Starting phenix.real_space_refine on Sat Mar 16 15:47:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0i_34412/03_2024/8h0i_34412.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0i_34412/03_2024/8h0i_34412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0i_34412/03_2024/8h0i_34412.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0i_34412/03_2024/8h0i_34412.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0i_34412/03_2024/8h0i_34412.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0i_34412/03_2024/8h0i_34412.pdb" } resolution = 2.8 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= 1.000 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 36 5.49 5 S 80 5.16 5 Cl 2 4.86 5 C 9428 2.51 5 N 2686 2.21 5 O 2782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 2": "OD1" <-> "OD2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2": "OD1" <-> "OD2" Residue "B PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 37": "OD1" <-> "OD2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 76": "OE1" <-> "OE2" Residue "C ASP 78": "OD1" <-> "OD2" Residue "C TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 172": "OD1" <-> "OD2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 26": "OE1" <-> "OE2" Residue "D ASP 34": "OD1" <-> "OD2" Residue "D GLU 38": "OE1" <-> "OE2" Residue "D GLU 39": "OE1" <-> "OE2" Residue "D PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 120": "OD1" <-> "OD2" Residue "E PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 171": "OE1" <-> "OE2" Residue "F TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 37": "OD1" <-> "OD2" Residue "G TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 76": "OE1" <-> "OE2" Residue "G ASP 78": "OD1" <-> "OD2" Residue "G TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 172": "OD1" <-> "OD2" Residue "H PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 26": "OE1" <-> "OE2" Residue "H ASP 34": "OD1" <-> "OD2" Residue "H GLU 38": "OE1" <-> "OE2" Residue "H GLU 39": "OE1" <-> "OE2" Residue "H PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 120": "OD1" <-> "OD2" Residue "I PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 171": "OE1" <-> "OE2" Residue "J TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15018 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2797 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 14, 'TRANS': 330} Chain breaks: 3 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 73 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2797 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 14, 'TRANS': 330} Chain breaks: 3 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 73 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1117 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1076 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain breaks: 2 Chain: "E" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1102 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1023 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1117 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain breaks: 1 Chain: "H" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1076 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain breaks: 2 Chain: "I" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1102 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1023 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 391 Classifications: {'RNA': 19} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna2p': 14, 'rna3p': 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' U%rna3p_pyr:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "Y" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 391 Classifications: {'RNA': 19} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna2p': 14, 'rna3p': 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' U%rna3p_pyr:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 760 SG CYS A 84 62.480 55.613 51.523 1.00 28.54 S ATOM 782 SG CYS A 87 64.206 53.365 53.738 1.00 29.65 S ATOM 2190 SG CYS A 271 22.526 52.111 59.584 1.00152.44 S ATOM 2213 SG CYS A 274 25.489 52.841 58.094 1.00145.84 S ATOM 3557 SG CYS B 84 83.680 56.947 51.523 1.00 28.91 S ATOM 3579 SG CYS B 87 81.954 59.195 53.737 1.00 29.52 S ATOM 4987 SG CYS B 271 123.634 60.449 59.584 1.00151.31 S ATOM 5010 SG CYS B 274 120.671 59.719 58.094 1.00144.79 S Time building chain proxies: 8.91, per 1000 atoms: 0.59 Number of scatterers: 15018 At special positions: 0 Unit cell: (147, 113.4, 112.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Cl 2 17.00 S 80 16.00 P 36 15.00 O 2782 8.00 N 2686 7.00 C 9428 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.73 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" ND1 HIS A 53 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 87 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 84 " pdb=" ZN A 402 " pdb="ZN ZN A 402 " - pdb=" ND1 HIS A 240 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 274 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 271 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" ND1 HIS B 53 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 84 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 87 " pdb=" ZN B 402 " pdb="ZN ZN B 402 " - pdb=" ND1 HIS B 240 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 271 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 274 " 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3248 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 15 sheets defined 38.4% alpha, 30.9% beta 0 base pairs and 2 stacking pairs defined. Time for finding SS restraints: 4.35 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 53 through 66 removed outlier: 3.525A pdb=" N ARG A 57 " --> pdb=" O HIS A 53 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 98 removed outlier: 3.539A pdb=" N GLU A 97 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 136 through 148 removed outlier: 3.773A pdb=" N VAL A 148 " --> pdb=" O TRP A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 177 Processing helix chain 'A' and resid 181 through 189 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.606A pdb=" N CYS A 244 " --> pdb=" O HIS A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 253 Processing helix chain 'A' and resid 271 through 285 Processing helix chain 'A' and resid 306 through 315 removed outlier: 3.622A pdb=" N GLY A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 334 removed outlier: 3.808A pdb=" N VAL A 334 " --> pdb=" O TRP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 362 Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 53 through 66 removed outlier: 3.525A pdb=" N ARG B 57 " --> pdb=" O HIS B 53 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 98 removed outlier: 3.539A pdb=" N GLU B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 128 Processing helix chain 'B' and resid 136 through 148 removed outlier: 3.773A pdb=" N VAL B 148 " --> pdb=" O TRP B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 177 Processing helix chain 'B' and resid 181 through 189 Processing helix chain 'B' and resid 240 through 249 removed outlier: 3.607A pdb=" N CYS B 244 " --> pdb=" O HIS B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 253 Processing helix chain 'B' and resid 271 through 285 Processing helix chain 'B' and resid 306 through 315 removed outlier: 3.622A pdb=" N GLY B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 334 removed outlier: 3.808A pdb=" N VAL B 334 " --> pdb=" O TRP B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 362 Processing helix chain 'C' and resid 14 through 31 removed outlier: 3.514A pdb=" N ILE C 18 " --> pdb=" O ASP C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 111 Processing helix chain 'C' and resid 165 through 171 removed outlier: 3.737A pdb=" N LEU C 169 " --> pdb=" O SER C 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 15 Processing helix chain 'D' and resid 15 through 24 removed outlier: 4.087A pdb=" N GLU D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 51 removed outlier: 3.664A pdb=" N GLY D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 140 through 151 Processing helix chain 'E' and resid 14 through 31 removed outlier: 3.576A pdb=" N LYS E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 46 removed outlier: 3.712A pdb=" N GLU E 45 " --> pdb=" O HIS E 42 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER E 46 " --> pdb=" O HIS E 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 42 through 46' Processing helix chain 'E' and resid 99 through 111 Processing helix chain 'E' and resid 165 through 171 removed outlier: 3.684A pdb=" N LEU E 169 " --> pdb=" O SER E 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 21 Processing helix chain 'F' and resid 36 through 51 Processing helix chain 'F' and resid 70 through 74 Processing helix chain 'F' and resid 139 through 150 Processing helix chain 'G' and resid 14 through 31 removed outlier: 3.515A pdb=" N ILE G 18 " --> pdb=" O ASP G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 111 Processing helix chain 'G' and resid 165 through 171 removed outlier: 3.738A pdb=" N LEU G 169 " --> pdb=" O SER G 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 15 Processing helix chain 'H' and resid 15 through 24 removed outlier: 4.088A pdb=" N GLU H 24 " --> pdb=" O LYS H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 51 removed outlier: 3.664A pdb=" N GLY H 51 " --> pdb=" O ALA H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 74 No H-bonds generated for 'chain 'H' and resid 72 through 74' Processing helix chain 'H' and resid 140 through 151 Processing helix chain 'I' and resid 14 through 31 removed outlier: 3.576A pdb=" N LYS I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 46 removed outlier: 3.712A pdb=" N GLU I 45 " --> pdb=" O HIS I 42 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER I 46 " --> pdb=" O HIS I 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 42 through 46' Processing helix chain 'I' and resid 99 through 111 Processing helix chain 'I' and resid 165 through 171 removed outlier: 3.684A pdb=" N LEU I 169 " --> pdb=" O SER I 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 21 Processing helix chain 'J' and resid 36 through 51 Processing helix chain 'J' and resid 70 through 74 Processing helix chain 'J' and resid 139 through 150 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 47 removed outlier: 5.028A pdb=" N VAL A 28 " --> pdb=" O MET A 39 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N GLN A 41 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 10.058A pdb=" N TYR A 26 " --> pdb=" O GLN A 41 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N ARG A 43 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 11.542A pdb=" N LEU A 24 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N TRP A 23 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N TRP A 81 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 225 removed outlier: 10.451A pdb=" N ASN A 219 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 11.565A pdb=" N ARG A 209 " --> pdb=" O ASN A 219 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG A 221 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TYR A 260 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N CYS A 291 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL A 262 " --> pdb=" O CYS A 291 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LYS A 293 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N CYS A 264 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N LYS A 317 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU A 290 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N SER A 319 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE A 292 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 35 through 47 removed outlier: 5.029A pdb=" N VAL B 28 " --> pdb=" O MET B 39 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N GLN B 41 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 10.058A pdb=" N TYR B 26 " --> pdb=" O GLN B 41 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N ARG B 43 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 11.541A pdb=" N LEU B 24 " --> pdb=" O ARG B 43 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TRP B 23 " --> pdb=" O SER B 80 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N TRP B 81 " --> pdb=" O ALA B 108 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 215 through 225 removed outlier: 10.451A pdb=" N ASN B 219 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 11.565A pdb=" N ARG B 209 " --> pdb=" O ASN B 219 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG B 221 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TYR B 260 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N CYS B 291 " --> pdb=" O TYR B 260 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL B 262 " --> pdb=" O CYS B 291 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LYS B 293 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N CYS B 264 " --> pdb=" O LYS B 293 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N LYS B 317 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU B 290 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N SER B 319 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE B 292 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 39 through 41 removed outlier: 3.505A pdb=" N GLU C 54 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 53 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 39 through 41 removed outlier: 3.505A pdb=" N GLU C 54 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 53 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE C 87 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE C 9 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 11.572A pdb=" N TRP C 89 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 14.274A pdb=" N VAL C 7 " --> pdb=" O TRP C 89 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU D 64 " --> pdb=" O ALA D 59 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE D 55 " --> pdb=" O PHE D 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 85 through 87 removed outlier: 3.766A pdb=" N ILE D 109 " --> pdb=" O GLU D 126 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP D 120 " --> pdb=" O ASP D 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 39 through 41 removed outlier: 6.471A pdb=" N THR E 68 " --> pdb=" O SER E 52 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU E 54 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE E 66 " --> pdb=" O GLU E 54 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N HIS E 56 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU E 64 " --> pdb=" O HIS E 56 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY E 71 " --> pdb=" O GLY E 82 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLY E 82 " --> pdb=" O GLY E 71 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN E 83 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ILE E 87 " --> pdb=" O ILE E 9 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE E 9 " --> pdb=" O ILE E 87 " (cutoff:3.500A) removed outlier: 11.329A pdb=" N TRP E 89 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 13.932A pdb=" N VAL E 7 " --> pdb=" O TRP E 89 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LEU F 64 " --> pdb=" O ALA F 59 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL F 58 " --> pdb=" O LYS F 28 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS F 28 " --> pdb=" O VAL F 58 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP F 120 " --> pdb=" O ASP F 115 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 39 through 41 removed outlier: 6.471A pdb=" N THR E 68 " --> pdb=" O SER E 52 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU E 54 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE E 66 " --> pdb=" O GLU E 54 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N HIS E 56 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU E 64 " --> pdb=" O HIS E 56 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY E 71 " --> pdb=" O GLY E 82 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLY E 82 " --> pdb=" O GLY E 71 " (cutoff:3.500A) removed outlier: 11.394A pdb=" N SER E 95 " --> pdb=" O PRO F 100 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ILE F 102 " --> pdb=" O SER E 95 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 39 through 41 removed outlier: 3.505A pdb=" N GLU G 54 " --> pdb=" O ARG G 41 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER G 53 " --> pdb=" O THR G 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 39 through 41 removed outlier: 3.505A pdb=" N GLU G 54 " --> pdb=" O ARG G 41 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER G 53 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE G 87 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE G 9 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 11.572A pdb=" N TRP G 89 " --> pdb=" O VAL G 7 " (cutoff:3.500A) removed outlier: 14.274A pdb=" N VAL G 7 " --> pdb=" O TRP G 89 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU H 64 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE H 55 " --> pdb=" O PHE H 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 85 through 87 removed outlier: 3.766A pdb=" N ILE H 109 " --> pdb=" O GLU H 126 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP H 120 " --> pdb=" O ASP H 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 6 through 9 removed outlier: 3.514A pdb=" N VAL J 58 " --> pdb=" O LYS J 28 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS J 28 " --> pdb=" O VAL J 58 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP J 120 " --> pdb=" O ASP J 115 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 11 through 13 removed outlier: 4.245A pdb=" N GLN I 83 " --> pdb=" O VAL I 13 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLY I 82 " --> pdb=" O GLY I 71 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY I 71 " --> pdb=" O GLY I 82 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU I 64 " --> pdb=" O HIS I 56 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N HIS I 56 " --> pdb=" O LEU I 64 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE I 66 " --> pdb=" O GLU I 54 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU I 54 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR I 68 " --> pdb=" O SER I 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 11 through 13 removed outlier: 4.245A pdb=" N GLN I 83 " --> pdb=" O VAL I 13 " (cutoff:3.500A) 740 hydrogen bonds defined for protein. 2091 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 2 stacking parallelities Total time for adding SS restraints: 3.78 Time building geometry restraints manager: 6.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2328 1.31 - 1.44: 4902 1.44 - 1.56: 8076 1.56 - 1.69: 72 1.69 - 1.81: 122 Bond restraints: 15500 Sorted by residual: bond pdb=" C ILE G 51 " pdb=" O ILE G 51 " ideal model delta sigma weight residual 1.236 1.188 0.048 1.19e-02 7.06e+03 1.63e+01 bond pdb=" C ILE C 51 " pdb=" O ILE C 51 " ideal model delta sigma weight residual 1.236 1.190 0.047 1.19e-02 7.06e+03 1.53e+01 bond pdb=" C TYR C 69 " pdb=" O TYR C 69 " ideal model delta sigma weight residual 1.234 1.186 0.048 1.26e-02 6.30e+03 1.44e+01 bond pdb=" C TYR G 69 " pdb=" O TYR G 69 " ideal model delta sigma weight residual 1.234 1.186 0.047 1.26e-02 6.30e+03 1.42e+01 bond pdb=" C TRP G 70 " pdb=" O TRP G 70 " ideal model delta sigma weight residual 1.234 1.190 0.044 1.18e-02 7.18e+03 1.42e+01 ... (remaining 15495 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.29: 641 106.29 - 113.22: 7990 113.22 - 120.16: 5669 120.16 - 127.10: 6472 127.10 - 134.04: 352 Bond angle restraints: 21124 Sorted by residual: angle pdb=" N SER C 52 " pdb=" CA SER C 52 " pdb=" C SER C 52 " ideal model delta sigma weight residual 111.28 118.22 -6.94 1.09e+00 8.42e-01 4.05e+01 angle pdb=" N SER G 52 " pdb=" CA SER G 52 " pdb=" C SER G 52 " ideal model delta sigma weight residual 111.28 118.20 -6.92 1.09e+00 8.42e-01 4.03e+01 angle pdb=" N ILE G 51 " pdb=" CA ILE G 51 " pdb=" C ILE G 51 " ideal model delta sigma weight residual 109.34 102.93 6.41 2.08e+00 2.31e-01 9.50e+00 angle pdb=" N ILE C 51 " pdb=" CA ILE C 51 " pdb=" C ILE C 51 " ideal model delta sigma weight residual 109.34 102.98 6.36 2.08e+00 2.31e-01 9.36e+00 angle pdb=" C ILE G 51 " pdb=" CA ILE G 51 " pdb=" CB ILE G 51 " ideal model delta sigma weight residual 111.29 106.29 5.00 1.64e+00 3.72e-01 9.29e+00 ... (remaining 21119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.88: 8838 30.88 - 61.76: 254 61.76 - 92.64: 42 92.64 - 123.52: 0 123.52 - 154.40: 2 Dihedral angle restraints: 9136 sinusoidal: 4138 harmonic: 4998 Sorted by residual: dihedral pdb=" O4' C X 1 " pdb=" C1' C X 1 " pdb=" N1 C X 1 " pdb=" C2 C X 1 " ideal model delta sinusoidal sigma weight residual 200.00 45.60 154.40 1 1.50e+01 4.44e-03 8.11e+01 dihedral pdb=" O4' C Y 1 " pdb=" C1' C Y 1 " pdb=" N1 C Y 1 " pdb=" C2 C Y 1 " ideal model delta sinusoidal sigma weight residual 200.00 45.60 154.40 1 1.50e+01 4.44e-03 8.11e+01 dihedral pdb=" CA TYR I 69 " pdb=" C TYR I 69 " pdb=" N TRP I 70 " pdb=" CA TRP I 70 " ideal model delta harmonic sigma weight residual 180.00 157.08 22.92 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 9133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2152 0.110 - 0.220: 40 0.220 - 0.329: 2 0.329 - 0.439: 0 0.439 - 0.549: 2 Chirality restraints: 2196 Sorted by residual: chirality pdb=" CA SER C 52 " pdb=" N SER C 52 " pdb=" C SER C 52 " pdb=" CB SER C 52 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.53e+00 chirality pdb=" CA SER G 52 " pdb=" N SER G 52 " pdb=" C SER G 52 " pdb=" CB SER G 52 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.46e+00 chirality pdb=" CA ILE G 51 " pdb=" N ILE G 51 " pdb=" C ILE G 51 " pdb=" CB ILE G 51 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2193 not shown) Planarity restraints: 2562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP I 70 " 0.022 2.00e-02 2.50e+03 2.35e-02 1.39e+01 pdb=" CG TRP I 70 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP I 70 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP I 70 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP I 70 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP I 70 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP I 70 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 70 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 70 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP I 70 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 70 " 0.021 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" CG TRP E 70 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP E 70 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP E 70 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 70 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP E 70 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 70 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 70 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 70 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP E 70 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 67 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" C THR C 67 " -0.038 2.00e-02 2.50e+03 pdb=" O THR C 67 " 0.014 2.00e-02 2.50e+03 pdb=" N THR C 68 " 0.013 2.00e-02 2.50e+03 ... (remaining 2559 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 951 2.74 - 3.28: 13899 3.28 - 3.82: 24046 3.82 - 4.36: 28751 4.36 - 4.90: 51337 Nonbonded interactions: 118984 Sorted by model distance: nonbonded pdb=" OG1 THR B 322 " pdb=" OE1 GLU B 325 " model vdw 2.198 2.440 nonbonded pdb=" OG1 THR A 322 " pdb=" OE1 GLU A 325 " model vdw 2.199 2.440 nonbonded pdb=" OD1 ASN D 46 " pdb=" NH2 ARG D 49 " model vdw 2.261 2.520 nonbonded pdb=" OD1 ASN H 46 " pdb=" NH2 ARG H 49 " model vdw 2.261 2.520 nonbonded pdb=" OD1 ASN A 20 " pdb=" N2 G X 10 " model vdw 2.275 2.520 ... (remaining 118979 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 112 or resid 161 through 176)) selection = chain 'E' selection = (chain 'G' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 112 or resid 161 through 176)) selection = chain 'I' } ncs_group { reference = (chain 'D' and (resid 15 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 151)) selection = (chain 'F' and (resid 15 through 77 or resid 83 through 128 or resid 139 through \ 151)) selection = (chain 'H' and (resid 15 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 151)) selection = (chain 'J' and (resid 15 through 77 or resid 83 through 128 or resid 139 through \ 151)) } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 4.350 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 44.410 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.070 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:11.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 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 0.063 15500 Z= 0.201 Angle : 0.605 10.233 21124 Z= 0.339 Chirality : 0.047 0.549 2196 Planarity : 0.004 0.039 2562 Dihedral : 14.234 154.398 5888 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.81 % Allowed : 0.67 % Favored : 98.52 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.21), residues: 1654 helix: 1.68 (0.23), residues: 582 sheet: -0.07 (0.26), residues: 404 loop : -0.75 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.001 TRP I 70 HIS 0.002 0.001 HIS E 28 PHE 0.013 0.001 PHE A 245 TYR 0.011 0.001 TYR B 118 ARG 0.003 0.000 ARG B 222 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 275 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 0 residues processed: 281 average time/residue: 1.2467 time to fit residues: 385.7833 Evaluate side-chains 168 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 10.0000 chunk 125 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 67 optimal weight: 30.0000 chunk 130 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 79 optimal weight: 0.2980 chunk 96 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS B 199 HIS C 97 GLN F 37 HIS F 77 GLN F 117 GLN G 97 GLN J 37 HIS J 74 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15500 Z= 0.194 Angle : 0.638 9.265 21124 Z= 0.319 Chirality : 0.043 0.147 2196 Planarity : 0.005 0.053 2562 Dihedral : 13.022 156.584 2456 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.15 % Allowed : 11.81 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.21), residues: 1654 helix: 1.97 (0.23), residues: 578 sheet: 0.15 (0.26), residues: 408 loop : -0.75 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 70 HIS 0.004 0.001 HIS E 110 PHE 0.019 0.001 PHE H 127 TYR 0.016 0.001 TYR F 85 ARG 0.008 0.001 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 182 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 171 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7854 (pm20) outliers start: 32 outliers final: 13 residues processed: 196 average time/residue: 1.2061 time to fit residues: 261.1980 Evaluate side-chains 174 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 160 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 171 GLU Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 151 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN F 45 GLN F 77 GLN F 117 GLN J 117 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15500 Z= 0.242 Angle : 0.609 8.609 21124 Z= 0.308 Chirality : 0.042 0.162 2196 Planarity : 0.004 0.054 2562 Dihedral : 12.979 158.021 2456 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.89 % Allowed : 13.02 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.21), residues: 1654 helix: 2.02 (0.22), residues: 580 sheet: 0.16 (0.26), residues: 420 loop : -0.61 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 70 HIS 0.010 0.001 HIS A 199 PHE 0.016 0.001 PHE J 143 TYR 0.010 0.001 TYR G 69 ARG 0.006 0.000 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 170 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 149 ARG cc_start: 0.7105 (ttt180) cc_final: 0.6393 (tpm170) REVERT: H 11 LYS cc_start: 0.9101 (tttt) cc_final: 0.8871 (tptt) REVERT: H 149 ARG cc_start: 0.7136 (ttt180) cc_final: 0.6414 (tpm170) outliers start: 43 outliers final: 18 residues processed: 189 average time/residue: 1.2163 time to fit residues: 254.0749 Evaluate side-chains 171 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 153 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 29 MET Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 8.9990 chunk 113 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 16 optimal weight: 0.0670 chunk 72 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 chunk 143 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 overall best weight: 4.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN B 166 GLN F 117 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 GLN J 117 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 15500 Z= 0.326 Angle : 0.636 8.336 21124 Z= 0.323 Chirality : 0.043 0.153 2196 Planarity : 0.004 0.055 2562 Dihedral : 13.083 160.830 2456 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.89 % Allowed : 14.16 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.22), residues: 1654 helix: 2.03 (0.22), residues: 580 sheet: 0.22 (0.26), residues: 420 loop : -0.50 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 70 HIS 0.003 0.001 HIS B 42 PHE 0.018 0.002 PHE J 143 TYR 0.013 0.001 TYR G 69 ARG 0.004 0.000 ARG J 148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 161 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 8 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.6667 (pp30) REVERT: D 11 LYS cc_start: 0.9062 (tptt) cc_final: 0.8839 (tptt) REVERT: H 8 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6663 (pp30) outliers start: 43 outliers final: 24 residues processed: 183 average time/residue: 1.1474 time to fit residues: 233.4637 Evaluate side-chains 176 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain H residue 8 GLN Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 29 MET Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 119 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 117 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 117 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15500 Z= 0.211 Angle : 0.605 8.698 21124 Z= 0.304 Chirality : 0.042 0.153 2196 Planarity : 0.004 0.055 2562 Dihedral : 12.998 161.019 2456 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.75 % Allowed : 14.97 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.22), residues: 1654 helix: 2.11 (0.22), residues: 580 sheet: 0.45 (0.26), residues: 408 loop : -0.49 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 70 HIS 0.003 0.001 HIS B 42 PHE 0.014 0.001 PHE J 143 TYR 0.008 0.001 TYR G 69 ARG 0.002 0.000 ARG J 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 166 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 8 GLN cc_start: 0.7138 (OUTLIER) cc_final: 0.6521 (pp30) REVERT: H 8 GLN cc_start: 0.7159 (OUTLIER) cc_final: 0.6583 (pp30) outliers start: 41 outliers final: 20 residues processed: 188 average time/residue: 1.2143 time to fit residues: 252.7227 Evaluate side-chains 171 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 149 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 8 GLN Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 0.0570 chunk 144 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 94 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 117 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 117 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15500 Z= 0.194 Angle : 0.623 9.209 21124 Z= 0.308 Chirality : 0.041 0.152 2196 Planarity : 0.004 0.054 2562 Dihedral : 12.914 160.413 2456 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.62 % Allowed : 16.31 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.22), residues: 1654 helix: 2.14 (0.22), residues: 580 sheet: 0.53 (0.26), residues: 408 loop : -0.43 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 70 HIS 0.003 0.000 HIS I 80 PHE 0.013 0.001 PHE J 143 TYR 0.024 0.001 TYR F 85 ARG 0.003 0.000 ARG D 151 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 157 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 8 GLN cc_start: 0.7102 (OUTLIER) cc_final: 0.6378 (pp30) REVERT: H 8 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6391 (pp30) outliers start: 39 outliers final: 23 residues processed: 177 average time/residue: 1.1430 time to fit residues: 225.1766 Evaluate side-chains 172 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 8 GLN Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 127 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 117 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 135 optimal weight: 20.0000 chunk 89 optimal weight: 0.9990 chunk 159 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15500 Z= 0.267 Angle : 0.643 10.043 21124 Z= 0.321 Chirality : 0.042 0.143 2196 Planarity : 0.004 0.054 2562 Dihedral : 12.934 162.439 2456 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.42 % Allowed : 17.65 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.22), residues: 1654 helix: 2.17 (0.22), residues: 578 sheet: 0.54 (0.25), residues: 410 loop : -0.42 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 70 HIS 0.004 0.001 HIS E 80 PHE 0.015 0.001 PHE J 143 TYR 0.010 0.001 TYR G 69 ARG 0.003 0.000 ARG H 149 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 153 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 MET cc_start: 0.8012 (mmm) cc_final: 0.7288 (mpt) REVERT: B 321 MET cc_start: 0.8016 (mmm) cc_final: 0.7294 (mpt) REVERT: D 8 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.6399 (pp30) REVERT: H 8 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6409 (pp30) outliers start: 36 outliers final: 23 residues processed: 176 average time/residue: 1.1636 time to fit residues: 227.3237 Evaluate side-chains 168 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 143 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 8 GLN Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15500 Z= 0.335 Angle : 0.679 10.777 21124 Z= 0.340 Chirality : 0.043 0.142 2196 Planarity : 0.004 0.053 2562 Dihedral : 12.987 163.317 2456 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.35 % Allowed : 18.59 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.21), residues: 1654 helix: 1.96 (0.22), residues: 580 sheet: 0.56 (0.25), residues: 408 loop : -0.43 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 174 HIS 0.004 0.001 HIS I 80 PHE 0.015 0.001 PHE H 143 TYR 0.020 0.001 TYR J 85 ARG 0.009 0.000 ARG C 93 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 153 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 91 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7523 (ttpt) REVERT: I 174 TRP cc_start: 0.6832 (t-100) cc_final: 0.6588 (t-100) outliers start: 35 outliers final: 23 residues processed: 174 average time/residue: 1.1696 time to fit residues: 226.4857 Evaluate side-chains 166 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 127 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 141 optimal weight: 0.0970 chunk 148 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15500 Z= 0.218 Angle : 0.684 11.713 21124 Z= 0.337 Chirality : 0.042 0.155 2196 Planarity : 0.004 0.054 2562 Dihedral : 12.879 161.465 2456 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.61 % Allowed : 19.87 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.21), residues: 1654 helix: 2.02 (0.22), residues: 576 sheet: 0.64 (0.25), residues: 408 loop : -0.44 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 174 HIS 0.007 0.001 HIS I 80 PHE 0.010 0.001 PHE H 143 TYR 0.009 0.001 TYR B 202 ARG 0.007 0.000 ARG G 93 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 149 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 MET cc_start: 0.7938 (mmm) cc_final: 0.7590 (mpt) REVERT: B 321 MET cc_start: 0.7937 (mmm) cc_final: 0.7590 (mpt) REVERT: E 175 ASN cc_start: 0.7487 (p0) cc_final: 0.6835 (p0) REVERT: J 28 LYS cc_start: 0.9058 (ptmm) cc_final: 0.8686 (pptt) outliers start: 24 outliers final: 23 residues processed: 162 average time/residue: 1.1687 time to fit residues: 211.2255 Evaluate side-chains 164 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 165 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 101 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15500 Z= 0.213 Angle : 0.698 12.296 21124 Z= 0.341 Chirality : 0.042 0.169 2196 Planarity : 0.004 0.054 2562 Dihedral : 12.782 160.339 2456 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.61 % Allowed : 20.07 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.21), residues: 1654 helix: 2.01 (0.22), residues: 576 sheet: 0.71 (0.25), residues: 408 loop : -0.39 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 89 HIS 0.006 0.001 HIS I 80 PHE 0.010 0.001 PHE H 143 TYR 0.024 0.001 TYR F 85 ARG 0.006 0.000 ARG C 93 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 151 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 MET cc_start: 0.7990 (mmm) cc_final: 0.7386 (mpt) REVERT: B 321 MET cc_start: 0.7991 (mmm) cc_final: 0.7387 (mpt) REVERT: E 175 ASN cc_start: 0.7311 (p0) cc_final: 0.6635 (p0) outliers start: 24 outliers final: 21 residues processed: 166 average time/residue: 1.2184 time to fit residues: 226.1189 Evaluate side-chains 166 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 127 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 24 optimal weight: 0.0970 chunk 115 optimal weight: 7.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.071784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.048566 restraints weight = 57649.980| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.95 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15500 Z= 0.300 Angle : 0.711 12.358 21124 Z= 0.350 Chirality : 0.043 0.153 2196 Planarity : 0.004 0.053 2562 Dihedral : 12.816 160.975 2456 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.74 % Allowed : 19.80 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.21), residues: 1654 helix: 1.94 (0.22), residues: 576 sheet: 0.68 (0.25), residues: 410 loop : -0.40 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP E 174 HIS 0.007 0.001 HIS I 80 PHE 0.013 0.001 PHE D 143 TYR 0.009 0.001 TYR G 69 ARG 0.005 0.000 ARG C 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4578.15 seconds wall clock time: 82 minutes 10.45 seconds (4930.45 seconds total)