resid 1 through 195 or resid 201)) selection = (chain 'E' and (resid 1 through 195 or (resid 201 and (name C18 or name C19 or n \ ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29 or name C30 or name C31 or name O \ 7 or name O8 )))) selection = (chain 'F' and (resid 1 through 195 or (resid 201 and (name C18 or name C19 or n \ ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29 or name C30 or name C31 or name O \ 7 or name O8 )))) } 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: 0.260 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: 0.010 Extract box with map and model: 1.490 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 27.890 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.050 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:20.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 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 : 0.009 0.069 9396 Z= 0.590 Angle : 1.113 9.557 12804 Z= 0.577 Chirality : 0.060 0.169 1440 Planarity : 0.008 0.045 1470 Dihedral : 14.604 59.699 3186 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % 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: -3.23 (0.20), residues: 1068 helix: -1.94 (0.14), residues: 810 sheet: None (None), residues: 0 loop : -2.09 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP C 153 HIS 0.013 0.003 HIS D 95 PHE 0.031 0.003 PHE B 34 TYR 0.073 0.005 TYR D 90 ARG 0.001 0.000 ARG D 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.062 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.9330 time to fit residues: 154.2489 Evaluate side-chains 106 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.990 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS A 114 ASN B 114 ASN C 95 HIS D 95 HIS D 114 ASN E 114 ASN F 95 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9396 Z= 0.166 Angle : 0.556 6.894 12804 Z= 0.289 Chirality : 0.042 0.172 1440 Planarity : 0.005 0.033 1470 Dihedral : 15.417 59.439 1422 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.53 % Allowed : 9.69 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.25), residues: 1068 helix: 0.37 (0.17), residues: 834 sheet: None (None), residues: 0 loop : -1.72 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 153 HIS 0.002 0.001 HIS D 95 PHE 0.013 0.001 PHE D 34 TYR 0.024 0.002 TYR C 90 ARG 0.002 0.001 ARG D 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 1.051 Fit side-chains outliers start: 14 outliers final: 2 residues processed: 134 average time/residue: 0.8118 time to fit residues: 120.6104 Evaluate side-chains 111 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 0.875 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.1803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 87 optimal weight: 0.0000 chunk 97 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS F 44 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9396 Z= 0.241 Angle : 0.581 7.287 12804 Z= 0.298 Chirality : 0.043 0.165 1440 Planarity : 0.005 0.037 1470 Dihedral : 14.682 59.577 1422 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.61 % Allowed : 12.85 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1068 helix: 1.01 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -1.48 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 142 HIS 0.004 0.001 HIS F 54 PHE 0.013 0.002 PHE A 110 TYR 0.032 0.002 TYR C 90 ARG 0.001 0.000 ARG F 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 107 time to evaluate : 0.908 Fit side-chains outliers start: 24 outliers final: 14 residues processed: 119 average time/residue: 0.8020 time to fit residues: 105.3460 Evaluate side-chains 113 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.876 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.1228 time to fit residues: 1.5516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN D 160 ASN E 95 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9396 Z= 0.232 Angle : 0.561 7.203 12804 Z= 0.288 Chirality : 0.042 0.133 1440 Planarity : 0.005 0.038 1470 Dihedral : 14.080 59.854 1422 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.81 % Allowed : 13.40 % Favored : 82.79 % 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: 1.17 (0.26), residues: 1068 helix: 1.34 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -1.25 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 187 HIS 0.004 0.001 HIS F 54 PHE 0.014 0.001 PHE A 110 TYR 0.025 0.002 TYR C 90 ARG 0.001 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 112 time to evaluate : 0.978 Fit side-chains outliers start: 35 outliers final: 18 residues processed: 130 average time/residue: 0.8121 time to fit residues: 116.8180 Evaluate side-chains 123 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 0.910 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.0815 time to fit residues: 1.8218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 0 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN D 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9396 Z= 0.328 Angle : 0.624 7.648 12804 Z= 0.321 Chirality : 0.045 0.135 1440 Planarity : 0.005 0.040 1470 Dihedral : 13.827 59.377 1422 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.68 % Allowed : 12.31 % Favored : 83.01 % 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: 1.14 (0.26), residues: 1068 helix: 1.34 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -1.29 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 194 HIS 0.005 0.001 HIS C 70 PHE 0.014 0.002 PHE A 110 TYR 0.026 0.002 TYR F 90 ARG 0.001 0.000 ARG D 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 104 time to evaluate : 0.851 Fit side-chains outliers start: 43 outliers final: 17 residues processed: 130 average time/residue: 0.8329 time to fit residues: 120.1373 Evaluate side-chains 122 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 1.008 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.1200 time to fit residues: 1.9513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 20 optimal weight: 0.0970 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 54 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 160 ASN B 44 ASN D 160 ASN E 44 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9396 Z= 0.147 Angle : 0.507 6.875 12804 Z= 0.258 Chirality : 0.040 0.129 1440 Planarity : 0.004 0.037 1470 Dihedral : 12.722 59.998 1422 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.94 % Allowed : 13.73 % Favored : 83.33 % 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: 2.05 (0.27), residues: 1068 helix: 1.89 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.61 (0.46), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 153 HIS 0.003 0.001 HIS F 54 PHE 0.014 0.001 PHE A 110 TYR 0.012 0.001 TYR F 8 ARG 0.000 0.000 ARG F 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 117 time to evaluate : 0.987 Fit side-chains outliers start: 27 outliers final: 15 residues processed: 131 average time/residue: 0.8174 time to fit residues: 118.0987 Evaluate side-chains 123 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 0.966 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 0.0851 time to fit residues: 1.7330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 44 ASN D 160 ASN E 44 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9396 Z= 0.153 Angle : 0.500 6.719 12804 Z= 0.253 Chirality : 0.040 0.173 1440 Planarity : 0.004 0.038 1470 Dihedral : 12.002 57.053 1422 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.51 % Allowed : 14.38 % Favored : 83.12 % 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: 2.38 (0.27), residues: 1068 helix: 2.11 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.41 (0.46), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 153 HIS 0.003 0.001 HIS C 54 PHE 0.013 0.001 PHE B 110 TYR 0.017 0.001 TYR D 88 ARG 0.000 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 1.003 Fit side-chains outliers start: 23 outliers final: 14 residues processed: 123 average time/residue: 0.8479 time to fit residues: 115.0385 Evaluate side-chains 125 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 0.963 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.1327 time to fit residues: 1.6874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.0870 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN D 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9396 Z= 0.129 Angle : 0.478 6.514 12804 Z= 0.241 Chirality : 0.040 0.154 1440 Planarity : 0.004 0.038 1470 Dihedral : 11.036 59.144 1422 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.18 % Allowed : 14.92 % Favored : 82.90 % 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: 2.70 (0.27), residues: 1068 helix: 2.32 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.26 (0.47), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 153 HIS 0.003 0.000 HIS F 54 PHE 0.013 0.001 PHE D 110 TYR 0.012 0.001 TYR B 88 ARG 0.001 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 1.007 Fit side-chains outliers start: 20 outliers final: 12 residues processed: 139 average time/residue: 0.7382 time to fit residues: 114.2417 Evaluate side-chains 136 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 1.3067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN D 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9396 Z= 0.226 Angle : 0.549 7.077 12804 Z= 0.281 Chirality : 0.045 0.220 1440 Planarity : 0.004 0.041 1470 Dihedral : 11.457 58.815 1422 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.61 % Allowed : 15.03 % Favored : 82.35 % 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: 2.41 (0.27), residues: 1068 helix: 2.11 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.32 (0.46), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 153 HIS 0.004 0.001 HIS F 54 PHE 0.011 0.001 PHE E 110 TYR 0.014 0.002 TYR A 88 ARG 0.000 0.000 ARG D 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 0.996 Fit side-chains outliers start: 24 outliers final: 14 residues processed: 130 average time/residue: 0.7698 time to fit residues: 111.0670 Evaluate side-chains 122 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 0.894 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 1.0449 time to fit residues: 3.4190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.6527 > 50: distance: 20 - 42: 16.039 distance: 27 - 50: 10.173 distance: 35 - 58: 29.062 distance: 39 - 42: 15.742 distance: 40 - 68: 9.977 distance: 42 - 43: 31.195 distance: 43 - 44: 30.727 distance: 43 - 46: 27.040 distance: 44 - 45: 23.166 distance: 44 - 50: 18.182 distance: 45 - 75: 6.968 distance: 46 - 47: 9.470 distance: 46 - 48: 4.290 distance: 47 - 49: 20.357 distance: 50 - 51: 20.241 distance: 51 - 52: 23.692 distance: 51 - 54: 19.088 distance: 52 - 53: 28.995 distance: 52 - 58: 32.698 distance: 54 - 55: 11.429 distance: 55 - 56: 21.955 distance: 55 - 57: 23.741 distance: 58 - 59: 12.287 distance: 59 - 60: 12.487 distance: 59 - 62: 9.527 distance: 60 - 61: 12.209 distance: 60 - 68: 15.408 distance: 62 - 63: 4.102 distance: 63 - 64: 14.955 distance: 63 - 65: 29.673 distance: 64 - 66: 17.390 distance: 65 - 67: 11.568 distance: 66 - 67: 25.046 distance: 68 - 69: 10.787 distance: 69 - 70: 5.574 distance: 69 - 72: 11.062 distance: 70 - 71: 4.983 distance: 70 - 75: 12.529 distance: 72 - 73: 3.281 distance: 72 - 74: 9.877 distance: 75 - 76: 17.974 distance: 76 - 77: 39.171 distance: 76 - 79: 15.598 distance: 77 - 78: 39.072 distance: 77 - 86: 52.041 distance: 79 - 80: 20.041 distance: 80 - 81: 15.976 distance: 80 - 82: 17.478 distance: 81 - 83: 11.888 distance: 82 - 84: 14.054 distance: 83 - 85: 22.383 distance: 84 - 85: 13.353 distance: 86 - 87: 38.034 distance: 87 - 88: 28.252 distance: 88 - 89: 5.603 distance: 88 - 90: 16.561 distance: 90 - 91: 28.862 distance: 91 - 92: 17.550 distance: 91 - 94: 11.268 distance: 92 - 93: 7.702 distance: 92 - 98: 12.446 distance: 94 - 95: 20.400 distance: 95 - 96: 5.358 distance: 95 - 97: 16.667 distance: 98 - 99: 17.441 distance: 99 - 100: 9.767 distance: 99 - 102: 11.216 distance: 100 - 101: 16.609 distance: 100 - 106: 15.929 distance: 102 - 103: 12.508 distance: 103 - 104: 11.614 distance: 103 - 105: 10.002 distance: 106 - 107: 27.285 distance: 107 - 108: 18.546 distance: 107 - 110: 19.181 distance: 108 - 109: 18.004 distance: 108 - 120: 36.912 distance: 110 - 111: 20.975 distance: 111 - 112: 13.770 distance: 111 - 113: 5.962 distance: 112 - 114: 8.562 distance: 113 - 115: 12.640 distance: 113 - 116: 16.058 distance: 114 - 115: 11.272 distance: 115 - 117: 6.643 distance: 116 - 118: 9.599 distance: 117 - 119: 17.379 distance: 118 - 119: 7.857 distance: 120 - 121: 46.091 distance: 121 - 122: 51.300 distance: 121 - 124: 47.950 distance: 122 - 123: 20.133 distance: 122 - 131: 28.473 distance: 123 - 156: 18.086 distance: 124 - 125: 38.345 distance: 125 - 126: 13.381 distance: 126 - 127: 22.748 distance: 127 - 128: 10.990 distance: 128 - 129: 4.923 distance: 128 - 130: 11.635