Starting phenix.real_space_refine on Fri Nov 15 13:47:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0q_35106/11_2024/8i0q_35106.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0q_35106/11_2024/8i0q_35106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0q_35106/11_2024/8i0q_35106.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0q_35106/11_2024/8i0q_35106.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0q_35106/11_2024/8i0q_35106.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0q_35106/11_2024/8i0q_35106.cif" } resolution = 4.45 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= 0.019 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 10 5.49 5 S 30 5.16 5 C 5601 2.51 5 N 1489 2.21 5 O 1712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8842 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2683 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 334} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 14, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 130 Chain: "B" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2679 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 334} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 134 Chain: "H" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 892 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 893 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 769 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "M" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 773 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "U" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 79 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "V" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 5.94, per 1000 atoms: 0.67 Number of scatterers: 8842 At special positions: 0 Unit cell: (130.058, 153.106, 85.6076, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 10 15.00 O 1712 8.00 N 1489 7.00 C 5601 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS I 25 " - pdb=" SG CYS I 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 24 " - pdb=" SG CYS M 89 " 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: 2.52 Conformation dependent library (CDL) restraints added in 1.2 seconds 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2232 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 24 sheets defined 7.7% alpha, 43.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 278 through 282 removed outlier: 3.876A pdb=" N ARG A 282 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.893A pdb=" N ASN A 311 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.805A pdb=" N ALA A 339 " --> pdb=" O GLY A 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 94 Processing helix chain 'B' and resid 98 through 109 removed outlier: 3.605A pdb=" N GLU B 102 " --> pdb=" O THR B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 removed outlier: 3.896A pdb=" N ARG B 282 " --> pdb=" O ALA B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 311 removed outlier: 3.931A pdb=" N ASN B 311 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.539A pdb=" N LEU B 338 " --> pdb=" O LEU B 335 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA B 339 " --> pdb=" O GLY B 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 335 through 339' Processing helix chain 'H' and resid 65 through 68 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'I' and resid 65 through 68 Processing helix chain 'I' and resid 90 through 94 Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'M' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 118 removed outlier: 4.196A pdb=" N VAL A 40 " --> pdb=" O TYR A 21 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 21 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 22 " --> pdb=" O PHE A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28 removed outlier: 4.090A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A 62 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP A 143 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 60 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL A 53 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N PHE A 61 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ASP A 78 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N TYR A 63 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ARG A 76 " --> pdb=" O TYR A 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 28 removed outlier: 4.090A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A 127 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 188 Processing sheet with id=AA5, first strand: chain 'A' and resid 246 through 258 removed outlier: 5.481A pdb=" N GLN A 248 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE A 241 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LYS A 250 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA A 239 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLN A 237 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 254 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL A 328 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE A 231 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LYS A 326 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILE A 233 " --> pdb=" O LYS A 324 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS A 324 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N VAL A 235 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LYS A 322 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLN A 237 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N SER A 320 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ALA A 239 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE A 318 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 112 through 118 removed outlier: 4.213A pdb=" N VAL B 40 " --> pdb=" O TYR B 21 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR B 21 " --> pdb=" O VAL B 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 26 through 29 removed outlier: 4.048A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 9.211A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 62 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP B 143 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 60 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL B 53 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N PHE B 61 " --> pdb=" O ASP B 78 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ASP B 78 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N TYR B 63 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ARG B 76 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 29 removed outlier: 4.048A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 9.211A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL B 127 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 183 through 188 Processing sheet with id=AB1, first strand: chain 'B' and resid 246 through 258 removed outlier: 5.531A pdb=" N GLN B 248 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE B 241 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS B 250 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA B 239 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLN B 237 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 254 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL B 328 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE B 231 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LYS B 326 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE B 233 " --> pdb=" O LYS B 324 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LYS B 324 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N VAL B 235 " --> pdb=" O LYS B 322 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LYS B 322 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLN B 237 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N SER B 320 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ALA B 239 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE B 318 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 8 through 10 removed outlier: 3.895A pdb=" N LEU H 23 " --> pdb=" O LEU H 84 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR H 81 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 14 through 15 Processing sheet with id=AB4, first strand: chain 'H' and resid 61 through 63 removed outlier: 3.581A pdb=" N TYR H 62 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA H 100 " --> pdb=" O HIS H 38 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL H 40 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 61 through 63 removed outlier: 3.581A pdb=" N TYR H 62 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA H 100 " --> pdb=" O HIS H 38 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL H 40 " --> pdb=" O TYR H 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 8 through 10 removed outlier: 3.852A pdb=" N LEU I 23 " --> pdb=" O LEU I 84 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR I 81 " --> pdb=" O ASP I 76 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 14 through 15 Processing sheet with id=AB8, first strand: chain 'I' and resid 61 through 63 removed outlier: 3.625A pdb=" N TYR I 62 " --> pdb=" O SER I 53 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TRP I 39 " --> pdb=" O VAL I 51 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER I 53 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE I 37 " --> pdb=" O SER I 53 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS I 38 " --> pdb=" O ALA I 100 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA I 100 " --> pdb=" O HIS I 38 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL I 40 " --> pdb=" O TYR I 98 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TYR I 112 " --> pdb=" O ARG I 101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 61 through 63 removed outlier: 3.625A pdb=" N TYR I 62 " --> pdb=" O SER I 53 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TRP I 39 " --> pdb=" O VAL I 51 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER I 53 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE I 37 " --> pdb=" O SER I 53 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS I 38 " --> pdb=" O ALA I 100 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA I 100 " --> pdb=" O HIS I 38 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL I 40 " --> pdb=" O TYR I 98 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 6 through 8 removed outlier: 3.537A pdb=" N VAL L 20 " --> pdb=" O ILE L 76 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.362A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.498A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 5 through 8 removed outlier: 3.519A pdb=" N VAL M 20 " --> pdb=" O ILE M 76 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.293A pdb=" N LEU M 12 " --> pdb=" O GLU M 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'M' and resid 54 through 55 removed outlier: 6.557A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N TYR M 50 " --> pdb=" O VAL M 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2858 1.34 - 1.46: 2084 1.46 - 1.58: 4026 1.58 - 1.69: 37 1.69 - 1.81: 38 Bond restraints: 9043 Sorted by residual: bond pdb=" O2P SEP V 351 " pdb=" P SEP V 351 " ideal model delta sigma weight residual 1.610 1.514 0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" O3P SEP V 351 " pdb=" P SEP V 351 " ideal model delta sigma weight residual 1.610 1.515 0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" O1P SEP V 351 " pdb=" P SEP V 351 " ideal model delta sigma weight residual 1.610 1.516 0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C MET B 352 " pdb=" N HIS B 353 " ideal model delta sigma weight residual 1.331 1.381 -0.050 2.83e-02 1.25e+03 3.06e+00 bond pdb=" C MET A 352 " pdb=" N HIS A 353 " ideal model delta sigma weight residual 1.331 1.380 -0.049 2.83e-02 1.25e+03 3.03e+00 ... (remaining 9038 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 12088 1.68 - 3.36: 241 3.36 - 5.04: 41 5.04 - 6.71: 2 6.71 - 8.39: 1 Bond angle restraints: 12373 Sorted by residual: angle pdb=" C GLU B 308 " pdb=" CA GLU B 308 " pdb=" CB GLU B 308 " ideal model delta sigma weight residual 115.79 110.62 5.17 1.19e+00 7.06e-01 1.89e+01 angle pdb=" N ARG A 103 " pdb=" CA ARG A 103 " pdb=" C ARG A 103 " ideal model delta sigma weight residual 111.02 106.97 4.05 1.22e+00 6.72e-01 1.10e+01 angle pdb=" CB SEP V 351 " pdb=" OG SEP V 351 " pdb=" P SEP V 351 " ideal model delta sigma weight residual 110.00 118.39 -8.39 3.00e+00 1.11e-01 7.83e+00 angle pdb=" O ARG A 103 " pdb=" C ARG A 103 " pdb=" N LEU A 104 " ideal model delta sigma weight residual 122.08 124.67 -2.59 1.07e+00 8.73e-01 5.84e+00 angle pdb=" N PHE B 149 " pdb=" CA PHE B 149 " pdb=" C PHE B 149 " ideal model delta sigma weight residual 107.73 110.83 -3.10 1.34e+00 5.57e-01 5.36e+00 ... (remaining 12368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 4986 16.96 - 33.91: 334 33.91 - 50.87: 52 50.87 - 67.83: 11 67.83 - 84.79: 12 Dihedral angle restraints: 5395 sinusoidal: 1923 harmonic: 3472 Sorted by residual: dihedral pdb=" CA GLN L 4 " pdb=" C GLN L 4 " pdb=" N MET L 5 " pdb=" CA MET L 5 " ideal model delta harmonic sigma weight residual -180.00 -158.43 -21.57 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA PHE B 190 " pdb=" C PHE B 190 " pdb=" N LEU B 191 " pdb=" CA LEU B 191 " ideal model delta harmonic sigma weight residual 180.00 -161.36 -18.64 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PHE A 190 " pdb=" C PHE A 190 " pdb=" N LEU A 191 " pdb=" CA LEU A 191 " ideal model delta harmonic sigma weight residual 180.00 -162.81 -17.19 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 5392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 877 0.029 - 0.058: 381 0.058 - 0.088: 52 0.088 - 0.117: 100 0.117 - 0.146: 26 Chirality restraints: 1436 Sorted by residual: chirality pdb=" CA ILE A 241 " pdb=" N ILE A 241 " pdb=" C ILE A 241 " pdb=" CB ILE A 241 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA VAL A 343 " pdb=" N VAL A 343 " pdb=" C VAL A 343 " pdb=" CB VAL A 343 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA VAL B 345 " pdb=" N VAL B 345 " pdb=" C VAL B 345 " pdb=" CB VAL B 345 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 1433 not shown) Planarity restraints: 1587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 275 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO B 276 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 276 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 276 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 275 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO A 276 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN I 16 " 0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO I 17 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO I 17 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO I 17 " 0.018 5.00e-02 4.00e+02 ... (remaining 1584 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 552 2.71 - 3.26: 9440 3.26 - 3.81: 14042 3.81 - 4.35: 16614 4.35 - 4.90: 27916 Nonbonded interactions: 68564 Sorted by model distance: nonbonded pdb=" NE2 GLN B 172 " pdb=" O TYR B 173 " model vdw 2.167 3.120 nonbonded pdb=" NZ LYS A 107 " pdb=" O1P SEP V 347 " model vdw 2.203 3.120 nonbonded pdb=" O GLN I 6 " pdb=" OG SER I 28 " model vdw 2.226 3.040 nonbonded pdb=" ND2 ASN A 222 " pdb=" O ALA A 263 " model vdw 2.229 3.120 nonbonded pdb=" NE ARG B 62 " pdb=" OG1 THR B 74 " model vdw 2.236 3.120 ... (remaining 68559 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 6 through 133 or (resid 134 and (name N or name CA or name \ C or name O or name CB )) or resid 135 through 368)) selection = chain 'B' } ncs_group { reference = chain 'H' selection = (chain 'I' and (resid 5 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 122)) } ncs_group { reference = chain 'L' selection = (chain 'M' and (resid 1 through 90 or (resid 91 and (name N or name CA or name C \ or name O or name CB )) or resid 92 through 106)) } ncs_group { reference = (chain 'U' and (resid 343 through 349 or (resid 350 and (name N or name CA or na \ me C or name O or name CB )) or resid 351)) 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: 1.330 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.960 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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 0.096 9043 Z= 0.204 Angle : 0.593 8.393 12373 Z= 0.329 Chirality : 0.043 0.146 1436 Planarity : 0.004 0.047 1587 Dihedral : 12.560 84.785 3151 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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: -1.41 (0.25), residues: 1162 helix: -1.43 (1.04), residues: 22 sheet: -1.01 (0.23), residues: 464 loop : -0.79 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 106 HIS 0.004 0.001 HIS B 210 PHE 0.009 0.001 PHE L 72 TYR 0.008 0.001 TYR B 113 ARG 0.006 0.000 ARG H 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 7 LEU cc_start: 0.6995 (pt) cc_final: 0.6702 (pp) REVERT: H 21 LEU cc_start: 0.9417 (mt) cc_final: 0.9197 (mp) REVERT: H 86 MET cc_start: 0.7768 (pmm) cc_final: 0.7361 (pmm) REVERT: I 7 LEU cc_start: 0.7424 (pt) cc_final: 0.7080 (pp) REVERT: I 21 LEU cc_start: 0.9413 (mt) cc_final: 0.9194 (mp) REVERT: I 86 MET cc_start: 0.7567 (pmm) cc_final: 0.7110 (pmm) REVERT: L 5 MET cc_start: 0.7409 (ttt) cc_final: 0.6658 (pmm) REVERT: L 101 GLN cc_start: 0.8947 (mp10) cc_final: 0.8647 (pm20) REVERT: M 5 MET cc_start: 0.7713 (ttp) cc_final: 0.6691 (pmm) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1633 time to fit residues: 11.1971 Evaluate side-chains 29 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 54 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS B 219 HIS ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9043 Z= 0.256 Angle : 0.651 5.545 12373 Z= 0.340 Chirality : 0.044 0.151 1436 Planarity : 0.004 0.032 1587 Dihedral : 8.050 88.905 1314 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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: -1.22 (0.25), residues: 1162 helix: -0.99 (1.00), residues: 24 sheet: -0.99 (0.22), residues: 482 loop : -0.55 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 39 HIS 0.007 0.002 HIS B 210 PHE 0.018 0.003 PHE B 190 TYR 0.019 0.002 TYR I 107 ARG 0.005 0.001 ARG M 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 CYS cc_start: 0.8018 (p) cc_final: 0.7543 (p) REVERT: A 352 MET cc_start: 0.9075 (ptm) cc_final: 0.8069 (ptm) REVERT: B 150 CYS cc_start: 0.8225 (p) cc_final: 0.7709 (p) REVERT: H 21 LEU cc_start: 0.9467 (mt) cc_final: 0.9206 (tp) REVERT: H 86 MET cc_start: 0.7743 (pmm) cc_final: 0.7487 (pmm) REVERT: I 21 LEU cc_start: 0.9577 (mt) cc_final: 0.9244 (tp) REVERT: I 86 MET cc_start: 0.7735 (pmm) cc_final: 0.7471 (pmm) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1721 time to fit residues: 10.4115 Evaluate side-chains 27 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 4 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9043 Z= 0.354 Angle : 0.724 7.270 12373 Z= 0.381 Chirality : 0.045 0.175 1436 Planarity : 0.005 0.042 1587 Dihedral : 8.481 81.411 1314 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 0.22 % Allowed : 6.90 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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: -1.49 (0.25), residues: 1162 helix: -1.39 (0.91), residues: 24 sheet: -1.25 (0.22), residues: 472 loop : -0.67 (0.26), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 39 HIS 0.008 0.003 HIS A 219 PHE 0.023 0.003 PHE A 190 TYR 0.025 0.002 TYR I 107 ARG 0.004 0.001 ARG H 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 CYS cc_start: 0.8099 (p) cc_final: 0.7762 (p) REVERT: A 352 MET cc_start: 0.8803 (ptm) cc_final: 0.7773 (ptm) REVERT: B 150 CYS cc_start: 0.8189 (p) cc_final: 0.7839 (p) REVERT: H 21 LEU cc_start: 0.9493 (mt) cc_final: 0.9287 (tp) REVERT: H 86 MET cc_start: 0.8560 (pmm) cc_final: 0.8314 (pmm) REVERT: I 21 LEU cc_start: 0.9620 (mt) cc_final: 0.9309 (tp) REVERT: I 86 MET cc_start: 0.8551 (pmm) cc_final: 0.8312 (pmm) outliers start: 2 outliers final: 0 residues processed: 35 average time/residue: 0.1652 time to fit residues: 9.7942 Evaluate side-chains 24 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 29 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9043 Z= 0.157 Angle : 0.569 5.285 12373 Z= 0.290 Chirality : 0.043 0.161 1436 Planarity : 0.004 0.030 1587 Dihedral : 7.696 83.321 1314 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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: -1.01 (0.25), residues: 1162 helix: -0.39 (1.11), residues: 24 sheet: -0.77 (0.23), residues: 474 loop : -0.50 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 36 HIS 0.004 0.001 HIS B 210 PHE 0.013 0.002 PHE L 72 TYR 0.008 0.001 TYR M 37 ARG 0.003 0.000 ARG I 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 CYS cc_start: 0.7785 (p) cc_final: 0.7381 (p) REVERT: A 352 MET cc_start: 0.8582 (ptm) cc_final: 0.7436 (ptm) REVERT: B 150 CYS cc_start: 0.7609 (p) cc_final: 0.7108 (p) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1800 time to fit residues: 11.4191 Evaluate side-chains 27 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 56 optimal weight: 0.0670 chunk 98 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9043 Z= 0.300 Angle : 0.672 6.564 12373 Z= 0.348 Chirality : 0.043 0.154 1436 Planarity : 0.004 0.042 1587 Dihedral : 8.131 83.613 1314 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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: -1.30 (0.25), residues: 1162 helix: -1.02 (0.99), residues: 24 sheet: -0.97 (0.23), residues: 468 loop : -0.68 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 39 HIS 0.007 0.002 HIS A 219 PHE 0.018 0.003 PHE B 190 TYR 0.021 0.002 TYR I 107 ARG 0.004 0.001 ARG I 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: A 150 CYS cc_start: 0.8075 (p) cc_final: 0.7720 (p) REVERT: A 352 MET cc_start: 0.8656 (ptm) cc_final: 0.7554 (ptm) REVERT: B 150 CYS cc_start: 0.8005 (p) cc_final: 0.7620 (p) REVERT: B 352 MET cc_start: 0.8848 (ttt) cc_final: 0.8636 (ttt) REVERT: H 107 TYR cc_start: 0.8677 (t80) cc_final: 0.8430 (t80) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1688 time to fit residues: 9.9771 Evaluate side-chains 22 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 27 optimal weight: 0.3980 chunk 110 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.0670 chunk 36 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 overall best weight: 1.4922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9043 Z= 0.185 Angle : 0.580 5.116 12373 Z= 0.294 Chirality : 0.043 0.155 1436 Planarity : 0.004 0.028 1587 Dihedral : 7.741 85.255 1314 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.11 % Allowed : 2.56 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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 (0.25), residues: 1162 helix: -0.38 (1.14), residues: 24 sheet: -0.79 (0.23), residues: 474 loop : -0.56 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 39 HIS 0.004 0.001 HIS B 210 PHE 0.013 0.002 PHE M 72 TYR 0.009 0.001 TYR B 113 ARG 0.003 0.000 ARG H 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: A 150 CYS cc_start: 0.7694 (p) cc_final: 0.7311 (p) REVERT: A 352 MET cc_start: 0.8863 (ptm) cc_final: 0.7779 (ptm) REVERT: B 150 CYS cc_start: 0.7574 (p) cc_final: 0.7155 (p) REVERT: B 352 MET cc_start: 0.8846 (ttt) cc_final: 0.8576 (ttt) outliers start: 1 outliers final: 0 residues processed: 36 average time/residue: 0.1923 time to fit residues: 11.2646 Evaluate side-chains 25 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 5.9990 chunk 12 optimal weight: 0.2980 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9043 Z= 0.235 Angle : 0.606 5.159 12373 Z= 0.312 Chirality : 0.042 0.149 1436 Planarity : 0.004 0.029 1587 Dihedral : 7.863 85.204 1314 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.25), residues: 1162 helix: -0.60 (1.08), residues: 24 sheet: -0.88 (0.23), residues: 474 loop : -0.60 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 39 HIS 0.005 0.002 HIS B 210 PHE 0.036 0.002 PHE H 105 TYR 0.016 0.001 TYR H 107 ARG 0.005 0.000 ARG H 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: A 150 CYS cc_start: 0.7950 (p) cc_final: 0.7585 (p) REVERT: A 352 MET cc_start: 0.8864 (ptm) cc_final: 0.7830 (ptm) REVERT: B 150 CYS cc_start: 0.7790 (p) cc_final: 0.7400 (p) REVERT: B 352 MET cc_start: 0.8830 (ttt) cc_final: 0.8569 (ttt) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1363 time to fit residues: 7.9425 Evaluate side-chains 23 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9043 Z= 0.377 Angle : 0.736 7.790 12373 Z= 0.384 Chirality : 0.044 0.207 1436 Planarity : 0.005 0.041 1587 Dihedral : 8.575 86.067 1314 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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: -1.61 (0.25), residues: 1162 helix: -1.54 (0.88), residues: 24 sheet: -1.20 (0.23), residues: 460 loop : -0.87 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP H 39 HIS 0.008 0.002 HIS B 210 PHE 0.043 0.003 PHE I 105 TYR 0.025 0.002 TYR I 107 ARG 0.011 0.001 ARG I 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 CYS cc_start: 0.8243 (p) cc_final: 0.7894 (p) REVERT: A 352 MET cc_start: 0.8861 (ptm) cc_final: 0.7945 (ptm) REVERT: B 150 CYS cc_start: 0.8090 (p) cc_final: 0.7713 (p) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1379 time to fit residues: 8.1205 Evaluate side-chains 21 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 61 optimal weight: 0.3980 chunk 44 optimal weight: 0.3980 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 108 optimal weight: 0.0070 chunk 66 optimal weight: 5.9990 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9043 Z= 0.132 Angle : 0.562 6.271 12373 Z= 0.280 Chirality : 0.043 0.158 1436 Planarity : 0.003 0.028 1587 Dihedral : 7.487 88.521 1314 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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 (0.25), residues: 1162 helix: -0.53 (1.03), residues: 24 sheet: -0.62 (0.23), residues: 466 loop : -0.66 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 36 HIS 0.005 0.001 HIS B 159 PHE 0.029 0.002 PHE I 105 TYR 0.007 0.001 TYR B 249 ARG 0.003 0.000 ARG H 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: A 150 CYS cc_start: 0.7701 (p) cc_final: 0.7344 (p) REVERT: A 352 MET cc_start: 0.8824 (ptm) cc_final: 0.7646 (ptm) REVERT: B 150 CYS cc_start: 0.7477 (p) cc_final: 0.7096 (p) REVERT: L 24 CYS cc_start: 0.2065 (t) cc_final: 0.1138 (t) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1345 time to fit residues: 9.0661 Evaluate side-chains 28 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.0050 chunk 75 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9043 Z= 0.162 Angle : 0.560 11.420 12373 Z= 0.279 Chirality : 0.042 0.149 1436 Planarity : 0.004 0.029 1587 Dihedral : 7.420 87.326 1314 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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: -0.96 (0.25), residues: 1162 helix: -0.11 (1.05), residues: 24 sheet: -0.61 (0.23), residues: 468 loop : -0.59 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 39 HIS 0.004 0.001 HIS B 210 PHE 0.025 0.002 PHE I 105 TYR 0.011 0.001 TYR H 107 ARG 0.003 0.000 ARG I 90 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 150 CYS cc_start: 0.7775 (p) cc_final: 0.7470 (p) REVERT: A 352 MET cc_start: 0.8797 (ptm) cc_final: 0.7734 (ptm) REVERT: B 150 CYS cc_start: 0.7597 (p) cc_final: 0.7202 (p) REVERT: H 21 LEU cc_start: 0.9456 (pt) cc_final: 0.9219 (pt) REVERT: I 86 MET cc_start: 0.7564 (pmm) cc_final: 0.7325 (pmm) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1377 time to fit residues: 9.2376 Evaluate side-chains 26 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 0.0000 chunk 25 optimal weight: 0.0980 chunk 90 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 GLN ** 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 = 0.3052 r_free = 0.3052 target = 0.039384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.031862 restraints weight = 86654.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.032832 restraints weight = 54729.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.033524 restraints weight = 39799.648| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9043 Z= 0.131 Angle : 0.526 5.366 12373 Z= 0.260 Chirality : 0.042 0.151 1436 Planarity : 0.003 0.029 1587 Dihedral : 7.136 87.866 1314 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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: -0.74 (0.25), residues: 1162 helix: 0.41 (1.04), residues: 24 sheet: -0.41 (0.24), residues: 464 loop : -0.50 (0.26), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 36 HIS 0.003 0.001 HIS B 210 PHE 0.024 0.001 PHE I 105 TYR 0.007 0.001 TYR A 113 ARG 0.003 0.000 ARG H 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1537.63 seconds wall clock time: 29 minutes 21.28 seconds (1761.28 seconds total)