Starting phenix.real_space_refine on Sun Nov 17 08:20:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0z_35114/11_2024/8i0z_35114.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0z_35114/11_2024/8i0z_35114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0z_35114/11_2024/8i0z_35114.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0z_35114/11_2024/8i0z_35114.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0z_35114/11_2024/8i0z_35114.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0z_35114/11_2024/8i0z_35114.cif" } resolution = 4.33 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= 0.015 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 15 5.49 5 S 24 5.16 5 C 8342 2.51 5 N 2234 2.21 5 O 2548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13163 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2620 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2620 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2595 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "D" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 910 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 786 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 81 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TPO:plan-1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 921 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 771 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "M" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 920 Classifications: {'peptide': 119} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 115} Chain: "N" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 782 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "U" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 81 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TPO:plan-1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "V" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 76 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TPO:plan-1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 8.99, per 1000 atoms: 0.68 Number of scatterers: 13163 At special positions: 0 Unit cell: (149.844, 151.093, 89.9064, 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 24 16.00 P 15 15.00 O 2548 8.00 N 2234 7.00 C 8342 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.05 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.05 Simple disulfide: pdb=" SG CYS M 25 " - pdb=" SG CYS M 99 " distance=2.04 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 89 " distance=2.04 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: 3.13 Conformation dependent library (CDL) restraints added in 1.7 seconds 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3228 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 26 sheets defined 5.0% alpha, 43.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 279 through 283 removed outlier: 4.002A pdb=" N ARG A 283 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 110 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.836A pdb=" N ARG B 283 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 110 Processing helix chain 'C' and resid 279 through 283 removed outlier: 3.987A pdb=" N ARG C 283 " --> pdb=" O ALA C 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 65 through 68 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'H' and resid 31 through 34 Processing helix chain 'H' and resid 65 through 68 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'M' and resid 31 through 34 Processing helix chain 'M' and resid 65 through 68 Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 115 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 29 removed outlier: 6.056A pdb=" N PHE A 28 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 169 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE A 145 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LYS A 171 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 10.587A pdb=" N VAL A 143 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 148 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL A 54 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLN A 86 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL A 56 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN A 84 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 58 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE A 82 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL A 60 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 27 through 29 removed outlier: 6.056A pdb=" N PHE A 28 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 169 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE A 145 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LYS A 171 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 10.587A pdb=" N VAL A 143 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 128 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 190 Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 209 removed outlier: 4.309A pdb=" N TYR A 322 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N LEU A 344 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 10.137A pdb=" N VAL A 320 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLN A 238 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ALA A 240 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LYS A 251 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE A 242 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLN A 249 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 113 through 115 Processing sheet with id=AA7, first strand: chain 'B' and resid 27 through 29 removed outlier: 6.028A pdb=" N PHE B 28 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE B 145 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LYS B 171 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 10.713A pdb=" N VAL B 143 " --> pdb=" O LYS B 171 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL B 54 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLN B 86 " --> pdb=" O VAL B 54 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL B 56 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASN B 84 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU B 58 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE B 82 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL B 60 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 27 through 29 removed outlier: 6.028A pdb=" N PHE B 28 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE B 145 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LYS B 171 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 10.713A pdb=" N VAL B 143 " --> pdb=" O LYS B 171 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL B 128 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 184 through 190 Processing sheet with id=AB1, first strand: chain 'B' and resid 208 through 209 removed outlier: 3.589A pdb=" N PHE B 342 " --> pdb=" O TYR B 322 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR B 322 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N LEU B 344 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 10.020A pdb=" N VAL B 320 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLN B 238 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA B 240 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LYS B 251 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE B 242 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLN B 249 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N THR B 247 " --> pdb=" O PHE C 76 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE C 76 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ASP C 79 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE C 62 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C 81 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL C 54 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 10.506A pdb=" N VAL C 143 " --> pdb=" O LYS C 171 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LYS C 171 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE C 145 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE C 28 " --> pdb=" O VAL C 172 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 208 through 209 removed outlier: 3.589A pdb=" N PHE B 342 " --> pdb=" O TYR B 322 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR B 322 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N LEU B 344 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 10.020A pdb=" N VAL B 320 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLN B 238 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA B 240 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LYS B 251 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE B 242 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLN B 249 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N THR B 247 " --> pdb=" O PHE C 76 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE C 76 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ASP C 79 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE C 62 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C 81 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL C 54 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL C 128 " --> pdb=" O VAL C 143 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 113 through 115 removed outlier: 3.700A pdb=" N ARG V 337 " --> pdb=" O LYS C 11 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 184 through 187 Processing sheet with id=AB5, first strand: chain 'C' and resid 208 through 209 removed outlier: 3.528A pdb=" N PHE C 342 " --> pdb=" O TYR C 322 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR C 322 " --> pdb=" O PHE C 342 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N LEU C 344 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N VAL C 320 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE C 232 " --> pdb=" O GLU C 258 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLU C 258 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL C 234 " --> pdb=" O GLN C 256 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLN C 256 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL C 236 " --> pdb=" O VAL C 254 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 6 through 10 removed outlier: 3.682A pdb=" N GLN D 6 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER D 28 " --> pdb=" O GLN D 6 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL D 8 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR D 81 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 14 through 15 removed outlier: 3.854A pdb=" N ALA D 52 " --> pdb=" O TRP D 39 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR D 62 " --> pdb=" O SER D 53 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 5 through 8 Processing sheet with id=AB9, first strand: chain 'E' and resid 54 through 55 removed outlier: 6.686A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN E 39 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR E 86 " --> pdb=" O GLN E 39 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.577A pdb=" N SER H 24 " --> pdb=" O SER H 10 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR H 81 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 60 through 63 removed outlier: 3.652A pdb=" N TYR H 62 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER H 53 " --> pdb=" O TYR H 62 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AC4, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.835A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN L 39 " --> pdb=" O THR L 86 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR L 86 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 14 through 15 removed outlier: 6.799A pdb=" N ILE M 37 " --> pdb=" O SER M 53 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N SER M 53 " --> pdb=" O ILE M 37 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N TRP M 39 " --> pdb=" O VAL M 51 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR M 62 " --> pdb=" O SER M 53 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR M 60 " --> pdb=" O SER M 55 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 23 through 26 Processing sheet with id=AC7, first strand: chain 'N' and resid 5 through 8 Processing sheet with id=AC8, first strand: chain 'N' and resid 54 through 55 removed outlier: 6.882A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TYR N 50 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN N 39 " --> pdb=" O THR N 86 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR N 86 " --> pdb=" O GLN N 39 " (cutoff:3.500A) 507 hydrogen bonds defined for protein. 1305 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: 4.54 Time building geometry restraints manager: 3.68 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: 4237 1.34 - 1.47: 3295 1.47 - 1.59: 5854 1.59 - 1.71: 40 1.71 - 1.83: 33 Bond restraints: 13459 Sorted by residual: bond pdb=" OG1 TPO V 342 " pdb=" P TPO V 342 " ideal model delta sigma weight residual 1.717 1.610 0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" OG1 TPO V 339 " pdb=" P TPO V 339 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.78e+01 bond pdb=" OG1 TPO U 339 " pdb=" P TPO U 339 " ideal model delta sigma weight residual 1.717 1.612 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" OG1 TPO G 339 " pdb=" P TPO G 339 " ideal model delta sigma weight residual 1.717 1.612 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" OG1 TPO V 336 " pdb=" P TPO V 336 " ideal model delta sigma weight residual 1.717 1.613 0.104 2.00e-02 2.50e+03 2.69e+01 ... (remaining 13454 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 17789 2.22 - 4.44: 469 4.44 - 6.67: 64 6.67 - 8.89: 14 8.89 - 11.11: 10 Bond angle restraints: 18346 Sorted by residual: angle pdb=" N GLY D 12 " pdb=" CA GLY D 12 " pdb=" C GLY D 12 " ideal model delta sigma weight residual 111.42 120.68 -9.26 1.51e+00 4.39e-01 3.76e+01 angle pdb=" C PHE H 105 " pdb=" N TRP H 106 " pdb=" CA TRP H 106 " ideal model delta sigma weight residual 121.70 129.23 -7.53 1.80e+00 3.09e-01 1.75e+01 angle pdb=" N GLU A 314 " pdb=" CA GLU A 314 " pdb=" CB GLU A 314 " ideal model delta sigma weight residual 114.17 109.67 4.50 1.14e+00 7.69e-01 1.56e+01 angle pdb=" C PHE D 105 " pdb=" N TRP D 106 " pdb=" CA TRP D 106 " ideal model delta sigma weight residual 121.70 128.77 -7.07 1.80e+00 3.09e-01 1.54e+01 angle pdb=" C PHE M 105 " pdb=" N TRP M 106 " pdb=" CA TRP M 106 " ideal model delta sigma weight residual 121.70 128.75 -7.05 1.80e+00 3.09e-01 1.53e+01 ... (remaining 18341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7454 17.96 - 35.93: 463 35.93 - 53.89: 68 53.89 - 71.85: 15 71.85 - 89.82: 10 Dihedral angle restraints: 8010 sinusoidal: 2988 harmonic: 5022 Sorted by residual: dihedral pdb=" CB CYS D 25 " pdb=" SG CYS D 25 " pdb=" SG CYS D 99 " pdb=" CB CYS D 99 " ideal model delta sinusoidal sigma weight residual 93.00 40.30 52.70 1 1.00e+01 1.00e-02 3.78e+01 dihedral pdb=" CA MET H 86 " pdb=" C MET H 86 " pdb=" N ASN H 87 " pdb=" CA ASN H 87 " ideal model delta harmonic sigma weight residual -180.00 -150.18 -29.82 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA MET D 86 " pdb=" C MET D 86 " pdb=" N ASN D 87 " pdb=" CA ASN D 87 " ideal model delta harmonic sigma weight residual -180.00 -152.64 -27.36 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 8007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1371 0.038 - 0.076: 461 0.076 - 0.115: 190 0.115 - 0.153: 65 0.153 - 0.191: 9 Chirality restraints: 2096 Sorted by residual: chirality pdb=" CG LEU M 7 " pdb=" CB LEU M 7 " pdb=" CD1 LEU M 7 " pdb=" CD2 LEU M 7 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CB ILE L 107 " pdb=" CA ILE L 107 " pdb=" CG1 ILE L 107 " pdb=" CG2 ILE L 107 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" CB ILE E 76 " pdb=" CA ILE E 76 " pdb=" CG1 ILE E 76 " pdb=" CG2 ILE E 76 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.37e-01 ... (remaining 2093 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE N 107 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C ILE N 107 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE N 107 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS N 108 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 340 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO A 341 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 341 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 341 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 124 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO C 125 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 125 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 125 " 0.025 5.00e-02 4.00e+02 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 157 2.63 - 3.20: 12543 3.20 - 3.77: 19192 3.77 - 4.33: 25591 4.33 - 4.90: 42448 Nonbonded interactions: 99931 Sorted by model distance: nonbonded pdb=" NE2 GLN E 39 " pdb=" O LYS E 40 " model vdw 2.066 3.120 nonbonded pdb=" NE2 GLN L 39 " pdb=" O LYS L 40 " model vdw 2.095 3.120 nonbonded pdb=" NE2 GLN N 39 " pdb=" O LYS N 40 " model vdw 2.109 3.120 nonbonded pdb=" OD1 ASP N 18 " pdb=" N ARG N 19 " model vdw 2.149 3.120 nonbonded pdb=" OD1 ASP E 18 " pdb=" N ARG E 19 " model vdw 2.254 3.120 ... (remaining 99926 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 8 through 119 or (resid 120 and (name N or name CA or name \ C or name O or name CB )) or resid 121 through 188 or (resid 189 and (name N or \ name CA or name C or name O or name CB )) or resid 190 through 229 or (resid 23 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 231 through \ 259 or (resid 260 and (name N or name CA or name C or name O or name CB )) or re \ sid 261 through 314 or (resid 315 through 316 and (name N or name CA or name C o \ r name O or name CB )) or resid 317 through 324 or (resid 325 and (name N or nam \ e CA or name C or name O or name CB )) or resid 326 through 338 or (resid 339 an \ d (name N or name CA or name C or name O or name CB )) or resid 340 through 350) \ ) selection = (chain 'B' and (resid 8 through 49 or (resid 50 and (name N or name CA or name C \ or name O or name CB )) or resid 51 through 155 or (resid 156 and (name N or na \ me CA or name C or name O or name CB )) or resid 157 or (resid 158 and (name N o \ r name CA or name C or name O or name CB )) or resid 159 through 188 or (resid 1 \ 89 and (name N or name CA or name C or name O or name CB )) or resid 190 through \ 194 or (resid 195 and (name N or name CA or name C or name O or name CB )) or r \ esid 196 through 229 or (resid 230 and (name N or name CA or name C or name O or \ name CB )) or resid 231 through 315 or (resid 316 and (name N or name CA or nam \ e C or name O or name CB )) or resid 317 through 324 or (resid 325 and (name N o \ r name CA or name C or name O or name CB )) or resid 326 through 338 or (resid 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 through \ 350)) selection = (chain 'C' and (resid 8 through 157 or (resid 158 and (name N or name CA or name \ C or name O or name CB )) or resid 159 through 350)) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 5 through 122) selection = (chain 'M' and (resid 5 through 41 or (resid 42 through 43 and (name N or name C \ A or name C or name O or name CB )) or resid 44 through 122)) } ncs_group { reference = (chain 'E' and (resid 2 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 107)) selection = (chain 'L' and (resid 2 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 107)) selection = (chain 'N' and (resid 2 through 92 or (resid 93 and (name N or name CA or name C \ or name O or name CB )) or resid 94 through 107)) } ncs_group { reference = (chain 'G' and resid 334 through 342) selection = (chain 'U' and resid 334 through 342) selection = chain 'V' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 33.080 Find NCS groups from input model: 0.640 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: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 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 : 0.007 0.107 13459 Z= 0.461 Angle : 0.914 11.110 18346 Z= 0.472 Chirality : 0.049 0.191 2096 Planarity : 0.006 0.059 2340 Dihedral : 12.708 89.817 4764 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.29 % Allowed : 0.58 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % 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: -1.50 (0.20), residues: 1672 helix: -2.36 (0.59), residues: 42 sheet: -0.64 (0.20), residues: 658 loop : -1.16 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 36 HIS 0.006 0.001 HIS C 114 PHE 0.020 0.002 PHE L 99 TYR 0.028 0.002 TYR M 33 ARG 0.007 0.001 ARG E 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 1.455 Fit side-chains revert: symmetry clash REVERT: B 295 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7744 (ptpp) REVERT: E 36 TRP cc_start: 0.7569 (m100) cc_final: 0.7248 (m100) REVERT: E 107 ILE cc_start: 0.6561 (mp) cc_final: 0.6308 (pt) outliers start: 4 outliers final: 2 residues processed: 97 average time/residue: 0.2132 time to fit residues: 32.8073 Evaluate side-chains 58 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 85 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 13459 Z= 0.291 Angle : 0.740 8.029 18346 Z= 0.384 Chirality : 0.049 0.315 2096 Planarity : 0.005 0.045 2340 Dihedral : 7.067 47.568 1898 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.29 % Allowed : 5.48 % Favored : 94.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % 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: -1.28 (0.20), residues: 1672 helix: -0.29 (0.81), residues: 36 sheet: -0.57 (0.18), residues: 772 loop : -1.07 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 106 HIS 0.005 0.001 HIS D 38 PHE 0.020 0.002 PHE B 145 TYR 0.016 0.002 TYR D 63 ARG 0.004 0.001 ARG H 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 31 ASN cc_start: 0.8823 (t0) cc_final: 0.8524 (t0) outliers start: 4 outliers final: 3 residues processed: 77 average time/residue: 0.2139 time to fit residues: 26.5771 Evaluate side-chains 49 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 151 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 GLN ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13459 Z= 0.200 Angle : 0.636 7.591 18346 Z= 0.327 Chirality : 0.045 0.222 2096 Planarity : 0.004 0.039 2340 Dihedral : 6.171 43.534 1898 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % 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: -1.04 (0.20), residues: 1672 helix: 0.93 (0.85), residues: 36 sheet: -0.31 (0.18), residues: 780 loop : -1.07 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 39 HIS 0.004 0.001 HIS A 346 PHE 0.015 0.002 PHE C 145 TYR 0.018 0.001 TYR M 33 ARG 0.003 0.000 ARG M 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 1.420 Fit side-chains revert: symmetry clash REVERT: M 31 ASN cc_start: 0.8848 (t0) cc_final: 0.8590 (p0) REVERT: M 86 MET cc_start: 0.8254 (ppp) cc_final: 0.8018 (ppp) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1887 time to fit residues: 22.6990 Evaluate side-chains 50 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 16 optimal weight: 0.0060 chunk 72 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN A 238 GLN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 13459 Z= 0.303 Angle : 0.677 8.959 18346 Z= 0.350 Chirality : 0.046 0.282 2096 Planarity : 0.004 0.038 2340 Dihedral : 6.196 43.051 1898 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.20), residues: 1672 helix: 1.08 (0.93), residues: 36 sheet: -0.23 (0.19), residues: 772 loop : -1.15 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP M 106 HIS 0.004 0.001 HIS A 114 PHE 0.019 0.002 PHE E 99 TYR 0.013 0.002 TYR L 37 ARG 0.003 0.000 ARG H 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 1.466 Fit side-chains revert: symmetry clash REVERT: M 86 MET cc_start: 0.8418 (ppp) cc_final: 0.8090 (ppp) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1929 time to fit residues: 21.6557 Evaluate side-chains 41 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 120 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 0.0060 chunk 144 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 overall best weight: 2.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN N 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 13459 Z= 0.275 Angle : 0.657 6.935 18346 Z= 0.339 Chirality : 0.046 0.327 2096 Planarity : 0.004 0.036 2340 Dihedral : 6.058 42.381 1898 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.20), residues: 1672 helix: 0.97 (0.92), residues: 36 sheet: -0.24 (0.19), residues: 759 loop : -1.18 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 39 HIS 0.004 0.001 HIS A 114 PHE 0.020 0.002 PHE E 99 TYR 0.015 0.001 TYR D 33 ARG 0.002 0.000 ARG M 70 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.492 Fit side-chains REVERT: E 94 TYR cc_start: 0.9185 (m-80) cc_final: 0.8980 (m-10) REVERT: H 86 MET cc_start: 0.7970 (pmm) cc_final: 0.7726 (pmm) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2028 time to fit residues: 23.2877 Evaluate side-chains 43 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 161 optimal weight: 0.0970 chunk 134 optimal weight: 1.9990 chunk 74 optimal weight: 0.0170 chunk 13 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 overall best weight: 1.2020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 HIS B 300 ASN ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13459 Z= 0.188 Angle : 0.604 6.263 18346 Z= 0.307 Chirality : 0.044 0.201 2096 Planarity : 0.004 0.032 2340 Dihedral : 5.666 41.093 1898 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.07 % Allowed : 2.23 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % 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: -0.90 (0.20), residues: 1672 helix: 1.06 (0.87), residues: 36 sheet: -0.07 (0.19), residues: 759 loop : -1.12 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 39 HIS 0.003 0.001 HIS C 114 PHE 0.017 0.001 PHE E 99 TYR 0.011 0.001 TYR C 250 ARG 0.003 0.000 ARG D 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 1.593 Fit side-chains REVERT: B 300 ASN cc_start: 0.8953 (OUTLIER) cc_final: 0.8290 (p0) outliers start: 1 outliers final: 0 residues processed: 71 average time/residue: 0.1804 time to fit residues: 22.5021 Evaluate side-chains 47 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 155 optimal weight: 2.9990 chunk 18 optimal weight: 0.0270 chunk 92 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN B 211 HIS ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 GLN L 7 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13459 Z= 0.221 Angle : 0.617 6.262 18346 Z= 0.313 Chirality : 0.045 0.286 2096 Planarity : 0.004 0.032 2340 Dihedral : 5.633 40.259 1898 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % 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: -0.88 (0.20), residues: 1672 helix: 1.01 (0.87), residues: 36 sheet: -0.00 (0.19), residues: 759 loop : -1.17 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 39 HIS 0.003 0.001 HIS B 114 PHE 0.015 0.002 PHE L 99 TYR 0.010 0.001 TYR L 37 ARG 0.003 0.000 ARG M 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.758 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1818 time to fit residues: 23.5493 Evaluate side-chains 47 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS B 211 HIS ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13459 Z= 0.239 Angle : 0.623 6.588 18346 Z= 0.318 Chirality : 0.045 0.307 2096 Planarity : 0.004 0.034 2340 Dihedral : 5.673 39.906 1898 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.20), residues: 1672 helix: 1.03 (0.87), residues: 36 sheet: -0.07 (0.19), residues: 771 loop : -1.15 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 39 HIS 0.004 0.001 HIS A 114 PHE 0.022 0.002 PHE L 99 TYR 0.010 0.001 TYR L 37 ARG 0.002 0.000 ARG M 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.570 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1844 time to fit residues: 23.0951 Evaluate side-chains 46 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 141 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 GLN C 182 GLN ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 13459 Z= 0.337 Angle : 0.704 8.291 18346 Z= 0.363 Chirality : 0.047 0.396 2096 Planarity : 0.004 0.043 2340 Dihedral : 6.069 40.455 1898 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % 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: -1.13 (0.21), residues: 1672 helix: 0.84 (0.95), residues: 36 sheet: -0.22 (0.19), residues: 788 loop : -1.31 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP M 50 HIS 0.007 0.001 HIS C 114 PHE 0.033 0.002 PHE L 99 TYR 0.014 0.002 TYR L 37 ARG 0.003 0.001 ARG D 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.588 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1830 time to fit residues: 21.0250 Evaluate side-chains 45 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 4.9990 chunk 75 optimal weight: 0.0020 chunk 110 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 chunk 81 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 chunk 141 optimal weight: 10.0000 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13459 Z= 0.169 Angle : 0.600 7.148 18346 Z= 0.301 Chirality : 0.044 0.216 2096 Planarity : 0.004 0.032 2340 Dihedral : 5.502 38.940 1898 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % 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: -0.88 (0.21), residues: 1672 helix: 0.97 (0.85), residues: 36 sheet: 0.04 (0.20), residues: 776 loop : -1.24 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 39 HIS 0.003 0.001 HIS M 38 PHE 0.021 0.001 PHE L 99 TYR 0.008 0.001 TYR A 273 ARG 0.005 0.000 ARG M 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.621 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1965 time to fit residues: 25.1515 Evaluate side-chains 49 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 116 optimal weight: 0.0980 chunk 7 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 GLN L 7 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.083045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.073007 restraints weight = 73531.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.075165 restraints weight = 88677.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.075175 restraints weight = 41896.209| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13459 Z= 0.154 Angle : 0.591 10.125 18346 Z= 0.293 Chirality : 0.044 0.166 2096 Planarity : 0.004 0.033 2340 Dihedral : 5.174 36.920 1898 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % 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: -0.73 (0.21), residues: 1672 helix: 1.25 (0.82), residues: 36 sheet: 0.18 (0.20), residues: 770 loop : -1.18 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 39 HIS 0.003 0.001 HIS B 346 PHE 0.019 0.001 PHE L 99 TYR 0.010 0.001 TYR L 94 ARG 0.004 0.000 ARG M 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2079.66 seconds wall clock time: 39 minutes 33.15 seconds (2373.15 seconds total)