Starting phenix.real_space_refine on Wed Sep 25 14:49:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpg_29363/09_2024/8fpg_29363.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpg_29363/09_2024/8fpg_29363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpg_29363/09_2024/8fpg_29363.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpg_29363/09_2024/8fpg_29363.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpg_29363/09_2024/8fpg_29363.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpg_29363/09_2024/8fpg_29363.cif" } resolution = 2.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 S 72 5.16 5 Cl 4 4.86 5 C 6927 2.51 5 N 1657 2.21 5 O 2014 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10674 Number of models: 1 Model: "" Number of chains: 20 Chain: "H" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1157 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 148, 1146 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 148, 1146 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1164 Chain: "B" Number of atoms: 1165 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1154 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 149, 1154 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 1172 Chain: "A" Number of atoms: 1152 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 148, 1141 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 148, 1141 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1159 Chain: "D" Number of atoms: 1161 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1150 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 149, 1150 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 1168 Chain: "E" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "F" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "G" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N APHE C 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 623 " occ=0.50 residue: pdb=" N APHE B 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 623 " occ=0.50 residue: pdb=" N APHE A 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 623 " occ=0.50 residue: pdb=" N APHE D 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.50 Time building chain proxies: 9.21, per 1000 atoms: 0.86 Number of scatterers: 10674 At special positions: 0 Unit cell: (108.994, 105.716, 92.6035, 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) Cl 4 17.00 S 72 16.00 O 2014 8.00 N 1657 7.00 C 6927 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.42 Conformation dependent library (CDL) restraints added in 2.0 seconds 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2480 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 74.5% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'H' and resid 5 through 30 Processing helix chain 'H' and resid 92 through 105 removed outlier: 3.989A pdb=" N TYR H 96 " --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 128 removed outlier: 4.146A pdb=" N GLU H 126 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR H 128 " --> pdb=" O ALA H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 162 removed outlier: 3.737A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 214 Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 92 through 105 removed outlier: 3.925A pdb=" N TYR F 96 " --> pdb=" O ASP F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 128 removed outlier: 4.019A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR F 128 " --> pdb=" O ALA F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 162 removed outlier: 3.769A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 214 Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.709A pdb=" N LEU C 518 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 551 Processing helix chain 'C' and resid 572 through 586 Processing helix chain 'C' and resid 595 through 629 Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 825 removed outlier: 3.619A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.572A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 547 through 551 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 825 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.711A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 629 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 825 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.574A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 825 removed outlier: 3.660A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 105 through 125 Processing helix chain 'E' and resid 132 through 161 removed outlier: 3.596A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 214 Processing helix chain 'G' and resid 6 through 30 Processing helix chain 'G' and resid 92 through 105 Processing helix chain 'G' and resid 105 through 125 Processing helix chain 'G' and resid 132 through 161 removed outlier: 3.587A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 214 Processing sheet with id=AA1, first strand: chain 'H' and resid 77 through 79 removed outlier: 3.895A pdb=" N VAL H 57 " --> pdb=" O GLY H 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 77 through 79 removed outlier: 3.947A pdb=" N VAL F 57 " --> pdb=" O GLY F 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 34 through 38 Processing sheet with id=AA4, first strand: chain 'G' and resid 34 through 38 854 hydrogen bonds defined for protein. 2494 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: 3.18 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3155 1.34 - 1.46: 2703 1.46 - 1.58: 4779 1.58 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 10749 Sorted by residual: bond pdb=" CB MET E 200 " pdb=" CG MET E 200 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.40e+00 bond pdb=" CB MET G 200 " pdb=" CG MET G 200 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" CB MET H 200 " pdb=" CG MET H 200 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.95e-01 bond pdb=" CB MET F 200 " pdb=" CG MET F 200 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.41e-01 bond pdb=" CG MET G 200 " pdb=" SD MET G 200 " ideal model delta sigma weight residual 1.803 1.781 0.022 2.50e-02 1.60e+03 7.74e-01 ... (remaining 10744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 14387 1.83 - 3.66: 158 3.66 - 5.48: 17 5.48 - 7.31: 0 7.31 - 9.14: 3 Bond angle restraints: 14565 Sorted by residual: angle pdb=" C CYS H 40 " pdb=" N LYS H 41 " pdb=" CA LYS H 41 " ideal model delta sigma weight residual 121.54 126.54 -5.00 1.91e+00 2.74e-01 6.87e+00 angle pdb=" CA LEU A 542 " pdb=" CB LEU A 542 " pdb=" CG LEU A 542 " ideal model delta sigma weight residual 116.30 125.44 -9.14 3.50e+00 8.16e-02 6.82e+00 angle pdb=" CA LEU C 542 " pdb=" CB LEU C 542 " pdb=" CG LEU C 542 " ideal model delta sigma weight residual 116.30 125.36 -9.06 3.50e+00 8.16e-02 6.71e+00 angle pdb=" CA LEU E 98 " pdb=" CB LEU E 98 " pdb=" CG LEU E 98 " ideal model delta sigma weight residual 116.30 124.89 -8.59 3.50e+00 8.16e-02 6.02e+00 angle pdb=" C CYS F 40 " pdb=" N LYS F 41 " pdb=" CA LYS F 41 " ideal model delta sigma weight residual 121.54 125.50 -3.96 1.91e+00 2.74e-01 4.29e+00 ... (remaining 14560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 5329 17.15 - 34.30: 559 34.30 - 51.45: 164 51.45 - 68.59: 39 68.59 - 85.74: 8 Dihedral angle restraints: 6099 sinusoidal: 2227 harmonic: 3872 Sorted by residual: dihedral pdb=" CB CYS G 40 " pdb=" SG CYS G 40 " pdb=" SG CYS G 68 " pdb=" CB CYS G 68 " ideal model delta sinusoidal sigma weight residual 93.00 121.57 -28.57 1 1.00e+01 1.00e-02 1.17e+01 dihedral pdb=" CA ASP A 590 " pdb=" CB ASP A 590 " pdb=" CG ASP A 590 " pdb=" OD1 ASP A 590 " ideal model delta sinusoidal sigma weight residual -30.00 -88.27 58.27 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASP C 590 " pdb=" CB ASP C 590 " pdb=" CG ASP C 590 " pdb=" OD1 ASP C 590 " ideal model delta sinusoidal sigma weight residual -30.00 -87.82 57.82 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 6096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1152 0.035 - 0.071: 393 0.071 - 0.106: 89 0.106 - 0.142: 13 0.142 - 0.177: 1 Chirality restraints: 1648 Sorted by residual: chirality pdb=" CB ILE E 106 " pdb=" CA ILE E 106 " pdb=" CG1 ILE E 106 " pdb=" CG2 ILE E 106 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.84e-01 chirality pdb=" CA PHE H 107 " pdb=" N PHE H 107 " pdb=" C PHE H 107 " pdb=" CB PHE H 107 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA PHE G 107 " pdb=" N PHE G 107 " pdb=" C PHE G 107 " pdb=" CB PHE G 107 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 1645 not shown) Planarity restraints: 1778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E 32 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C TYR E 32 " -0.029 2.00e-02 2.50e+03 pdb=" O TYR E 32 " 0.011 2.00e-02 2.50e+03 pdb=" N TRP E 33 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR G 32 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C TYR G 32 " 0.028 2.00e-02 2.50e+03 pdb=" O TYR G 32 " -0.011 2.00e-02 2.50e+03 pdb=" N TRP G 33 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE E 107 " 0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO E 108 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO E 108 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 108 " 0.018 5.00e-02 4.00e+02 ... (remaining 1775 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 370 2.71 - 3.26: 10886 3.26 - 3.81: 18809 3.81 - 4.35: 22219 4.35 - 4.90: 37551 Nonbonded interactions: 89835 Sorted by model distance: nonbonded pdb=" OD1 ASN G 160 " pdb=" O HOH G 501 " model vdw 2.165 3.040 nonbonded pdb=" OD1 ASN E 160 " pdb=" O HOH E 501 " model vdw 2.167 3.040 nonbonded pdb=" O PHE A 579 " pdb=" O HOH A 901 " model vdw 2.169 3.040 nonbonded pdb=" O HOH D 911 " pdb=" O HOH D 920 " model vdw 2.172 3.040 nonbonded pdb=" O HOH C 923 " pdb=" O HOH B1001 " model vdw 2.174 3.040 ... (remaining 89830 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 511 through 575 or (resid 576 and (name N or name CA or na \ me C or name O or name CB )) or resid 577 through 622 or resid 624 through 626 o \ r (resid 627 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 28 through 629 or resid 784 through 812 or (resid 813 and (name N or name CA or \ name C or name O or name CB )) or resid 814 through 818 or (resid 819 through 82 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 821 through \ 825)) selection = (chain 'B' and ((resid 511 and (name N or name CA or name C or name O or name CB \ )) or resid 512 through 575 or (resid 576 and (name N or name CA or name C or n \ ame O or name CB )) or resid 577 through 593 or (resid 594 and (name N or name C \ A or name C or name O or name CB )) or resid 595 through 622 or resid 624 throug \ h 626 or (resid 627 and (name N or name CA or name C or name O or name CB )) or \ resid 628 through 629 or (resid 784 and (name N or name CA or name C or name O o \ r name CB )) or resid 785 through 825)) selection = (chain 'C' and (resid 511 through 593 or (resid 594 and (name N or name CA or na \ me C or name O or name CB )) or resid 595 through 622 or resid 624 through 626 o \ r (resid 627 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 28 through 629 or resid 784 through 812 or (resid 813 and (name N or name CA or \ name C or name O or name CB )) or resid 814 through 818 or (resid 819 through 82 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 821 through \ 825)) selection = (chain 'D' and ((resid 511 and (name N or name CA or name C or name O or name CB \ )) or resid 512 through 575 or (resid 576 and (name N or name CA or name C or n \ ame O or name CB )) or resid 577 through 593 or (resid 594 and (name N or name C \ A or name C or name O or name CB )) or resid 595 through 622 or resid 624 throug \ h 629 or (resid 784 and (name N or name CA or name C or name O or name CB )) or \ resid 785 through 825)) } ncs_group { reference = (chain 'E' and (resid 5 through 214 or resid 401)) selection = (chain 'F' and (resid 5 through 41 or resid 55 through 214 or resid 401)) selection = (chain 'G' and (resid 5 through 214 or resid 401)) selection = (chain 'H' and (resid 5 through 41 or resid 55 through 214 or resid 401)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 29.300 Find NCS groups from input model: 0.560 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: 0.010 Load rotamer database and sin/cos tables:11.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 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 : 0.003 0.035 10749 Z= 0.200 Angle : 0.490 9.141 14565 Z= 0.263 Chirality : 0.037 0.177 1648 Planarity : 0.003 0.031 1778 Dihedral : 16.030 85.743 3595 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.84 % Allowed : 17.42 % Favored : 80.74 % 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: 3.31 (0.23), residues: 1312 helix: 3.19 (0.16), residues: 948 sheet: 0.46 (0.78), residues: 48 loop : -0.87 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 64 HIS 0.006 0.001 HIS E 132 PHE 0.017 0.002 PHE C 584 TYR 0.015 0.002 TYR C 523 ARG 0.003 0.000 ARG C 545 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 158 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: E 11 LEU cc_start: 0.7721 (tp) cc_final: 0.7037 (tp) outliers start: 20 outliers final: 14 residues processed: 171 average time/residue: 1.0675 time to fit residues: 198.8914 Evaluate side-chains 168 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 154 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 150 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 chunk 61 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS F 199 HIS C 791 ASN E 79 GLN G 9 GLN G 79 GLN G 132 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10749 Z= 0.142 Angle : 0.445 8.302 14565 Z= 0.246 Chirality : 0.035 0.138 1648 Planarity : 0.003 0.034 1778 Dihedral : 4.115 42.513 1462 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.04 % Allowed : 16.50 % Favored : 80.46 % 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: 4.23 (0.23), residues: 1312 helix: 3.93 (0.15), residues: 950 sheet: 1.01 (1.30), residues: 10 loop : -0.61 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 33 HIS 0.003 0.001 HIS E 132 PHE 0.014 0.001 PHE G 107 TYR 0.013 0.001 TYR H 181 ARG 0.002 0.000 ARG G 209 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 153 time to evaluate : 1.115 Fit side-chains REVERT: H 113 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7835 (mt) REVERT: F 113 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7815 (mt) outliers start: 33 outliers final: 6 residues processed: 176 average time/residue: 0.9239 time to fit residues: 178.7304 Evaluate side-chains 156 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 148 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 117 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 116 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 HIS H 199 HIS F 60 HIS F 199 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10749 Z= 0.182 Angle : 0.475 7.063 14565 Z= 0.266 Chirality : 0.037 0.142 1648 Planarity : 0.003 0.035 1778 Dihedral : 3.486 18.769 1444 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.23 % Allowed : 15.58 % Favored : 81.20 % 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: 4.15 (0.23), residues: 1312 helix: 3.85 (0.15), residues: 950 sheet: 1.35 (1.31), residues: 10 loop : -0.59 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 33 HIS 0.004 0.001 HIS E 132 PHE 0.015 0.002 PHE C 584 TYR 0.015 0.001 TYR F 181 ARG 0.002 0.000 ARG E 6 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 156 time to evaluate : 1.052 Fit side-chains REVERT: H 78 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.7055 (tmmt) REVERT: H 113 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7807 (mt) REVERT: F 78 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6943 (tmmt) REVERT: F 113 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7796 (mt) outliers start: 35 outliers final: 13 residues processed: 181 average time/residue: 0.9775 time to fit residues: 193.8596 Evaluate side-chains 168 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 151 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 61 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS F 199 HIS E 132 HIS ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10749 Z= 0.148 Angle : 0.441 7.218 14565 Z= 0.248 Chirality : 0.036 0.128 1648 Planarity : 0.003 0.035 1778 Dihedral : 3.369 17.110 1444 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.04 % Allowed : 15.58 % Favored : 81.38 % 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: 4.32 (0.23), residues: 1312 helix: 4.00 (0.16), residues: 950 sheet: 0.81 (1.15), residues: 10 loop : -0.60 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 33 HIS 0.004 0.001 HIS E 132 PHE 0.012 0.001 PHE C 584 TYR 0.013 0.001 TYR H 181 ARG 0.001 0.000 ARG G 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 158 time to evaluate : 1.127 Fit side-chains REVERT: H 78 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.7075 (tmmt) REVERT: H 113 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7809 (mt) REVERT: F 113 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7789 (mt) REVERT: E 12 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7387 (mp) REVERT: E 120 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6665 (tp) outliers start: 33 outliers final: 12 residues processed: 182 average time/residue: 1.0336 time to fit residues: 205.1380 Evaluate side-chains 171 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 chunk 85 optimal weight: 0.3980 chunk 0 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS F 199 HIS E 132 HIS G 60 HIS ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10749 Z= 0.138 Angle : 0.433 7.520 14565 Z= 0.242 Chirality : 0.035 0.122 1648 Planarity : 0.003 0.035 1778 Dihedral : 3.307 17.024 1444 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.12 % Allowed : 16.59 % Favored : 81.29 % 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: 4.39 (0.23), residues: 1312 helix: 4.05 (0.16), residues: 952 sheet: 0.83 (1.17), residues: 10 loop : -0.58 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 33 HIS 0.017 0.001 HIS G 60 PHE 0.011 0.001 PHE A 584 TYR 0.013 0.001 TYR F 181 ARG 0.001 0.000 ARG G 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 160 time to evaluate : 1.016 Fit side-chains REVERT: H 78 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.7128 (tmmt) REVERT: H 113 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7817 (mt) REVERT: F 113 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7802 (mt) REVERT: C 589 CYS cc_start: 0.5411 (p) cc_final: 0.4346 (m) REVERT: A 589 CYS cc_start: 0.5463 (p) cc_final: 0.4452 (m) outliers start: 23 outliers final: 11 residues processed: 176 average time/residue: 0.9919 time to fit residues: 191.2139 Evaluate side-chains 167 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 153 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 123 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 0.0170 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS F 199 HIS E 132 HIS G 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10749 Z= 0.132 Angle : 0.426 7.708 14565 Z= 0.237 Chirality : 0.035 0.120 1648 Planarity : 0.003 0.035 1778 Dihedral : 3.225 16.541 1442 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.76 % Allowed : 16.31 % Favored : 80.92 % 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: 4.44 (0.23), residues: 1312 helix: 4.09 (0.16), residues: 952 sheet: 0.84 (1.17), residues: 10 loop : -0.58 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 33 HIS 0.003 0.001 HIS G 132 PHE 0.010 0.001 PHE C 584 TYR 0.012 0.001 TYR H 181 ARG 0.001 0.000 ARG G 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 154 time to evaluate : 1.060 Fit side-chains REVERT: H 78 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.7162 (tmmt) REVERT: C 589 CYS cc_start: 0.5371 (p) cc_final: 0.4247 (m) REVERT: A 589 CYS cc_start: 0.5323 (p) cc_final: 0.4277 (m) REVERT: G 12 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7174 (tp) outliers start: 30 outliers final: 16 residues processed: 177 average time/residue: 0.9997 time to fit residues: 193.8117 Evaluate side-chains 172 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10749 Z= 0.145 Angle : 0.440 7.853 14565 Z= 0.246 Chirality : 0.036 0.125 1648 Planarity : 0.003 0.035 1778 Dihedral : 3.280 17.248 1442 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.13 % Allowed : 15.76 % Favored : 81.11 % 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: 4.35 (0.23), residues: 1312 helix: 4.02 (0.16), residues: 950 sheet: 0.92 (1.17), residues: 10 loop : -0.58 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 33 HIS 0.004 0.001 HIS G 205 PHE 0.015 0.001 PHE A 531 TYR 0.014 0.001 TYR H 181 ARG 0.001 0.000 ARG G 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 159 time to evaluate : 1.155 Fit side-chains REVERT: H 78 LYS cc_start: 0.7421 (OUTLIER) cc_final: 0.7174 (tmmt) REVERT: H 199 HIS cc_start: 0.8042 (OUTLIER) cc_final: 0.7575 (m-70) REVERT: F 199 HIS cc_start: 0.8016 (OUTLIER) cc_final: 0.7474 (m-70) REVERT: C 589 CYS cc_start: 0.5493 (p) cc_final: 0.4328 (m) REVERT: A 589 CYS cc_start: 0.5531 (p) cc_final: 0.4366 (m) outliers start: 34 outliers final: 21 residues processed: 184 average time/residue: 0.9871 time to fit residues: 198.8949 Evaluate side-chains 180 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 156 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10749 Z= 0.150 Angle : 0.444 8.036 14565 Z= 0.248 Chirality : 0.036 0.123 1648 Planarity : 0.003 0.035 1778 Dihedral : 3.300 17.302 1442 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.04 % Allowed : 15.76 % Favored : 81.20 % 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: 4.34 (0.23), residues: 1312 helix: 4.01 (0.16), residues: 950 sheet: 0.87 (1.16), residues: 10 loop : -0.58 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 33 HIS 0.004 0.001 HIS G 205 PHE 0.012 0.001 PHE A 584 TYR 0.014 0.001 TYR F 181 ARG 0.001 0.000 ARG G 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 152 time to evaluate : 0.999 Fit side-chains REVERT: H 78 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.7151 (tmmt) REVERT: H 199 HIS cc_start: 0.8037 (OUTLIER) cc_final: 0.7496 (m-70) REVERT: F 199 HIS cc_start: 0.8020 (OUTLIER) cc_final: 0.7480 (m-70) REVERT: C 589 CYS cc_start: 0.5493 (p) cc_final: 0.4310 (m) REVERT: A 589 CYS cc_start: 0.5506 (p) cc_final: 0.4352 (m) REVERT: G 11 LEU cc_start: 0.7574 (tp) cc_final: 0.6903 (tp) REVERT: G 12 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7175 (tp) REVERT: G 102 ARG cc_start: 0.7930 (tpt90) cc_final: 0.7599 (tpt90) REVERT: G 141 PHE cc_start: 0.7497 (m-80) cc_final: 0.7256 (m-80) outliers start: 33 outliers final: 20 residues processed: 177 average time/residue: 0.9581 time to fit residues: 186.1581 Evaluate side-chains 172 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 148 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 103 optimal weight: 0.1980 chunk 108 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 60 HIS E 132 HIS ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10749 Z= 0.172 Angle : 0.472 8.533 14565 Z= 0.263 Chirality : 0.037 0.129 1648 Planarity : 0.003 0.036 1778 Dihedral : 3.388 17.855 1442 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.86 % Allowed : 15.85 % Favored : 81.29 % 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: 4.21 (0.23), residues: 1312 helix: 3.90 (0.16), residues: 950 sheet: 1.01 (1.18), residues: 10 loop : -0.57 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 33 HIS 0.017 0.001 HIS E 60 PHE 0.014 0.001 PHE A 584 TYR 0.015 0.001 TYR H 181 ARG 0.001 0.000 ARG A 545 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 148 time to evaluate : 1.020 Fit side-chains REVERT: H 78 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.7122 (tmmt) REVERT: H 113 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7688 (mt) REVERT: H 199 HIS cc_start: 0.8034 (OUTLIER) cc_final: 0.7564 (m-70) REVERT: F 113 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7685 (mt) REVERT: F 199 HIS cc_start: 0.7992 (OUTLIER) cc_final: 0.7445 (m-70) REVERT: C 589 CYS cc_start: 0.5467 (p) cc_final: 0.4302 (m) REVERT: G 11 LEU cc_start: 0.7524 (tp) cc_final: 0.6939 (tp) REVERT: G 120 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6775 (tp) outliers start: 31 outliers final: 19 residues processed: 171 average time/residue: 0.9896 time to fit residues: 185.6577 Evaluate side-chains 173 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 10 MET Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 7.9990 chunk 57 optimal weight: 0.0040 chunk 84 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 205 HIS E 60 HIS E 132 HIS ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10749 Z= 0.137 Angle : 0.438 8.609 14565 Z= 0.244 Chirality : 0.035 0.129 1648 Planarity : 0.003 0.034 1778 Dihedral : 3.270 16.850 1442 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.40 % Allowed : 16.41 % Favored : 81.20 % 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: 4.41 (0.23), residues: 1312 helix: 4.07 (0.16), residues: 950 sheet: 0.89 (1.14), residues: 10 loop : -0.58 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 33 HIS 0.015 0.001 HIS E 60 PHE 0.010 0.001 PHE C 584 TYR 0.013 0.001 TYR H 181 ARG 0.001 0.000 ARG F 6 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 1.136 Fit side-chains REVERT: H 78 LYS cc_start: 0.7421 (OUTLIER) cc_final: 0.7173 (tmmt) REVERT: H 199 HIS cc_start: 0.8036 (OUTLIER) cc_final: 0.7501 (m-70) REVERT: F 199 HIS cc_start: 0.8019 (OUTLIER) cc_final: 0.7484 (m-70) REVERT: C 589 CYS cc_start: 0.5440 (p) cc_final: 0.4170 (m) REVERT: A 589 CYS cc_start: 0.5304 (p) cc_final: 0.4176 (m) REVERT: G 11 LEU cc_start: 0.7467 (tp) cc_final: 0.6859 (tp) REVERT: G 102 ARG cc_start: 0.7926 (tpt90) cc_final: 0.7596 (tpt90) outliers start: 26 outliers final: 17 residues processed: 169 average time/residue: 0.9926 time to fit residues: 183.6225 Evaluate side-chains 168 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 10 MET Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 chunk 104 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 10.9990 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 0.0020 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.192289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.136175 restraints weight = 23738.473| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 3.20 r_work: 0.3104 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10749 Z= 0.127 Angle : 0.427 8.712 14565 Z= 0.237 Chirality : 0.035 0.136 1648 Planarity : 0.003 0.034 1778 Dihedral : 3.203 16.137 1442 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.21 % Allowed : 16.77 % Favored : 81.01 % 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: 4.48 (0.23), residues: 1312 helix: 4.12 (0.16), residues: 952 sheet: 0.84 (1.17), residues: 10 loop : -0.55 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 33 HIS 0.004 0.001 HIS E 132 PHE 0.020 0.001 PHE C 531 TYR 0.011 0.001 TYR H 181 ARG 0.001 0.000 ARG G 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3921.22 seconds wall clock time: 69 minutes 11.50 seconds (4151.50 seconds total)