Starting phenix.real_space_refine on Thu Mar 14 14:45:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsk_0499/03_2024/6nsk_0499_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsk_0499/03_2024/6nsk_0499.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsk_0499/03_2024/6nsk_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_0499/03_2024/6nsk_0499_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsk_0499/03_2024/6nsk_0499_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsk_0499/03_2024/6nsk_0499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsk_0499/03_2024/6nsk_0499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsk_0499/03_2024/6nsk_0499_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsk_0499/03_2024/6nsk_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-dev-5265/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: 5.26, per 1000 atoms: 0.58 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: 3.71 Conformation dependent library (CDL) restraints added in 1.8 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: 1.33 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: 2.10 Time building geometry restraints manager: 4.02 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: 0.190 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: 1.460 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.160 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 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:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.760 ------------------------------------------------------------------------------- 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 : 0.883 Fit side-chains REVERT: A 15 SER cc_start: 0.8629 (t) cc_final: 0.8293 (m) REVERT: A 88 TYR cc_start: 0.8657 (m-80) cc_final: 0.8377 (m-80) REVERT: D 15 SER cc_start: 0.8645 (t) cc_final: 0.8321 (m) REVERT: D 88 TYR cc_start: 0.8677 (m-80) cc_final: 0.8399 (m-80) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.9110 time to fit residues: 150.4872 Evaluate side-chains 108 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.0970 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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: 0.7315 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9396 Z= 0.169 Angle : 0.548 6.363 12804 Z= 0.284 Chirality : 0.042 0.173 1440 Planarity : 0.005 0.033 1470 Dihedral : 15.166 59.321 1422 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.87 % Allowed : 10.68 % Favored : 88.45 % 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: 0.04 (0.25), residues: 1068 helix: 0.55 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -1.64 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 153 HIS 0.003 0.001 HIS D 95 PHE 0.013 0.001 PHE D 34 TYR 0.023 0.002 TYR E 90 ARG 0.002 0.001 ARG B 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 142 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 134 time to evaluate : 0.900 Fit side-chains REVERT: A 40 SER cc_start: 0.7775 (t) cc_final: 0.7468 (m) REVERT: A 88 TYR cc_start: 0.8640 (m-80) cc_final: 0.8326 (m-80) REVERT: B 32 MET cc_start: 0.8316 (tpt) cc_final: 0.7868 (tpt) REVERT: B 40 SER cc_start: 0.8074 (t) cc_final: 0.7611 (m) REVERT: D 40 SER cc_start: 0.7828 (t) cc_final: 0.7527 (m) REVERT: D 88 TYR cc_start: 0.8663 (m-80) cc_final: 0.8351 (m-80) REVERT: E 32 MET cc_start: 0.8314 (tpt) cc_final: 0.7865 (tpt) REVERT: E 40 SER cc_start: 0.8089 (t) cc_final: 0.7625 (m) outliers start: 8 outliers final: 0 residues processed: 134 average time/residue: 0.7196 time to fit residues: 107.3191 Evaluate side-chains 110 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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: 4.9990 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: 1.9990 chunk 87 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.7447 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9396 Z= 0.314 Angle : 0.629 7.613 12804 Z= 0.324 Chirality : 0.045 0.157 1440 Planarity : 0.005 0.036 1470 Dihedral : 14.834 59.853 1422 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.94 % Allowed : 12.64 % Favored : 84.42 % 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: 0.52 (0.26), residues: 1068 helix: 0.85 (0.18), residues: 846 sheet: None (None), residues: 0 loop : -1.40 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 153 HIS 0.005 0.001 HIS C 70 PHE 0.014 0.002 PHE F 84 TYR 0.039 0.003 TYR C 90 ARG 0.001 0.000 ARG A 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 125 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 0.997 Fit side-chains REVERT: A 88 TYR cc_start: 0.8679 (m-80) cc_final: 0.8348 (m-80) REVERT: D 88 TYR cc_start: 0.8701 (m-80) cc_final: 0.8371 (m-80) outliers start: 27 outliers final: 15 residues processed: 109 average time/residue: 0.8412 time to fit residues: 100.9276 Evaluate side-chains 109 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 137 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.0870 chunk 65 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9396 Z= 0.134 Angle : 0.492 6.618 12804 Z= 0.251 Chirality : 0.039 0.127 1440 Planarity : 0.004 0.035 1470 Dihedral : 13.634 59.874 1422 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.63 % Allowed : 14.92 % Favored : 83.44 % 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: 1.65 (0.27), residues: 1068 helix: 1.66 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.97 (0.45), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 187 HIS 0.003 0.001 HIS A 123 PHE 0.014 0.001 PHE D 110 TYR 0.012 0.001 TYR B 88 ARG 0.001 0.000 ARG F 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 143 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 1.001 Fit side-chains REVERT: A 88 TYR cc_start: 0.8590 (m-80) cc_final: 0.8366 (m-80) REVERT: D 88 TYR cc_start: 0.8611 (m-80) cc_final: 0.8391 (m-80) outliers start: 15 outliers final: 6 residues processed: 134 average time/residue: 0.7849 time to fit residues: 116.4549 Evaluate side-chains 126 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain F residue 12 VAL 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: 0.9980 chunk 1 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 0 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9396 Z= 0.162 Angle : 0.509 6.736 12804 Z= 0.257 Chirality : 0.041 0.165 1440 Planarity : 0.004 0.037 1470 Dihedral : 13.087 59.686 1422 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.72 % Allowed : 14.49 % 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: 2.03 (0.27), residues: 1068 helix: 1.91 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.78 (0.45), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 153 HIS 0.003 0.001 HIS F 54 PHE 0.012 0.001 PHE B 110 TYR 0.013 0.001 TYR E 90 ARG 0.000 0.000 ARG C 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 140 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 115 time to evaluate : 1.023 Fit side-chains REVERT: A 88 TYR cc_start: 0.8627 (m-80) cc_final: 0.8332 (m-80) REVERT: B 32 MET cc_start: 0.8338 (tpt) cc_final: 0.7953 (tpt) REVERT: D 88 TYR cc_start: 0.8648 (m-80) cc_final: 0.8359 (m-80) REVERT: E 32 MET cc_start: 0.8330 (tpt) cc_final: 0.7939 (tpt) REVERT: E 44 ASN cc_start: 0.8489 (m-40) cc_final: 0.8088 (m110) REVERT: F 4 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8671 (tt) outliers start: 25 outliers final: 18 residues processed: 127 average time/residue: 0.7910 time to fit residues: 111.0960 Evaluate side-chains 133 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 137 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 104 optimal weight: 0.0060 chunk 86 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9396 Z= 0.218 Angle : 0.542 7.062 12804 Z= 0.276 Chirality : 0.042 0.151 1440 Planarity : 0.004 0.039 1470 Dihedral : 12.790 59.289 1422 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.38 % Allowed : 13.51 % 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: 2.02 (0.27), residues: 1068 helix: 1.89 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.69 (0.45), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 153 HIS 0.004 0.001 HIS F 54 PHE 0.012 0.001 PHE D 110 TYR 0.017 0.002 TYR B 90 ARG 0.001 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 143 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 112 time to evaluate : 0.924 Fit side-chains REVERT: A 88 TYR cc_start: 0.8676 (m-80) cc_final: 0.8416 (m-80) REVERT: B 44 ASN cc_start: 0.8378 (m-40) cc_final: 0.7975 (m110) REVERT: D 88 TYR cc_start: 0.8696 (m-80) cc_final: 0.8442 (m-80) REVERT: E 44 ASN cc_start: 0.8446 (m-40) cc_final: 0.8028 (m110) outliers start: 31 outliers final: 20 residues processed: 130 average time/residue: 0.7516 time to fit residues: 108.1100 Evaluate side-chains 131 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 137 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.0060 chunk 11 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 0.1980 chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9396 Z= 0.133 Angle : 0.483 6.609 12804 Z= 0.243 Chirality : 0.040 0.148 1440 Planarity : 0.004 0.036 1470 Dihedral : 11.789 59.418 1422 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % 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: 2.53 (0.27), residues: 1068 helix: 2.22 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.36 (0.47), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 153 HIS 0.003 0.001 HIS F 54 PHE 0.014 0.001 PHE A 110 TYR 0.011 0.001 TYR B 88 ARG 0.000 0.000 ARG F 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 147 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 0.920 Fit side-chains REVERT: A 88 TYR cc_start: 0.8658 (m-80) cc_final: 0.8406 (m-80) REVERT: B 44 ASN cc_start: 0.8371 (m-40) cc_final: 0.8090 (m-40) REVERT: C 159 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6572 (mt-10) REVERT: D 88 TYR cc_start: 0.8679 (m-80) cc_final: 0.8437 (m-80) REVERT: E 44 ASN cc_start: 0.8404 (m-40) cc_final: 0.8119 (m-40) REVERT: F 5 VAL cc_start: 0.8258 (t) cc_final: 0.8014 (m) REVERT: F 159 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6617 (mt-10) outliers start: 23 outliers final: 18 residues processed: 136 average time/residue: 0.7378 time to fit residues: 111.3137 Evaluate side-chains 138 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 137 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9396 Z= 0.311 Angle : 0.606 7.680 12804 Z= 0.309 Chirality : 0.045 0.185 1440 Planarity : 0.005 0.041 1470 Dihedral : 12.407 59.590 1422 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.72 % Allowed : 14.71 % Favored : 82.57 % 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: 2.01 (0.27), residues: 1068 helix: 1.80 (0.18), residues: 846 sheet: None (None), residues: 0 loop : -0.39 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 153 HIS 0.005 0.001 HIS F 54 PHE 0.012 0.002 PHE A 84 TYR 0.019 0.002 TYR E 90 ARG 0.001 0.000 ARG A 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 130 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 0.916 Fit side-chains REVERT: A 88 TYR cc_start: 0.8701 (m-80) cc_final: 0.8370 (m-80) REVERT: B 44 ASN cc_start: 0.8439 (m-40) cc_final: 0.8134 (m-40) REVERT: C 4 LEU cc_start: 0.8995 (tm) cc_final: 0.8786 (tt) REVERT: D 88 TYR cc_start: 0.8721 (m-80) cc_final: 0.8394 (m-80) REVERT: E 44 ASN cc_start: 0.8483 (m-40) cc_final: 0.8190 (m-40) outliers start: 25 outliers final: 21 residues processed: 121 average time/residue: 0.7918 time to fit residues: 105.8091 Evaluate side-chains 118 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 97 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 137 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9396 Z= 0.165 Angle : 0.516 6.926 12804 Z= 0.261 Chirality : 0.041 0.165 1440 Planarity : 0.004 0.041 1470 Dihedral : 11.795 59.395 1422 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.29 % Allowed : 15.25 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.27), residues: 1068 helix: 2.09 (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 0.009 0.001 TRP F 153 HIS 0.003 0.001 HIS C 54 PHE 0.012 0.001 PHE A 110 TYR 0.010 0.001 TYR E 88 ARG 0.001 0.000 ARG F 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 131 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 0.917 Fit side-chains REVERT: A 88 TYR cc_start: 0.8707 (m-80) cc_final: 0.8366 (m-80) REVERT: B 44 ASN cc_start: 0.8373 (m-40) cc_final: 0.8099 (m-40) REVERT: C 4 LEU cc_start: 0.8904 (tm) cc_final: 0.8698 (tt) REVERT: C 5 VAL cc_start: 0.8165 (t) cc_final: 0.7928 (m) REVERT: C 159 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6718 (mt-10) REVERT: D 88 TYR cc_start: 0.8727 (m-80) cc_final: 0.8392 (m-80) REVERT: E 44 ASN cc_start: 0.8404 (m-40) cc_final: 0.8142 (m-40) REVERT: F 159 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6669 (mt-10) outliers start: 21 outliers final: 21 residues processed: 126 average time/residue: 0.8161 time to fit residues: 113.4617 Evaluate side-chains 130 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9396 Z= 0.221 Angle : 0.548 7.207 12804 Z= 0.278 Chirality : 0.043 0.165 1440 Planarity : 0.004 0.040 1470 Dihedral : 11.766 59.704 1422 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.72 % Allowed : 14.81 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.27), residues: 1068 helix: 2.04 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.36 (0.45), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 153 HIS 0.004 0.001 HIS F 54 PHE 0.013 0.001 PHE A 110 TYR 0.013 0.002 TYR E 90 ARG 0.000 0.000 ARG A 102 ********************** REFINEMENT MACRO_CYCLE 10 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 132 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 0.968 Fit side-chains REVERT: A 88 TYR cc_start: 0.8727 (m-80) cc_final: 0.8433 (m-80) REVERT: B 44 ASN cc_start: 0.8375 (m-40) cc_final: 0.8125 (m-40) REVERT: C 4 LEU cc_start: 0.8973 (tm) cc_final: 0.8768 (tt) REVERT: C 5 VAL cc_start: 0.8211 (t) cc_final: 0.7969 (m) REVERT: C 159 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6812 (mt-10) REVERT: D 88 TYR cc_start: 0.8745 (m-80) cc_final: 0.8453 (m-80) REVERT: E 44 ASN cc_start: 0.8426 (m-40) cc_final: 0.8186 (m-40) REVERT: F 159 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6825 (mt-10) outliers start: 25 outliers final: 21 residues processed: 123 average time/residue: 0.8525 time to fit residues: 115.4521 Evaluate side-chains 127 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 12 optimal weight: 0.0050 chunk 23 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.148449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.118538 restraints weight = 10269.838| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.64 r_work: 0.3321 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9396 Z= 0.139 Angle : 0.494 6.684 12804 Z= 0.248 Chirality : 0.041 0.157 1440 Planarity : 0.004 0.041 1470 Dihedral : 10.899 59.747 1422 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.29 % Allowed : 15.03 % Favored : 82.68 % 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: 2.74 (0.27), residues: 1068 helix: 2.32 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.11 (0.47), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 153 HIS 0.003 0.001 HIS C 54 PHE 0.014 0.001 PHE A 110 TYR 0.012 0.001 TYR E 88 ARG 0.001 0.000 ARG C 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2637.74 seconds wall clock time: 47 minutes 36.67 seconds (2856.67 seconds total)