Starting phenix.real_space_refine on Thu Jun 27 21:56:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsh_24670/06_2024/7rsh_24670_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsh_24670/06_2024/7rsh_24670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsh_24670/06_2024/7rsh_24670.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsh_24670/06_2024/7rsh_24670.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsh_24670/06_2024/7rsh_24670_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsh_24670/06_2024/7rsh_24670_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 28 5.16 5 C 9244 2.51 5 N 2148 2.21 5 O 2316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 47": "OD1" <-> "OD2" Residue "A ASP 57": "OD1" <-> "OD2" Residue "A ASP 84": "OD1" <-> "OD2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 226": "OD1" <-> "OD2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 268": "NH1" <-> "NH2" Residue "A GLU 274": "OE1" <-> "OE2" Residue "A ASP 312": "OD1" <-> "OD2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A ASP 388": "OD1" <-> "OD2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "B ASP 47": "OD1" <-> "OD2" Residue "B ASP 57": "OD1" <-> "OD2" Residue "B ASP 84": "OD1" <-> "OD2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 226": "OD1" <-> "OD2" Residue "B ARG 233": "NH1" <-> "NH2" Residue "B ARG 247": "NH1" <-> "NH2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "B GLU 274": "OE1" <-> "OE2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B ASP 388": "OD1" <-> "OD2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C ASP 84": "OD1" <-> "OD2" Residue "C ARG 111": "NH1" <-> "NH2" Residue "C PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 226": "OD1" <-> "OD2" Residue "C ARG 233": "NH1" <-> "NH2" Residue "C ARG 247": "NH1" <-> "NH2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C GLU 274": "OE1" <-> "OE2" Residue "C ASP 312": "OD1" <-> "OD2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "C ASP 388": "OD1" <-> "OD2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "D ASP 47": "OD1" <-> "OD2" Residue "D ASP 57": "OD1" <-> "OD2" Residue "D ASP 84": "OD1" <-> "OD2" Residue "D ARG 111": "NH1" <-> "NH2" Residue "D PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 226": "OD1" <-> "OD2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D ARG 247": "NH1" <-> "NH2" Residue "D ARG 268": "NH1" <-> "NH2" Residue "D GLU 274": "OE1" <-> "OE2" Residue "D ASP 312": "OD1" <-> "OD2" Residue "D GLU 318": "OE1" <-> "OE2" Residue "D ASP 388": "OD1" <-> "OD2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D GLU 406": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 13744 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3191 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 25, 'TRANS': 375} Chain breaks: 1 Chain: "B" Number of atoms: 3191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3191 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 25, 'TRANS': 375} Chain breaks: 1 Chain: "C" Number of atoms: 3191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3191 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 25, 'TRANS': 375} Chain breaks: 1 Chain: "D" Number of atoms: 3191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3191 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 25, 'TRANS': 375} Chain breaks: 1 Chain: "A" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 245 Unusual residues: {'PGW': 14} Classifications: {'RNA': 1, 'undetermined': 14} Modifications used: {'rna3p': 1} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 491 Unresolved non-hydrogen angles: 580 Unresolved non-hydrogen dihedrals: 494 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'PGW:plan-1': 12, 'PGW:plan-2': 12, 'PGW:plan-3': 8} Unresolved non-hydrogen planarities: 119 Chain: "B" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 245 Unusual residues: {'PGW': 14} Classifications: {'RNA': 1, 'undetermined': 14} Modifications used: {'rna3p': 1} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 491 Unresolved non-hydrogen angles: 580 Unresolved non-hydrogen dihedrals: 494 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'PGW:plan-1': 12, 'PGW:plan-2': 12, 'PGW:plan-3': 8} Unresolved non-hydrogen planarities: 119 Chain: "C" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 245 Unusual residues: {'PGW': 14} Classifications: {'RNA': 1, 'undetermined': 14} Modifications used: {'rna3p': 1} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 491 Unresolved non-hydrogen angles: 580 Unresolved non-hydrogen dihedrals: 494 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'PGW:plan-1': 12, 'PGW:plan-2': 12, 'PGW:plan-3': 8} Unresolved non-hydrogen planarities: 119 Chain: "D" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 245 Unusual residues: {'PGW': 14} Classifications: {'RNA': 1, 'undetermined': 14} Modifications used: {'rna3p': 1} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 491 Unresolved non-hydrogen angles: 580 Unresolved non-hydrogen dihedrals: 494 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'PGW:plan-1': 12, 'PGW:plan-2': 12, 'PGW:plan-3': 8} Unresolved non-hydrogen planarities: 119 Time building chain proxies: 8.08, per 1000 atoms: 0.59 Number of scatterers: 13744 At special positions: 0 Unit cell: (106.937, 106.937, 123.877, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 8 15.00 O 2316 8.00 N 2148 7.00 C 9244 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: 5.18 Conformation dependent library (CDL) restraints added in 2.3 seconds 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3048 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 8 sheets defined 57.9% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 15 through 35 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 44 through 62 removed outlier: 4.385A pdb=" N ILE A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 95 through 98 No H-bonds generated for 'chain 'A' and resid 95 through 98' Processing helix chain 'A' and resid 102 through 125 removed outlier: 4.081A pdb=" N LEU A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N SER A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ARG A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 157 removed outlier: 3.588A pdb=" N LEU A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 181 Processing helix chain 'A' and resid 194 through 222 Processing helix chain 'A' and resid 228 through 246 Processing helix chain 'A' and resid 250 through 267 removed outlier: 3.727A pdb=" N ILE A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 275 No H-bonds generated for 'chain 'A' and resid 272 through 275' Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 307 through 314 Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.538A pdb=" N LEU A 371 " --> pdb=" O GLU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 401 Processing helix chain 'A' and resid 405 through 416 Processing helix chain 'B' and resid 15 through 35 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 44 through 62 removed outlier: 4.385A pdb=" N ILE B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 95 through 98 No H-bonds generated for 'chain 'B' and resid 95 through 98' Processing helix chain 'B' and resid 102 through 125 removed outlier: 4.080A pdb=" N LEU B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N SER B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ARG B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 157 removed outlier: 3.588A pdb=" N LEU B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 181 Processing helix chain 'B' and resid 194 through 222 Processing helix chain 'B' and resid 228 through 246 Processing helix chain 'B' and resid 250 through 267 removed outlier: 3.727A pdb=" N ILE B 257 " --> pdb=" O GLN B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 275 No H-bonds generated for 'chain 'B' and resid 272 through 275' Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 307 through 314 Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.538A pdb=" N LEU B 371 " --> pdb=" O GLU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 401 Processing helix chain 'B' and resid 405 through 416 Processing helix chain 'C' and resid 15 through 35 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 44 through 62 removed outlier: 4.385A pdb=" N ILE C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 95 through 98 No H-bonds generated for 'chain 'C' and resid 95 through 98' Processing helix chain 'C' and resid 102 through 125 removed outlier: 4.080A pdb=" N LEU C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU C 107 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N SER C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ARG C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU C 115 " --> pdb=" O ARG C 111 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 157 removed outlier: 3.589A pdb=" N LEU C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 181 Processing helix chain 'C' and resid 194 through 222 Processing helix chain 'C' and resid 228 through 246 Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.727A pdb=" N ILE C 257 " --> pdb=" O GLN C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 275 No H-bonds generated for 'chain 'C' and resid 272 through 275' Processing helix chain 'C' and resid 281 through 293 Processing helix chain 'C' and resid 307 through 314 Processing helix chain 'C' and resid 368 through 372 removed outlier: 3.538A pdb=" N LEU C 371 " --> pdb=" O GLU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 401 Processing helix chain 'C' and resid 405 through 416 Processing helix chain 'D' and resid 15 through 35 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 44 through 62 removed outlier: 4.386A pdb=" N ILE D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 95 through 98 No H-bonds generated for 'chain 'D' and resid 95 through 98' Processing helix chain 'D' and resid 102 through 125 removed outlier: 4.081A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N SER D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ARG D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU D 112 " --> pdb=" O SER D 108 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU D 115 " --> pdb=" O ARG D 111 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 157 removed outlier: 3.589A pdb=" N LEU D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 181 Processing helix chain 'D' and resid 194 through 222 Processing helix chain 'D' and resid 228 through 246 Processing helix chain 'D' and resid 250 through 267 removed outlier: 3.727A pdb=" N ILE D 257 " --> pdb=" O GLN D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 275 No H-bonds generated for 'chain 'D' and resid 272 through 275' Processing helix chain 'D' and resid 281 through 293 Processing helix chain 'D' and resid 307 through 314 Processing helix chain 'D' and resid 368 through 372 removed outlier: 3.538A pdb=" N LEU D 371 " --> pdb=" O GLU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 401 Processing helix chain 'D' and resid 405 through 416 Processing sheet with id= A, first strand: chain 'A' and resid 318 through 320 Processing sheet with id= B, first strand: chain 'A' and resid 380 through 383 removed outlier: 3.610A pdb=" N ALA A 358 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 318 through 320 Processing sheet with id= D, first strand: chain 'B' and resid 380 through 383 removed outlier: 3.610A pdb=" N ALA B 358 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 318 through 320 Processing sheet with id= F, first strand: chain 'C' and resid 380 through 383 removed outlier: 3.610A pdb=" N ALA C 358 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 318 through 320 Processing sheet with id= H, first strand: chain 'D' and resid 380 through 383 removed outlier: 3.610A pdb=" N ALA D 358 " --> pdb=" O VAL D 348 " (cutoff:3.500A) 644 hydrogen bonds defined for protein. 1872 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.48 Time building geometry restraints manager: 5.69 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: 1992 1.31 - 1.43: 3463 1.43 - 1.56: 8473 1.56 - 1.68: 16 1.68 - 1.80: 48 Bond restraints: 13992 Sorted by residual: bond pdb=" C10 PGW D 515 " pdb=" C9 PGW D 515 " ideal model delta sigma weight residual 1.333 1.529 -0.196 2.00e-02 2.50e+03 9.63e+01 bond pdb=" C10 PGW A 514 " pdb=" C9 PGW A 514 " ideal model delta sigma weight residual 1.333 1.529 -0.196 2.00e-02 2.50e+03 9.58e+01 bond pdb=" C10 PGW B 514 " pdb=" C9 PGW B 514 " ideal model delta sigma weight residual 1.333 1.529 -0.196 2.00e-02 2.50e+03 9.58e+01 bond pdb=" C10 PGW C 514 " pdb=" C9 PGW C 514 " ideal model delta sigma weight residual 1.333 1.528 -0.195 2.00e-02 2.50e+03 9.54e+01 bond pdb=" C10 PGW B 509 " pdb=" C9 PGW B 509 " ideal model delta sigma weight residual 1.333 1.528 -0.195 2.00e-02 2.50e+03 9.52e+01 ... (remaining 13987 not shown) Histogram of bond angle deviations from ideal: 100.48 - 107.57: 593 107.57 - 114.66: 8532 114.66 - 121.75: 7115 121.75 - 128.83: 2420 128.83 - 135.92: 100 Bond angle restraints: 18760 Sorted by residual: angle pdb=" C06 PGW D 511 " pdb=" C10 PGW D 511 " pdb=" C9 PGW D 511 " ideal model delta sigma weight residual 126.92 107.33 19.59 3.00e+00 1.11e-01 4.27e+01 angle pdb=" C06 PGW A 510 " pdb=" C10 PGW A 510 " pdb=" C9 PGW A 510 " ideal model delta sigma weight residual 126.92 107.33 19.59 3.00e+00 1.11e-01 4.27e+01 angle pdb=" C06 PGW B 510 " pdb=" C10 PGW B 510 " pdb=" C9 PGW B 510 " ideal model delta sigma weight residual 126.92 107.33 19.59 3.00e+00 1.11e-01 4.27e+01 angle pdb=" C06 PGW C 510 " pdb=" C10 PGW C 510 " pdb=" C9 PGW C 510 " ideal model delta sigma weight residual 126.92 107.37 19.55 3.00e+00 1.11e-01 4.25e+01 angle pdb=" C06 PGW D 504 " pdb=" C10 PGW D 504 " pdb=" C9 PGW D 504 " ideal model delta sigma weight residual 126.92 108.41 18.51 3.00e+00 1.11e-01 3.81e+01 ... (remaining 18755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.70: 8272 33.70 - 67.40: 288 67.40 - 101.10: 20 101.10 - 134.80: 20 134.80 - 168.50: 12 Dihedral angle restraints: 8612 sinusoidal: 3896 harmonic: 4716 Sorted by residual: dihedral pdb=" C5' CMP B 501 " pdb=" O5' CMP B 501 " pdb=" P CMP B 501 " pdb=" O1P CMP B 501 " ideal model delta sinusoidal sigma weight residual 60.00 168.92 -108.92 1 2.00e+01 2.50e-03 3.18e+01 dihedral pdb=" C5' CMP A 501 " pdb=" O5' CMP A 501 " pdb=" P CMP A 501 " pdb=" O1P CMP A 501 " ideal model delta sinusoidal sigma weight residual 60.00 168.89 -108.89 1 2.00e+01 2.50e-03 3.18e+01 dihedral pdb=" C5' CMP D 502 " pdb=" O5' CMP D 502 " pdb=" P CMP D 502 " pdb=" O1P CMP D 502 " ideal model delta sinusoidal sigma weight residual 60.00 168.86 -108.86 1 2.00e+01 2.50e-03 3.18e+01 ... (remaining 8609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1408 0.041 - 0.081: 519 0.081 - 0.122: 205 0.122 - 0.162: 12 0.162 - 0.203: 4 Chirality restraints: 2148 Sorted by residual: chirality pdb=" C02 PGW C 502 " pdb=" C01 PGW C 502 " pdb=" C03 PGW C 502 " pdb=" O01 PGW C 502 " both_signs ideal model delta sigma weight residual False 2.36 2.56 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C02 PGW D 503 " pdb=" C01 PGW D 503 " pdb=" C03 PGW D 503 " pdb=" O01 PGW D 503 " both_signs ideal model delta sigma weight residual False 2.36 2.56 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C02 PGW B 502 " pdb=" C01 PGW B 502 " pdb=" C03 PGW B 502 " pdb=" O01 PGW B 502 " both_signs ideal model delta sigma weight residual False 2.36 2.56 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 2145 not shown) Planarity restraints: 2248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW A 503 " 0.109 2.00e-02 2.50e+03 3.57e-01 1.27e+03 pdb=" C10 PGW A 503 " 0.136 2.00e-02 2.50e+03 pdb=" C8 PGW A 503 " 0.351 2.00e-02 2.50e+03 pdb=" C9 PGW A 503 " -0.596 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW B 503 " 0.109 2.00e-02 2.50e+03 3.57e-01 1.27e+03 pdb=" C10 PGW B 503 " 0.136 2.00e-02 2.50e+03 pdb=" C8 PGW B 503 " 0.351 2.00e-02 2.50e+03 pdb=" C9 PGW B 503 " -0.596 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW D 504 " -0.112 2.00e-02 2.50e+03 3.57e-01 1.27e+03 pdb=" C10 PGW D 504 " -0.132 2.00e-02 2.50e+03 pdb=" C8 PGW D 504 " -0.352 2.00e-02 2.50e+03 pdb=" C9 PGW D 504 " 0.596 2.00e-02 2.50e+03 ... (remaining 2245 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2014 2.76 - 3.29: 12817 3.29 - 3.83: 21249 3.83 - 4.36: 26352 4.36 - 4.90: 44928 Nonbonded interactions: 107360 Sorted by model distance: nonbonded pdb=" OH TYR B 186 " pdb=" OG1 THR C 180 " model vdw 2.221 2.440 nonbonded pdb=" OG1 THR A 180 " pdb=" OH TYR D 186 " model vdw 2.228 2.440 nonbonded pdb=" OH TYR A 186 " pdb=" OG1 THR B 180 " model vdw 2.228 2.440 nonbonded pdb=" OH TYR C 186 " pdb=" OG1 THR D 180 " model vdw 2.249 2.440 nonbonded pdb=" NH2 ARG B 238 " pdb=" OE2 GLU C 278 " model vdw 2.267 2.520 ... (remaining 107355 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' and (resid 10 through 418 or (resid 503 and (name C06 or name C07 or \ name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or \ (resid 505 and (name C20 or name C21 or name C22 or name C23 or name C24 or name \ C25 or name C26 or name C27)) or (resid 506 and (name C15 or name C22 or name C \ 23 or name C24 or name C25 or name C26 or name C27)) or (resid 507 and (name C22 \ or name C23 or name C24 or name C25 or name C26 or name C27)) or resid 509 thro \ ugh 510 or (resid 512 and (name C15 or name C16 or name C17 or name C18 or name \ C25 or name C26 or name C27)) or (resid 513 and (name C15 or name C16 or name C1 \ 7 or name C18 or name C25 or name C26 or name C27 or name C28)))) selection = (chain 'B' and (resid 10 through 418 or (resid 503 and (name C06 or name C07 or \ name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or \ (resid 505 and (name C20 or name C21 or name C22 or name C23 or name C24 or name \ C25 or name C26 or name C27)) or (resid 506 and (name C15 or name C22 or name C \ 23 or name C24 or name C25 or name C26 or name C27)) or (resid 507 and (name C22 \ or name C23 or name C24 or name C25 or name C26 or name C27)) or resid 509 thro \ ugh 510 or (resid 512 and (name C15 or name C16 or name C17 or name C18 or name \ C25 or name C26 or name C27)) or (resid 513 and (name C15 or name C16 or name C1 \ 7 or name C18 or name C25 or name C26 or name C27 or name C28)))) selection = (chain 'C' and (resid 10 through 418 or (resid 503 and (name C06 or name C07 or \ name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or \ (resid 505 and (name C20 or name C21 or name C22 or name C23 or name C24 or name \ C25 or name C26 or name C27)) or (resid 506 and (name C15 or name C22 or name C \ 23 or name C24 or name C25 or name C26 or name C27)) or (resid 507 and (name C22 \ or name C23 or name C24 or name C25 or name C26 or name C27)) or resid 509 thro \ ugh 510 or (resid 512 and (name C15 or name C16 or name C17 or name C18 or name \ C25 or name C26 or name C27)) or (resid 513 and (name C15 or name C16 or name C1 \ 7 or name C18 or name C25 or name C26 or name C27 or name C28)))) selection = (chain 'D' and (resid 10 through 418 or (resid 503 and (name C06 or name C07 or \ name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or \ (resid 505 and (name C20 or name C21 or name C22 or name C23 or name C24 or name \ C25 or name C26 or name C27)) or (resid 506 and (name C15 or name C22 or name C \ 23 or name C24 or name C25 or name C26 or name C27)) or (resid 507 and (name C22 \ or name C23 or name C24 or name C25 or name C26 or name C27)) or resid 509 thro \ ugh 510 or (resid 512 and (name C15 or name C16 or name C17 or name C18 or name \ C25 or name C26 or name C27)) or resid 513)) } 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: 0.780 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: 3.210 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 37.670 Find NCS groups from input model: 0.870 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: 0.010 Load rotamer database and sin/cos tables:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 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 : 0.009 0.196 13992 Z= 0.574 Angle : 1.428 19.594 18760 Z= 0.569 Chirality : 0.047 0.203 2148 Planarity : 0.017 0.357 2248 Dihedral : 19.070 168.500 5564 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.58 % Allowed : 0.07 % Favored : 99.35 % 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: -0.72 (0.22), residues: 1588 helix: 0.10 (0.17), residues: 1004 sheet: -0.50 (0.56), residues: 88 loop : -1.48 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 264 HIS 0.002 0.001 HIS C 149 PHE 0.018 0.002 PHE C 64 TYR 0.008 0.001 TYR C 170 ARG 0.006 0.001 ARG B 111 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 180 time to evaluate : 1.424 Fit side-chains REVERT: A 330 ARG cc_start: 0.7096 (mtt90) cc_final: 0.6623 (mtm-85) REVERT: B 330 ARG cc_start: 0.7097 (mtt90) cc_final: 0.6593 (mtm-85) REVERT: C 330 ARG cc_start: 0.7058 (mtt90) cc_final: 0.6605 (mtm-85) REVERT: D 327 TYR cc_start: 0.7900 (m-10) cc_final: 0.7134 (m-80) REVERT: D 330 ARG cc_start: 0.7055 (mtt90) cc_final: 0.6630 (mtm-85) REVERT: D 403 ARG cc_start: 0.7457 (mtt180) cc_final: 0.7057 (mtt180) outliers start: 8 outliers final: 2 residues processed: 184 average time/residue: 1.2827 time to fit residues: 257.4187 Evaluate side-chains 147 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 145 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain B residue 276 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.5980 chunk 121 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 145 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7623 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13992 Z= 0.190 Angle : 0.659 8.489 18760 Z= 0.303 Chirality : 0.041 0.125 2148 Planarity : 0.006 0.082 2248 Dihedral : 18.112 162.471 2528 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.00 % Allowed : 10.54 % Favored : 85.47 % 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: 0.04 (0.23), residues: 1588 helix: 0.78 (0.18), residues: 1000 sheet: -0.27 (0.59), residues: 88 loop : -1.36 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 264 HIS 0.002 0.001 HIS A 232 PHE 0.012 0.001 PHE D 64 TYR 0.007 0.001 TYR A 170 ARG 0.003 0.000 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 146 time to evaluate : 1.375 Fit side-chains REVERT: A 203 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8104 (mp) REVERT: A 333 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: B 156 MET cc_start: 0.7966 (ttp) cc_final: 0.7753 (ttm) REVERT: B 203 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8102 (mp) REVERT: B 273 ARG cc_start: 0.7797 (ptt90) cc_final: 0.7595 (ptm-80) REVERT: C 156 MET cc_start: 0.7947 (ttp) cc_final: 0.7732 (ttm) REVERT: C 203 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8099 (mp) REVERT: C 273 ARG cc_start: 0.7769 (ptt90) cc_final: 0.7568 (ptm-80) REVERT: D 203 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8093 (mp) REVERT: D 333 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7362 (mp0) outliers start: 55 outliers final: 7 residues processed: 173 average time/residue: 1.4031 time to fit residues: 263.8397 Evaluate side-chains 148 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 135 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 333 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 8.9990 chunk 45 optimal weight: 0.4980 chunk 120 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.7659 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13992 Z= 0.260 Angle : 0.660 7.651 18760 Z= 0.307 Chirality : 0.042 0.127 2148 Planarity : 0.005 0.064 2248 Dihedral : 17.570 162.807 2524 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 5.60 % Allowed : 12.79 % Favored : 81.61 % 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: 0.54 (0.23), residues: 1588 helix: 1.17 (0.18), residues: 940 sheet: -0.07 (0.59), residues: 88 loop : -0.89 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 264 HIS 0.003 0.001 HIS B 149 PHE 0.007 0.001 PHE D 64 TYR 0.009 0.001 TYR A 170 ARG 0.002 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 145 time to evaluate : 1.292 Fit side-chains REVERT: A 330 ARG cc_start: 0.7067 (mtt90) cc_final: 0.6678 (ttm-80) REVERT: A 333 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: B 273 ARG cc_start: 0.7749 (ptt90) cc_final: 0.7508 (ptm-80) REVERT: B 330 ARG cc_start: 0.7112 (mtt90) cc_final: 0.6768 (ttm-80) REVERT: C 273 ARG cc_start: 0.7712 (ptt90) cc_final: 0.7471 (ptm-80) REVERT: D 330 ARG cc_start: 0.7119 (mtt90) cc_final: 0.6700 (mtm-85) REVERT: D 403 ARG cc_start: 0.7274 (mtt180) cc_final: 0.7062 (mtt180) outliers start: 77 outliers final: 35 residues processed: 194 average time/residue: 1.1255 time to fit residues: 240.7266 Evaluate side-chains 172 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 136 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 393 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.4980 chunk 109 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13992 Z= 0.199 Angle : 0.628 7.789 18760 Z= 0.290 Chirality : 0.041 0.166 2148 Planarity : 0.005 0.053 2248 Dihedral : 16.906 161.765 2524 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.87 % Allowed : 14.10 % Favored : 81.03 % 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 (0.23), residues: 1588 helix: 1.37 (0.18), residues: 940 sheet: 0.15 (0.61), residues: 88 loop : -0.89 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 264 HIS 0.002 0.001 HIS D 232 PHE 0.007 0.001 PHE B 40 TYR 0.009 0.001 TYR C 170 ARG 0.005 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 146 time to evaluate : 1.377 Fit side-chains REVERT: A 55 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7558 (tp) REVERT: A 77 LEU cc_start: 0.2981 (OUTLIER) cc_final: 0.2519 (tt) REVERT: A 203 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8084 (mp) REVERT: A 273 ARG cc_start: 0.7538 (ptm-80) cc_final: 0.7075 (mtm-85) REVERT: A 330 ARG cc_start: 0.7090 (mtt90) cc_final: 0.6696 (ttm-80) REVERT: A 333 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: B 77 LEU cc_start: 0.3088 (OUTLIER) cc_final: 0.2628 (tt) REVERT: B 203 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8085 (mp) REVERT: B 273 ARG cc_start: 0.7672 (ptt90) cc_final: 0.7105 (mtm-85) REVERT: B 330 ARG cc_start: 0.7127 (mtt90) cc_final: 0.6803 (ttm-80) REVERT: C 77 LEU cc_start: 0.3085 (OUTLIER) cc_final: 0.2626 (tt) REVERT: C 203 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8081 (mp) REVERT: C 273 ARG cc_start: 0.7652 (ptt90) cc_final: 0.7102 (mtm-85) REVERT: C 330 ARG cc_start: 0.7140 (mtt90) cc_final: 0.6722 (ttm-80) REVERT: D 77 LEU cc_start: 0.2891 (OUTLIER) cc_final: 0.2412 (tt) REVERT: D 203 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8088 (mp) REVERT: D 273 ARG cc_start: 0.7548 (ptm-80) cc_final: 0.7089 (mtm-85) REVERT: D 330 ARG cc_start: 0.7170 (mtt90) cc_final: 0.6852 (mtm-85) outliers start: 67 outliers final: 19 residues processed: 190 average time/residue: 1.1500 time to fit residues: 240.7977 Evaluate side-chains 166 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 393 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 0.9980 chunk 87 optimal weight: 0.4980 chunk 2 optimal weight: 0.1980 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 131 optimal weight: 0.0070 chunk 106 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 78 optimal weight: 0.4980 chunk 138 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN C 164 ASN D 164 ASN D 253 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13992 Z= 0.147 Angle : 0.597 7.808 18760 Z= 0.271 Chirality : 0.040 0.129 2148 Planarity : 0.004 0.047 2248 Dihedral : 15.962 161.182 2524 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.07 % Allowed : 16.35 % Favored : 79.58 % 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 (0.23), residues: 1588 helix: 1.46 (0.18), residues: 952 sheet: 0.43 (0.64), residues: 88 loop : -0.72 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 264 HIS 0.001 0.000 HIS A 232 PHE 0.008 0.001 PHE D 40 TYR 0.006 0.001 TYR A 170 ARG 0.001 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 157 time to evaluate : 1.492 Fit side-chains REVERT: A 44 LEU cc_start: 0.6129 (OUTLIER) cc_final: 0.5853 (mm) REVERT: A 77 LEU cc_start: 0.2960 (OUTLIER) cc_final: 0.2527 (tt) REVERT: A 203 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8174 (mp) REVERT: A 273 ARG cc_start: 0.7492 (ptm-80) cc_final: 0.7081 (mtm-85) REVERT: A 330 ARG cc_start: 0.7098 (mtt90) cc_final: 0.6710 (ttm-80) REVERT: A 333 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: B 44 LEU cc_start: 0.6107 (OUTLIER) cc_final: 0.5845 (mm) REVERT: B 77 LEU cc_start: 0.2961 (OUTLIER) cc_final: 0.2528 (tt) REVERT: B 203 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8172 (mp) REVERT: B 273 ARG cc_start: 0.7638 (ptt90) cc_final: 0.7105 (mtm-85) REVERT: B 330 ARG cc_start: 0.7124 (mtt90) cc_final: 0.6685 (ttm-80) REVERT: C 44 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.5851 (mm) REVERT: C 77 LEU cc_start: 0.2962 (OUTLIER) cc_final: 0.2528 (tt) REVERT: C 203 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8176 (mp) REVERT: C 273 ARG cc_start: 0.7630 (ptt90) cc_final: 0.7104 (mtm-85) REVERT: C 330 ARG cc_start: 0.7147 (mtt90) cc_final: 0.6845 (mtm-85) REVERT: D 44 LEU cc_start: 0.6116 (OUTLIER) cc_final: 0.5850 (mm) REVERT: D 77 LEU cc_start: 0.2869 (OUTLIER) cc_final: 0.2427 (tt) REVERT: D 203 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8176 (mp) REVERT: D 273 ARG cc_start: 0.7496 (ptm-80) cc_final: 0.7066 (mtm-85) REVERT: D 330 ARG cc_start: 0.7105 (mtt90) cc_final: 0.6766 (ttm-80) outliers start: 56 outliers final: 12 residues processed: 188 average time/residue: 1.1591 time to fit residues: 239.8773 Evaluate side-chains 172 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 253 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13992 Z= 0.258 Angle : 0.639 8.550 18760 Z= 0.296 Chirality : 0.043 0.127 2148 Planarity : 0.005 0.047 2248 Dihedral : 16.030 160.241 2524 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 4.36 % Allowed : 16.93 % Favored : 78.71 % 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: 0.87 (0.23), residues: 1588 helix: 1.41 (0.18), residues: 944 sheet: 0.24 (0.61), residues: 88 loop : -0.77 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 176 HIS 0.002 0.001 HIS D 149 PHE 0.006 0.001 PHE A 260 TYR 0.010 0.001 TYR D 170 ARG 0.005 0.000 ARG B 374 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 142 time to evaluate : 1.971 Fit side-chains REVERT: A 44 LEU cc_start: 0.6218 (OUTLIER) cc_final: 0.5944 (mm) REVERT: A 77 LEU cc_start: 0.2988 (OUTLIER) cc_final: 0.2574 (tt) REVERT: A 273 ARG cc_start: 0.7540 (ptm-80) cc_final: 0.7051 (mtm-85) REVERT: A 330 ARG cc_start: 0.7110 (mtt90) cc_final: 0.6684 (ttm-80) REVERT: A 333 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: B 44 LEU cc_start: 0.6264 (OUTLIER) cc_final: 0.5993 (mm) REVERT: B 77 LEU cc_start: 0.2990 (OUTLIER) cc_final: 0.2578 (tt) REVERT: B 273 ARG cc_start: 0.7649 (ptt90) cc_final: 0.7106 (mtm-85) REVERT: B 330 ARG cc_start: 0.7163 (mtt90) cc_final: 0.6777 (mtm-85) REVERT: B 333 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6863 (mp0) REVERT: C 44 LEU cc_start: 0.6215 (OUTLIER) cc_final: 0.5945 (mm) REVERT: C 77 LEU cc_start: 0.2983 (OUTLIER) cc_final: 0.2575 (tt) REVERT: C 273 ARG cc_start: 0.7614 (ptt90) cc_final: 0.7091 (mtm-85) REVERT: C 318 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7224 (tp30) REVERT: C 330 ARG cc_start: 0.7105 (mtt90) cc_final: 0.6760 (mtm-85) REVERT: D 44 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5944 (mm) REVERT: D 77 LEU cc_start: 0.2749 (OUTLIER) cc_final: 0.2350 (tt) REVERT: D 273 ARG cc_start: 0.7549 (ptm-80) cc_final: 0.7090 (mtm-85) REVERT: D 330 ARG cc_start: 0.7112 (mtt90) cc_final: 0.6604 (ttm-80) outliers start: 60 outliers final: 22 residues processed: 183 average time/residue: 1.1360 time to fit residues: 229.4519 Evaluate side-chains 175 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 142 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 393 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.7980 chunk 17 optimal weight: 0.1980 chunk 88 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 154 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7625 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13992 Z= 0.191 Angle : 0.620 11.637 18760 Z= 0.284 Chirality : 0.041 0.122 2148 Planarity : 0.004 0.046 2248 Dihedral : 15.620 160.441 2524 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 4.80 % Allowed : 17.95 % Favored : 77.25 % 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: 0.88 (0.23), residues: 1588 helix: 1.45 (0.18), residues: 948 sheet: 0.28 (0.61), residues: 88 loop : -0.86 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 264 HIS 0.001 0.001 HIS A 149 PHE 0.007 0.001 PHE D 40 TYR 0.009 0.001 TYR D 170 ARG 0.001 0.000 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 139 time to evaluate : 1.319 Fit side-chains REVERT: A 44 LEU cc_start: 0.6147 (OUTLIER) cc_final: 0.5927 (mm) REVERT: A 55 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7376 (tp) REVERT: A 77 LEU cc_start: 0.2797 (OUTLIER) cc_final: 0.2387 (tt) REVERT: A 203 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8093 (mp) REVERT: A 273 ARG cc_start: 0.7501 (ptm-80) cc_final: 0.7046 (mtm-85) REVERT: A 313 ILE cc_start: 0.8126 (pt) cc_final: 0.7796 (mm) REVERT: A 330 ARG cc_start: 0.7051 (mtt90) cc_final: 0.6625 (ttm-80) REVERT: A 333 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: B 55 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7376 (tp) REVERT: B 77 LEU cc_start: 0.2801 (OUTLIER) cc_final: 0.2390 (tt) REVERT: B 203 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8087 (mp) REVERT: B 273 ARG cc_start: 0.7602 (ptt90) cc_final: 0.7062 (mtm-85) REVERT: B 313 ILE cc_start: 0.8161 (pt) cc_final: 0.7808 (mm) REVERT: B 330 ARG cc_start: 0.7056 (mtt90) cc_final: 0.6782 (ttm-80) REVERT: C 44 LEU cc_start: 0.6143 (OUTLIER) cc_final: 0.5921 (mm) REVERT: C 55 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7374 (tp) REVERT: C 77 LEU cc_start: 0.2797 (OUTLIER) cc_final: 0.2379 (tt) REVERT: C 203 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8091 (mp) REVERT: C 273 ARG cc_start: 0.7600 (ptt90) cc_final: 0.7088 (mtm-85) REVERT: C 313 ILE cc_start: 0.8133 (pt) cc_final: 0.7788 (mm) REVERT: C 318 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7224 (tp30) REVERT: C 330 ARG cc_start: 0.7053 (mtt90) cc_final: 0.6705 (mtm-85) REVERT: D 44 LEU cc_start: 0.6139 (OUTLIER) cc_final: 0.5922 (mm) REVERT: D 55 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7370 (tp) REVERT: D 77 LEU cc_start: 0.2808 (OUTLIER) cc_final: 0.2412 (tt) REVERT: D 203 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8092 (mp) REVERT: D 273 ARG cc_start: 0.7533 (ptm-80) cc_final: 0.7087 (mtm-85) REVERT: D 313 ILE cc_start: 0.8151 (pt) cc_final: 0.7815 (mm) REVERT: D 330 ARG cc_start: 0.7156 (mtt90) cc_final: 0.6896 (ttm-80) outliers start: 66 outliers final: 19 residues processed: 186 average time/residue: 1.1241 time to fit residues: 230.6838 Evaluate side-chains 175 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 139 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 393 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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: 0.7653 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13992 Z= 0.257 Angle : 0.645 11.076 18760 Z= 0.297 Chirality : 0.042 0.126 2148 Planarity : 0.004 0.046 2248 Dihedral : 15.913 160.617 2524 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 4.58 % Allowed : 18.24 % Favored : 77.18 % 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: 0.78 (0.23), residues: 1588 helix: 1.39 (0.18), residues: 944 sheet: 0.13 (0.60), residues: 88 loop : -0.91 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 264 HIS 0.002 0.001 HIS A 149 PHE 0.005 0.001 PHE C 260 TYR 0.010 0.001 TYR B 170 ARG 0.003 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 144 time to evaluate : 1.272 Fit side-chains REVERT: A 44 LEU cc_start: 0.6214 (OUTLIER) cc_final: 0.5951 (mm) REVERT: A 55 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7383 (tp) REVERT: A 77 LEU cc_start: 0.2767 (OUTLIER) cc_final: 0.2379 (tt) REVERT: A 273 ARG cc_start: 0.7526 (ptm-80) cc_final: 0.7050 (mtm-85) REVERT: A 330 ARG cc_start: 0.7035 (mtt90) cc_final: 0.6598 (ttm-80) REVERT: A 333 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: B 55 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7382 (tp) REVERT: B 77 LEU cc_start: 0.2851 (OUTLIER) cc_final: 0.2460 (tt) REVERT: B 330 ARG cc_start: 0.7044 (mtt90) cc_final: 0.6701 (mtm-85) REVERT: C 44 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5946 (mm) REVERT: C 55 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7378 (tp) REVERT: C 77 LEU cc_start: 0.2751 (OUTLIER) cc_final: 0.2361 (tt) REVERT: C 318 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7235 (tp30) REVERT: C 330 ARG cc_start: 0.7122 (mtt90) cc_final: 0.6719 (mtm-85) REVERT: D 44 LEU cc_start: 0.6200 (OUTLIER) cc_final: 0.5948 (mm) REVERT: D 55 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7378 (tp) REVERT: D 77 LEU cc_start: 0.2690 (OUTLIER) cc_final: 0.2321 (tt) REVERT: D 273 ARG cc_start: 0.7527 (ptm-80) cc_final: 0.7068 (mtm-85) REVERT: D 330 ARG cc_start: 0.7103 (mtt90) cc_final: 0.6757 (mtm-85) outliers start: 63 outliers final: 27 residues processed: 191 average time/residue: 1.2160 time to fit residues: 254.1319 Evaluate side-chains 184 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 144 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 393 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 86 optimal weight: 0.0030 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 129 optimal weight: 0.0000 chunk 135 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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: 0.7600 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13992 Z= 0.151 Angle : 0.593 10.829 18760 Z= 0.270 Chirality : 0.040 0.121 2148 Planarity : 0.004 0.046 2248 Dihedral : 15.290 161.408 2524 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.42 % Allowed : 19.62 % Favored : 76.96 % 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: 0.99 (0.23), residues: 1588 helix: 1.52 (0.18), residues: 956 sheet: 0.33 (0.60), residues: 88 loop : -0.81 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 264 HIS 0.001 0.000 HIS D 232 PHE 0.008 0.001 PHE A 40 TYR 0.006 0.001 TYR B 170 ARG 0.001 0.000 ARG D 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 149 time to evaluate : 1.453 Fit side-chains REVERT: A 77 LEU cc_start: 0.2715 (OUTLIER) cc_final: 0.2351 (tt) REVERT: A 203 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8181 (mp) REVERT: A 273 ARG cc_start: 0.7493 (ptm-80) cc_final: 0.7061 (mtm-85) REVERT: A 313 ILE cc_start: 0.8057 (pt) cc_final: 0.7820 (mm) REVERT: A 330 ARG cc_start: 0.7068 (mtt90) cc_final: 0.6654 (ttm-80) REVERT: A 333 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6808 (mp0) REVERT: B 77 LEU cc_start: 0.2715 (OUTLIER) cc_final: 0.2356 (tt) REVERT: B 203 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8176 (mp) REVERT: B 273 ARG cc_start: 0.7454 (ptt90) cc_final: 0.6998 (mtm-85) REVERT: B 313 ILE cc_start: 0.8046 (pt) cc_final: 0.7816 (mm) REVERT: B 330 ARG cc_start: 0.7043 (mtt90) cc_final: 0.6651 (mtm-85) REVERT: C 77 LEU cc_start: 0.2691 (OUTLIER) cc_final: 0.2342 (tt) REVERT: C 203 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8179 (mp) REVERT: C 273 ARG cc_start: 0.7376 (ptt90) cc_final: 0.6916 (mtm-85) REVERT: C 313 ILE cc_start: 0.8064 (pt) cc_final: 0.7834 (mm) REVERT: C 318 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7197 (tp30) REVERT: C 330 ARG cc_start: 0.7071 (mtt90) cc_final: 0.6672 (mtm-85) REVERT: D 77 LEU cc_start: 0.2651 (OUTLIER) cc_final: 0.2299 (tt) REVERT: D 203 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8178 (mp) REVERT: D 273 ARG cc_start: 0.7488 (ptm-80) cc_final: 0.7061 (mtm-85) REVERT: D 330 ARG cc_start: 0.7083 (mtt90) cc_final: 0.6546 (mtm-85) outliers start: 47 outliers final: 17 residues processed: 180 average time/residue: 1.2482 time to fit residues: 246.0502 Evaluate side-chains 171 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 144 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 393 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.4948 > 50: distance: 16 - 22: 29.622 distance: 22 - 23: 41.769 distance: 23 - 24: 39.902 distance: 23 - 26: 19.593 distance: 26 - 27: 19.358 distance: 27 - 28: 26.164 distance: 27 - 29: 30.037 distance: 30 - 31: 39.567 distance: 32 - 35: 52.234 distance: 35 - 36: 41.602 distance: 35 - 41: 7.109 distance: 36 - 37: 39.912 distance: 36 - 39: 41.216 distance: 37 - 42: 46.115 distance: 39 - 40: 40.595 distance: 40 - 41: 39.714 distance: 42 - 43: 46.709 distance: 43 - 44: 46.822 distance: 43 - 46: 39.576 distance: 44 - 45: 43.467 distance: 44 - 48: 16.551 distance: 49 - 50: 39.710 distance: 49 - 52: 27.370 distance: 50 - 51: 40.337 distance: 52 - 53: 19.307 distance: 53 - 54: 43.249 distance: 55 - 56: 15.395 distance: 56 - 57: 41.816 distance: 56 - 58: 47.695 distance: 60 - 61: 41.903 distance: 60 - 63: 40.412 distance: 61 - 62: 27.688 distance: 61 - 67: 62.362 distance: 62 - 90: 69.501 distance: 63 - 64: 36.330 distance: 64 - 65: 41.220 distance: 64 - 66: 31.015 distance: 67 - 73: 38.899 distance: 68 - 69: 16.266 distance: 68 - 71: 46.912 distance: 69 - 70: 25.269 distance: 69 - 74: 25.842 distance: 70 - 98: 31.506 distance: 71 - 72: 48.032 distance: 72 - 73: 44.109 distance: 74 - 75: 29.672 distance: 75 - 76: 10.107 distance: 75 - 78: 11.627 distance: 77 - 103: 33.015 distance: 78 - 79: 49.670 distance: 79 - 80: 17.259 distance: 79 - 81: 45.526 distance: 82 - 83: 38.667 distance: 83 - 84: 38.850 distance: 83 - 86: 40.877 distance: 84 - 85: 37.440 distance: 84 - 90: 43.150 distance: 87 - 88: 38.536 distance: 91 - 92: 39.517 distance: 92 - 93: 6.075 distance: 92 - 98: 30.768 distance: 94 - 95: 42.916 distance: 95 - 96: 14.647 distance: 95 - 97: 14.046