Starting phenix.real_space_refine on Fri Feb 16 15:50:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9h_16510/02_2024/8c9h_16510_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9h_16510/02_2024/8c9h_16510.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9h_16510/02_2024/8c9h_16510_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9h_16510/02_2024/8c9h_16510_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9h_16510/02_2024/8c9h_16510_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9h_16510/02_2024/8c9h_16510.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9h_16510/02_2024/8c9h_16510.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9h_16510/02_2024/8c9h_16510_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9h_16510/02_2024/8c9h_16510_updated.pdb" } resolution = 3.2 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= 0.003 sd= 0.032 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: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 10472 2.51 5 N 2568 2.21 5 O 2632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15776 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1945 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "B" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1945 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "C" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1945 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "D" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1945 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "E" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1945 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "F" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1945 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "G" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1945 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "H" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1945 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'T60': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'T60': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'T60': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'T60': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'T60': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'T60': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'T60': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'T60': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.13, per 1000 atoms: 0.52 Number of scatterers: 15776 At special positions: 0 Unit cell: (87.1792, 87.1792, 119.342, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 2632 8.00 N 2568 7.00 C 10472 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: 5.40 Conformation dependent library (CDL) restraints added in 2.7 seconds 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 0 sheets defined 72.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 28 through 30 No H-bonds generated for 'chain 'A' and resid 28 through 30' Processing helix chain 'A' and resid 32 through 60 removed outlier: 3.677A pdb=" N GLU A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 84 removed outlier: 4.147A pdb=" N VAL A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET A 80 " --> pdb=" O PHE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 89 No H-bonds generated for 'chain 'A' and resid 86 through 89' Processing helix chain 'A' and resid 95 through 103 Processing helix chain 'A' and resid 109 through 133 Proline residue: A 113 - end of helix Processing helix chain 'A' and resid 135 through 142 Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 168 through 190 Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 227 through 240 Proline residue: A 232 - end of helix Processing helix chain 'A' and resid 244 through 275 removed outlier: 3.706A pdb=" N SER A 248 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN A 249 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLY A 250 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN A 252 " --> pdb=" O ASN A 249 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP A 253 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TRP A 254 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TRP A 255 " --> pdb=" O ASN A 252 " (cutoff:3.500A) Proline residue: A 257 - end of helix removed outlier: 4.912A pdb=" N ALA A 260 " --> pdb=" O PRO A 257 " (cutoff:3.500A) Proline residue: A 261 - end of helix Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 32 through 60 removed outlier: 3.780A pdb=" N GLU B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 84 removed outlier: 4.207A pdb=" N VAL B 78 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR B 79 " --> pdb=" O GLY B 75 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET B 80 " --> pdb=" O PHE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 89 No H-bonds generated for 'chain 'B' and resid 86 through 89' Processing helix chain 'B' and resid 95 through 103 Processing helix chain 'B' and resid 109 through 133 Proline residue: B 113 - end of helix Processing helix chain 'B' and resid 135 through 142 Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' Processing helix chain 'B' and resid 168 through 190 Processing helix chain 'B' and resid 202 through 216 Processing helix chain 'B' and resid 227 through 240 Proline residue: B 232 - end of helix Processing helix chain 'B' and resid 244 through 275 removed outlier: 3.707A pdb=" N SER B 248 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN B 249 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLY B 250 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN B 252 " --> pdb=" O ASN B 249 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TRP B 254 " --> pdb=" O GLU B 251 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TRP B 255 " --> pdb=" O ASN B 252 " (cutoff:3.500A) Proline residue: B 257 - end of helix removed outlier: 4.910A pdb=" N ALA B 260 " --> pdb=" O PRO B 257 " (cutoff:3.500A) Proline residue: B 261 - end of helix Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 32 through 60 removed outlier: 3.673A pdb=" N GLU C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 84 removed outlier: 4.302A pdb=" N VAL C 78 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR C 79 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET C 80 " --> pdb=" O PHE C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 89 No H-bonds generated for 'chain 'C' and resid 86 through 89' Processing helix chain 'C' and resid 95 through 103 Processing helix chain 'C' and resid 109 through 133 Proline residue: C 113 - end of helix Processing helix chain 'C' and resid 135 through 142 Processing helix chain 'C' and resid 155 through 157 No H-bonds generated for 'chain 'C' and resid 155 through 157' Processing helix chain 'C' and resid 168 through 190 removed outlier: 3.517A pdb=" N THR C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 216 Processing helix chain 'C' and resid 227 through 240 Proline residue: C 232 - end of helix Processing helix chain 'C' and resid 244 through 275 removed outlier: 3.708A pdb=" N SER C 248 " --> pdb=" O GLN C 245 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN C 249 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLY C 250 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU C 251 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN C 252 " --> pdb=" O ASN C 249 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP C 253 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TRP C 254 " --> pdb=" O GLU C 251 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TRP C 255 " --> pdb=" O ASN C 252 " (cutoff:3.500A) Proline residue: C 257 - end of helix removed outlier: 4.913A pdb=" N ALA C 260 " --> pdb=" O PRO C 257 " (cutoff:3.500A) Proline residue: C 261 - end of helix Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 32 through 60 removed outlier: 3.642A pdb=" N GLU D 40 " --> pdb=" O GLU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 84 removed outlier: 4.271A pdb=" N VAL D 78 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET D 80 " --> pdb=" O PHE D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 89 No H-bonds generated for 'chain 'D' and resid 86 through 89' Processing helix chain 'D' and resid 95 through 103 Processing helix chain 'D' and resid 109 through 133 Proline residue: D 113 - end of helix Processing helix chain 'D' and resid 135 through 142 Processing helix chain 'D' and resid 155 through 157 No H-bonds generated for 'chain 'D' and resid 155 through 157' Processing helix chain 'D' and resid 168 through 188 Processing helix chain 'D' and resid 202 through 216 Processing helix chain 'D' and resid 227 through 240 Proline residue: D 232 - end of helix Processing helix chain 'D' and resid 244 through 275 removed outlier: 3.707A pdb=" N SER D 248 " --> pdb=" O GLN D 245 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN D 249 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLY D 250 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU D 251 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN D 252 " --> pdb=" O ASN D 249 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP D 253 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N TRP D 254 " --> pdb=" O GLU D 251 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TRP D 255 " --> pdb=" O ASN D 252 " (cutoff:3.500A) Proline residue: D 257 - end of helix removed outlier: 4.885A pdb=" N ALA D 260 " --> pdb=" O PRO D 257 " (cutoff:3.500A) Proline residue: D 261 - end of helix Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 32 through 60 removed outlier: 3.728A pdb=" N GLU E 40 " --> pdb=" O GLU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 84 removed outlier: 4.240A pdb=" N VAL E 78 " --> pdb=" O PHE E 74 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR E 79 " --> pdb=" O GLY E 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET E 80 " --> pdb=" O PHE E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 89 No H-bonds generated for 'chain 'E' and resid 86 through 89' Processing helix chain 'E' and resid 95 through 103 Processing helix chain 'E' and resid 109 through 133 Proline residue: E 113 - end of helix Processing helix chain 'E' and resid 135 through 142 Processing helix chain 'E' and resid 155 through 157 No H-bonds generated for 'chain 'E' and resid 155 through 157' Processing helix chain 'E' and resid 168 through 190 Processing helix chain 'E' and resid 202 through 216 Processing helix chain 'E' and resid 227 through 240 Proline residue: E 232 - end of helix Processing helix chain 'E' and resid 244 through 275 removed outlier: 3.708A pdb=" N SER E 248 " --> pdb=" O GLN E 245 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASN E 249 " --> pdb=" O VAL E 246 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLY E 250 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU E 251 " --> pdb=" O SER E 248 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN E 252 " --> pdb=" O ASN E 249 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP E 253 " --> pdb=" O GLY E 250 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N TRP E 254 " --> pdb=" O GLU E 251 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TRP E 255 " --> pdb=" O ASN E 252 " (cutoff:3.500A) Proline residue: E 257 - end of helix removed outlier: 4.915A pdb=" N ALA E 260 " --> pdb=" O PRO E 257 " (cutoff:3.500A) Proline residue: E 261 - end of helix removed outlier: 3.699A pdb=" N PHE E 275 " --> pdb=" O TYR E 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'F' and resid 32 through 60 removed outlier: 3.774A pdb=" N GLU F 40 " --> pdb=" O GLU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 84 removed outlier: 4.219A pdb=" N VAL F 78 " --> pdb=" O PHE F 74 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR F 79 " --> pdb=" O GLY F 75 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET F 80 " --> pdb=" O PHE F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 89 No H-bonds generated for 'chain 'F' and resid 86 through 89' Processing helix chain 'F' and resid 95 through 103 Processing helix chain 'F' and resid 109 through 133 Proline residue: F 113 - end of helix Processing helix chain 'F' and resid 135 through 142 Processing helix chain 'F' and resid 155 through 157 No H-bonds generated for 'chain 'F' and resid 155 through 157' Processing helix chain 'F' and resid 168 through 190 Processing helix chain 'F' and resid 202 through 216 Processing helix chain 'F' and resid 227 through 240 Proline residue: F 232 - end of helix Processing helix chain 'F' and resid 244 through 275 removed outlier: 3.707A pdb=" N SER F 248 " --> pdb=" O GLN F 245 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASN F 249 " --> pdb=" O VAL F 246 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLY F 250 " --> pdb=" O PHE F 247 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU F 251 " --> pdb=" O SER F 248 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN F 252 " --> pdb=" O ASN F 249 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP F 253 " --> pdb=" O GLY F 250 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N TRP F 254 " --> pdb=" O GLU F 251 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TRP F 255 " --> pdb=" O ASN F 252 " (cutoff:3.500A) Proline residue: F 257 - end of helix removed outlier: 4.905A pdb=" N ALA F 260 " --> pdb=" O PRO F 257 " (cutoff:3.500A) Proline residue: F 261 - end of helix Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 32 through 60 Processing helix chain 'G' and resid 67 through 84 removed outlier: 4.211A pdb=" N VAL G 78 " --> pdb=" O PHE G 74 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR G 79 " --> pdb=" O GLY G 75 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET G 80 " --> pdb=" O PHE G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 89 No H-bonds generated for 'chain 'G' and resid 86 through 89' Processing helix chain 'G' and resid 95 through 103 Processing helix chain 'G' and resid 109 through 133 Proline residue: G 113 - end of helix Processing helix chain 'G' and resid 135 through 142 Processing helix chain 'G' and resid 155 through 157 No H-bonds generated for 'chain 'G' and resid 155 through 157' Processing helix chain 'G' and resid 168 through 190 Processing helix chain 'G' and resid 202 through 216 Processing helix chain 'G' and resid 227 through 240 Proline residue: G 232 - end of helix Processing helix chain 'G' and resid 244 through 275 removed outlier: 3.707A pdb=" N SER G 248 " --> pdb=" O GLN G 245 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN G 249 " --> pdb=" O VAL G 246 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLY G 250 " --> pdb=" O PHE G 247 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU G 251 " --> pdb=" O SER G 248 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN G 252 " --> pdb=" O ASN G 249 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP G 253 " --> pdb=" O GLY G 250 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TRP G 254 " --> pdb=" O GLU G 251 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TRP G 255 " --> pdb=" O ASN G 252 " (cutoff:3.500A) Proline residue: G 257 - end of helix removed outlier: 4.912A pdb=" N ALA G 260 " --> pdb=" O PRO G 257 " (cutoff:3.500A) Proline residue: G 261 - end of helix Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 32 through 60 removed outlier: 3.665A pdb=" N GLU H 40 " --> pdb=" O GLU H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 84 Processing helix chain 'H' and resid 86 through 89 No H-bonds generated for 'chain 'H' and resid 86 through 89' Processing helix chain 'H' and resid 95 through 103 Processing helix chain 'H' and resid 109 through 133 Proline residue: H 113 - end of helix Processing helix chain 'H' and resid 135 through 142 Processing helix chain 'H' and resid 155 through 157 No H-bonds generated for 'chain 'H' and resid 155 through 157' Processing helix chain 'H' and resid 168 through 190 Processing helix chain 'H' and resid 202 through 216 Processing helix chain 'H' and resid 227 through 240 Proline residue: H 232 - end of helix Processing helix chain 'H' and resid 244 through 275 removed outlier: 3.708A pdb=" N SER H 248 " --> pdb=" O GLN H 245 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASN H 249 " --> pdb=" O VAL H 246 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLY H 250 " --> pdb=" O PHE H 247 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU H 251 " --> pdb=" O SER H 248 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN H 252 " --> pdb=" O ASN H 249 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP H 253 " --> pdb=" O GLY H 250 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TRP H 254 " --> pdb=" O GLU H 251 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TRP H 255 " --> pdb=" O ASN H 252 " (cutoff:3.500A) Proline residue: H 257 - end of helix removed outlier: 4.913A pdb=" N ALA H 260 " --> pdb=" O PRO H 257 " (cutoff:3.500A) Proline residue: H 261 - end of helix 913 hydrogen bonds defined for protein. 1947 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.52 Time building geometry restraints manager: 5.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2344 1.31 - 1.43: 4896 1.43 - 1.56: 8816 1.56 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 16248 Sorted by residual: bond pdb=" C18 T60 E 401 " pdb=" N19 T60 E 401 " ideal model delta sigma weight residual 1.463 1.318 0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" C18 T60 D 401 " pdb=" N19 T60 D 401 " ideal model delta sigma weight residual 1.463 1.319 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" C18 T60 C 401 " pdb=" N19 T60 C 401 " ideal model delta sigma weight residual 1.463 1.319 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" C18 T60 F 401 " pdb=" N19 T60 F 401 " ideal model delta sigma weight residual 1.463 1.319 0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" C18 T60 A 401 " pdb=" N19 T60 A 401 " ideal model delta sigma weight residual 1.463 1.320 0.143 2.00e-02 2.50e+03 5.14e+01 ... (remaining 16243 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.65: 536 106.65 - 113.48: 8527 113.48 - 120.32: 6264 120.32 - 127.16: 6550 127.16 - 133.99: 243 Bond angle restraints: 22120 Sorted by residual: angle pdb=" C26 T60 D 401 " pdb=" C09 T60 D 401 " pdb=" N10 T60 D 401 " ideal model delta sigma weight residual 83.54 119.13 -35.59 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C26 T60 A 401 " pdb=" C09 T60 A 401 " pdb=" N10 T60 A 401 " ideal model delta sigma weight residual 83.54 119.12 -35.58 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C26 T60 B 401 " pdb=" C09 T60 B 401 " pdb=" N10 T60 B 401 " ideal model delta sigma weight residual 83.54 119.11 -35.57 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C26 T60 E 401 " pdb=" C09 T60 E 401 " pdb=" N10 T60 E 401 " ideal model delta sigma weight residual 83.54 119.05 -35.51 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C26 T60 G 401 " pdb=" C09 T60 G 401 " pdb=" N10 T60 G 401 " ideal model delta sigma weight residual 83.54 119.02 -35.48 3.00e+00 1.11e-01 1.40e+02 ... (remaining 22115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 8408 17.85 - 35.70: 464 35.70 - 53.54: 112 53.54 - 71.39: 16 71.39 - 89.24: 16 Dihedral angle restraints: 9016 sinusoidal: 3368 harmonic: 5648 Sorted by residual: dihedral pdb=" CA PHE D 76 " pdb=" C PHE D 76 " pdb=" N GLY D 77 " pdb=" CA GLY D 77 " ideal model delta harmonic sigma weight residual 180.00 163.17 16.83 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CG ARG D 35 " pdb=" CD ARG D 35 " pdb=" NE ARG D 35 " pdb=" CZ ARG D 35 " ideal model delta sinusoidal sigma weight residual -90.00 -134.34 44.34 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG H 35 " pdb=" CD ARG H 35 " pdb=" NE ARG H 35 " pdb=" CZ ARG H 35 " ideal model delta sinusoidal sigma weight residual 180.00 -136.28 -43.72 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 9013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1407 0.025 - 0.050: 617 0.050 - 0.076: 317 0.076 - 0.101: 59 0.101 - 0.126: 40 Chirality restraints: 2440 Sorted by residual: chirality pdb=" CA LEU C 231 " pdb=" N LEU C 231 " pdb=" C LEU C 231 " pdb=" CB LEU C 231 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA LEU G 231 " pdb=" N LEU G 231 " pdb=" C LEU G 231 " pdb=" CB LEU G 231 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA LEU D 231 " pdb=" N LEU D 231 " pdb=" C LEU D 231 " pdb=" CB LEU D 231 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.81e-01 ... (remaining 2437 not shown) Planarity restraints: 2752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 231 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO E 232 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO E 232 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 232 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 231 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.90e+00 pdb=" N PRO H 232 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO H 232 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO H 232 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 231 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO G 232 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO G 232 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO G 232 " -0.019 5.00e-02 4.00e+02 ... (remaining 2749 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 5062 2.84 - 3.35: 15874 3.35 - 3.87: 26241 3.87 - 4.38: 28773 4.38 - 4.90: 53032 Nonbonded interactions: 128982 Sorted by model distance: nonbonded pdb=" OG1 THR C 79 " pdb=" O ALA C 203 " model vdw 2.324 2.440 nonbonded pdb=" O PHE F 275 " pdb=" NH1 ARG G 35 " model vdw 2.380 2.520 nonbonded pdb=" OG1 THR A 79 " pdb=" O ALA A 203 " model vdw 2.437 2.440 nonbonded pdb=" OG1 THR G 79 " pdb=" O ALA G 203 " model vdw 2.445 2.440 nonbonded pdb=" OG1 THR F 79 " pdb=" O ALA F 203 " model vdw 2.447 2.440 ... (remaining 128977 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 6.280 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 40.600 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.110 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: 52.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 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 : 0.004 0.145 16248 Z= 0.260 Angle : 0.902 35.586 22120 Z= 0.360 Chirality : 0.036 0.126 2440 Planarity : 0.004 0.035 2752 Dihedral : 12.785 89.241 5464 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.44 % Allowed : 6.41 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.20), residues: 2008 helix: 2.48 (0.14), residues: 1424 sheet: None (None), residues: 0 loop : -0.14 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 177 HIS 0.002 0.001 HIS C 83 PHE 0.009 0.001 PHE E 37 TYR 0.018 0.001 TYR G 223 ARG 0.002 0.000 ARG G 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 186 time to evaluate : 1.746 Fit side-chains REVERT: D 74 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7882 (t80) REVERT: G 74 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.7849 (t80) outliers start: 7 outliers final: 4 residues processed: 191 average time/residue: 0.3189 time to fit residues: 87.3096 Evaluate side-chains 187 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 181 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain F residue 187 PHE Chi-restraints excluded: chain G residue 74 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 181 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16248 Z= 0.209 Angle : 0.557 7.486 22120 Z= 0.297 Chirality : 0.038 0.127 2440 Planarity : 0.007 0.036 2752 Dihedral : 8.678 89.402 2204 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.82 % Allowed : 6.41 % Favored : 91.77 % 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: 1.41 (0.19), residues: 2008 helix: 1.34 (0.14), residues: 1416 sheet: None (None), residues: 0 loop : 0.13 (0.29), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 169 HIS 0.002 0.001 HIS H 57 PHE 0.009 0.001 PHE F 37 TYR 0.021 0.001 TYR F 223 ARG 0.007 0.001 ARG C 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 171 time to evaluate : 1.724 Fit side-chains REVERT: A 74 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.8146 (t80) REVERT: B 74 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.7945 (t80) REVERT: C 74 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.8074 (t80) REVERT: D 74 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8066 (t80) REVERT: E 74 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8029 (t80) REVERT: F 74 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.8102 (t80) REVERT: G 74 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.8097 (t80) outliers start: 29 outliers final: 21 residues processed: 194 average time/residue: 0.2782 time to fit residues: 80.3958 Evaluate side-chains 199 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 171 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain F residue 74 PHE Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 187 PHE Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain H residue 270 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 123 optimal weight: 0.0170 chunk 50 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 180 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 145 optimal weight: 0.5980 overall best weight: 1.4622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 HIS C 165 HIS D 165 HIS E 165 HIS G 165 HIS H 165 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16248 Z= 0.219 Angle : 0.539 8.416 22120 Z= 0.284 Chirality : 0.038 0.130 2440 Planarity : 0.006 0.036 2752 Dihedral : 8.697 88.751 2200 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.20 % Allowed : 6.97 % Favored : 90.83 % 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: 0.77 (0.19), residues: 2008 helix: 0.94 (0.14), residues: 1376 sheet: None (None), residues: 0 loop : -0.28 (0.28), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 169 HIS 0.002 0.001 HIS A 57 PHE 0.009 0.001 PHE A 172 TYR 0.020 0.002 TYR F 223 ARG 0.007 0.001 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 1.696 Fit side-chains REVERT: A 74 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8133 (t80) REVERT: B 74 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.7914 (t80) REVERT: C 74 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.8034 (t80) REVERT: D 74 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8231 (t80) REVERT: E 74 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8070 (t80) REVERT: F 74 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8079 (t80) REVERT: G 74 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8290 (t80) outliers start: 35 outliers final: 26 residues processed: 196 average time/residue: 0.2677 time to fit residues: 79.7033 Evaluate side-chains 188 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 155 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain F residue 74 PHE Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 187 PHE Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 187 PHE Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 187 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS F 165 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16248 Z= 0.264 Angle : 0.563 7.546 22120 Z= 0.298 Chirality : 0.039 0.129 2440 Planarity : 0.006 0.036 2752 Dihedral : 8.869 89.233 2200 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.14 % Allowed : 8.48 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.19), residues: 2008 helix: 0.86 (0.14), residues: 1360 sheet: None (None), residues: 0 loop : -0.40 (0.27), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 169 HIS 0.003 0.001 HIS G 165 PHE 0.011 0.001 PHE A 172 TYR 0.023 0.002 TYR A 223 ARG 0.006 0.001 ARG G 106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 163 time to evaluate : 1.705 Fit side-chains REVERT: A 74 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8182 (t80) REVERT: B 74 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.7992 (t80) REVERT: C 74 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8064 (t80) REVERT: D 74 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.8313 (t80) REVERT: E 74 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8077 (t80) REVERT: F 74 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.8097 (t80) REVERT: G 74 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8376 (t80) outliers start: 34 outliers final: 27 residues processed: 197 average time/residue: 0.2525 time to fit residues: 76.0752 Evaluate side-chains 184 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 150 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain F residue 74 PHE Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 187 PHE Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 187 PHE Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 187 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 16248 Z= 0.328 Angle : 0.594 7.994 22120 Z= 0.314 Chirality : 0.040 0.138 2440 Planarity : 0.007 0.038 2752 Dihedral : 8.954 88.370 2200 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.43 % Favored : 94.47 % Rotamer: Outliers : 2.70 % Allowed : 8.67 % Favored : 88.63 % 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: 0.41 (0.19), residues: 2008 helix: 0.73 (0.14), residues: 1352 sheet: None (None), residues: 0 loop : -0.52 (0.27), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 169 HIS 0.003 0.001 HIS F 165 PHE 0.012 0.002 PHE C 172 TYR 0.024 0.002 TYR G 223 ARG 0.008 0.001 ARG G 106 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 153 time to evaluate : 1.905 Fit side-chains REVERT: A 74 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8184 (t80) REVERT: B 74 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.8000 (t80) REVERT: C 74 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8160 (t80) REVERT: D 74 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8300 (t80) REVERT: E 74 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8168 (t80) REVERT: F 74 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.8208 (t80) REVERT: G 74 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.8317 (t80) REVERT: H 47 MET cc_start: 0.8884 (tmm) cc_final: 0.8386 (ttt) outliers start: 43 outliers final: 28 residues processed: 196 average time/residue: 0.2545 time to fit residues: 79.2026 Evaluate side-chains 181 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 146 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain F residue 74 PHE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 187 PHE Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 187 PHE Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain H residue 259 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 4.9990 chunk 174 optimal weight: 0.0970 chunk 38 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 193 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 16248 Z= 0.136 Angle : 0.510 7.086 22120 Z= 0.265 Chirality : 0.036 0.125 2440 Planarity : 0.006 0.035 2752 Dihedral : 8.772 89.668 2200 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.69 % Favored : 96.02 % Rotamer: Outliers : 2.01 % Allowed : 9.80 % Favored : 88.19 % 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: 0.83 (0.19), residues: 2008 helix: 0.97 (0.14), residues: 1360 sheet: None (None), residues: 0 loop : -0.17 (0.28), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 169 HIS 0.002 0.000 HIS G 57 PHE 0.008 0.001 PHE F 37 TYR 0.014 0.001 TYR A 223 ARG 0.007 0.001 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 158 time to evaluate : 1.682 Fit side-chains REVERT: A 74 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8055 (t80) REVERT: B 74 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.7836 (t80) REVERT: C 74 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.7943 (t80) REVERT: D 74 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8265 (t80) REVERT: E 74 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.7951 (t80) REVERT: F 74 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.8048 (t80) REVERT: G 74 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8206 (t80) outliers start: 32 outliers final: 25 residues processed: 183 average time/residue: 0.2503 time to fit residues: 71.2342 Evaluate side-chains 184 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 152 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain F residue 74 PHE Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 187 PHE Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 147 MET Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 187 PHE Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 147 MET Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 187 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 162 optimal weight: 0.7980 chunk 108 optimal weight: 0.0050 chunk 192 optimal weight: 0.3980 chunk 120 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 chunk 88 optimal weight: 0.0870 overall best weight: 0.3572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 GLN ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16248 Z= 0.123 Angle : 0.492 7.034 22120 Z= 0.256 Chirality : 0.036 0.121 2440 Planarity : 0.006 0.034 2752 Dihedral : 8.465 89.965 2200 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.70 % Allowed : 10.30 % Favored : 88.00 % 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: 1.15 (0.20), residues: 2008 helix: 1.21 (0.14), residues: 1352 sheet: None (None), residues: 0 loop : -0.02 (0.27), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 169 HIS 0.002 0.001 HIS E 57 PHE 0.009 0.001 PHE H 172 TYR 0.014 0.001 TYR G 223 ARG 0.004 0.000 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 163 time to evaluate : 1.627 Fit side-chains REVERT: A 74 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.7964 (t80) REVERT: B 74 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.7730 (t80) REVERT: C 74 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.7891 (t80) REVERT: D 74 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8172 (t80) REVERT: E 74 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.7856 (t80) REVERT: F 74 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.7959 (t80) REVERT: G 74 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8118 (t80) outliers start: 27 outliers final: 19 residues processed: 187 average time/residue: 0.2659 time to fit residues: 75.8078 Evaluate side-chains 189 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 163 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain F residue 74 PHE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 187 PHE Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 187 PHE Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 187 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 16248 Z= 0.388 Angle : 0.619 8.086 22120 Z= 0.325 Chirality : 0.042 0.145 2440 Planarity : 0.006 0.038 2752 Dihedral : 8.766 87.378 2200 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.01 % Allowed : 10.62 % Favored : 87.37 % 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: 0.57 (0.19), residues: 2008 helix: 0.80 (0.14), residues: 1360 sheet: None (None), residues: 0 loop : -0.33 (0.28), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 255 HIS 0.003 0.001 HIS H 165 PHE 0.013 0.002 PHE B 74 TYR 0.028 0.002 TYR E 223 ARG 0.003 0.001 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 147 time to evaluate : 1.722 Fit side-chains REVERT: A 74 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8224 (t80) REVERT: B 74 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8043 (t80) REVERT: C 74 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8136 (t80) REVERT: D 74 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8307 (t80) REVERT: E 74 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8159 (t80) REVERT: F 74 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8231 (t80) REVERT: G 74 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8265 (t80) outliers start: 32 outliers final: 19 residues processed: 179 average time/residue: 0.2289 time to fit residues: 65.0678 Evaluate side-chains 168 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 142 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain F residue 74 PHE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 187 PHE Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 187 PHE Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 187 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 162 optimal weight: 0.0970 chunk 169 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16248 Z= 0.151 Angle : 0.516 7.222 22120 Z= 0.268 Chirality : 0.036 0.126 2440 Planarity : 0.006 0.034 2752 Dihedral : 8.715 89.977 2200 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.03 % Favored : 95.72 % Rotamer: Outliers : 1.63 % Allowed : 11.12 % Favored : 87.25 % 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: 0.83 (0.20), residues: 2008 helix: 0.99 (0.14), residues: 1368 sheet: None (None), residues: 0 loop : -0.23 (0.28), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 169 HIS 0.002 0.001 HIS H 57 PHE 0.008 0.001 PHE F 37 TYR 0.013 0.001 TYR F 223 ARG 0.005 0.000 ARG G 106 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 154 time to evaluate : 1.661 Fit side-chains REVERT: A 74 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8092 (t80) REVERT: B 74 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.7869 (t80) REVERT: C 74 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.7992 (t80) REVERT: D 74 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8271 (t80) REVERT: E 74 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.7991 (t80) REVERT: F 74 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8014 (t80) REVERT: G 74 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8232 (t80) outliers start: 26 outliers final: 19 residues processed: 180 average time/residue: 0.2450 time to fit residues: 68.5268 Evaluate side-chains 179 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 153 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain F residue 74 PHE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 187 PHE Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 187 PHE Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 187 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 199 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16248 Z= 0.208 Angle : 0.534 7.602 22120 Z= 0.279 Chirality : 0.038 0.125 2440 Planarity : 0.006 0.035 2752 Dihedral : 8.703 88.705 2200 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.43 % Favored : 95.42 % Rotamer: Outliers : 1.76 % Allowed : 10.74 % Favored : 87.50 % 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: 0.80 (0.20), residues: 2008 helix: 0.97 (0.14), residues: 1368 sheet: None (None), residues: 0 loop : -0.24 (0.28), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 169 HIS 0.002 0.001 HIS G 57 PHE 0.009 0.001 PHE B 37 TYR 0.020 0.001 TYR B 223 ARG 0.004 0.000 ARG D 106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 1.682 Fit side-chains REVERT: A 74 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8089 (t80) REVERT: B 74 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.7902 (t80) REVERT: C 74 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8036 (t80) REVERT: D 74 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.8258 (t80) REVERT: E 74 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8070 (t80) REVERT: F 74 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.8082 (t80) REVERT: G 74 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8209 (t80) outliers start: 28 outliers final: 21 residues processed: 180 average time/residue: 0.2432 time to fit residues: 68.6333 Evaluate side-chains 180 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain F residue 74 PHE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 187 PHE Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 187 PHE Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 187 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 0.9980 chunk 146 optimal weight: 0.0980 chunk 23 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 139 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** 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 = 0.3821 r_free = 0.3821 target = 0.151195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.127875 restraints weight = 18107.250| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.60 r_work: 0.3429 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16248 Z= 0.134 Angle : 0.502 7.110 22120 Z= 0.261 Chirality : 0.036 0.121 2440 Planarity : 0.006 0.034 2752 Dihedral : 8.606 89.995 2200 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.76 % Allowed : 10.74 % Favored : 87.50 % 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: 1.01 (0.20), residues: 2008 helix: 1.12 (0.14), residues: 1360 sheet: None (None), residues: 0 loop : -0.15 (0.28), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 169 HIS 0.002 0.000 HIS H 57 PHE 0.009 0.001 PHE F 172 TYR 0.013 0.001 TYR C 223 ARG 0.004 0.000 ARG D 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2983.89 seconds wall clock time: 55 minutes 6.05 seconds (3306.05 seconds total)