Starting phenix.real_space_refine on Mon Apr 8 15:34:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsh_24670/04_2024/7rsh_24670_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsh_24670/04_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_24670/04_2024/7rsh_24670.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsh_24670/04_2024/7rsh_24670.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsh_24670/04_2024/7rsh_24670_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsh_24670/04_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-5288/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: 7.20, per 1000 atoms: 0.52 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: 5.85 Conformation dependent library (CDL) restraints added in 2.2 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: 2.49 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: 3.90 Time building geometry restraints manager: 6.32 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: 1.190 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: 3.630 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 37.630 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.090 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:16.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.090 ------------------------------------------------------------------------------- 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 : 1.420 19.594 18760 Z= 0.567 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 : 1.404 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: 1.3854 time to fit residues: 278.3930 Evaluate side-chains 147 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 145 time to evaluate : 2.304 ------------------------------------------------------------------------------- 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: 0.7626 moved from start: 0.0968 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= 0.190 Angle : 0.665 9.332 18760 Z= 0.304 Chirality : 0.041 0.128 2148 Planarity : 0.006 0.082 2248 Dihedral : 18.570 162.211 2528 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.00 % Allowed : 10.76 % Favored : 85.25 % 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: 0.03 (0.23), residues: 1588 helix: 0.77 (0.18), residues: 1000 sheet: -0.26 (0.59), residues: 88 loop : -1.37 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 264 HIS 0.003 0.001 HIS A 232 PHE 0.012 0.001 PHE D 64 TYR 0.008 0.001 TYR B 170 ARG 0.003 0.000 ARG D 120 *********************** 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 200 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 145 time to evaluate : 1.379 Fit side-chains REVERT: A 203 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8095 (mp) REVERT: A 330 ARG cc_start: 0.7203 (mtt90) cc_final: 0.6775 (ttm-80) REVERT: A 333 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: B 203 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8091 (mp) REVERT: B 273 ARG cc_start: 0.7798 (ptt90) cc_final: 0.7595 (ptm-80) REVERT: C 203 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8094 (mp) REVERT: C 273 ARG cc_start: 0.7760 (ptt90) cc_final: 0.7558 (ptm-80) REVERT: D 203 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8080 (mp) REVERT: D 273 ARG cc_start: 0.7781 (ptt90) cc_final: 0.7576 (ptm-80) REVERT: D 333 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7341 (mp0) outliers start: 55 outliers final: 9 residues processed: 172 average time/residue: 1.4713 time to fit residues: 274.5634 Evaluate side-chains 147 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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 84 ASP 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 84 ASP 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: 0.9980 chunk 120 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.1266 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= 0.241 Angle : 0.651 8.008 18760 Z= 0.303 Chirality : 0.042 0.125 2148 Planarity : 0.005 0.064 2248 Dihedral : 17.428 162.596 2524 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 5.74 % Allowed : 12.57 % Favored : 81.69 % 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: 0.59 (0.23), residues: 1588 helix: 1.17 (0.18), residues: 944 sheet: -0.09 (0.59), residues: 88 loop : -0.79 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 264 HIS 0.003 0.001 HIS C 232 PHE 0.007 0.001 PHE D 64 TYR 0.010 0.001 TYR C 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 226 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 147 time to evaluate : 1.573 Fit side-chains REVERT: A 273 ARG cc_start: 0.7565 (ptm-80) cc_final: 0.7102 (mtm-85) REVERT: A 330 ARG cc_start: 0.7118 (mtt90) cc_final: 0.6684 (ttm-80) REVERT: A 333 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: B 273 ARG cc_start: 0.7764 (ptt90) cc_final: 0.7522 (ptm-80) REVERT: B 330 ARG cc_start: 0.7100 (mtt90) cc_final: 0.6770 (ttm-80) REVERT: C 273 ARG cc_start: 0.7742 (ptt90) cc_final: 0.7509 (ptm-80) REVERT: C 330 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6949 (mtm-85) REVERT: D 273 ARG cc_start: 0.7795 (ptt90) cc_final: 0.7562 (ptm-80) REVERT: D 330 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.5683 (mtt90) REVERT: D 333 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7257 (mp0) outliers start: 79 outliers final: 35 residues processed: 195 average time/residue: 1.2662 time to fit residues: 270.7495 Evaluate side-chains 176 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 137 time to evaluate : 1.449 ------------------------------------------------------------------------------- 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 164 ASN Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 224 LYS 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 330 ARG 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 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 330 ARG Chi-restraints excluded: chain D residue 333 GLU 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: 0.6980 chunk 109 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 146 optimal weight: 0.7980 chunk 154 optimal weight: 0.0030 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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: 0.7620 moved from start: 0.1522 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= 0.176 Angle : 0.618 7.859 18760 Z= 0.285 Chirality : 0.041 0.168 2148 Planarity : 0.005 0.053 2248 Dihedral : 16.650 161.649 2524 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 4.80 % Allowed : 14.17 % 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: 0.48 (0.23), residues: 1588 helix: 1.13 (0.18), residues: 988 sheet: 0.16 (0.61), residues: 88 loop : -1.20 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 264 HIS 0.002 0.001 HIS A 232 PHE 0.008 0.001 PHE A 40 TYR 0.008 0.001 TYR B 170 ARG 0.004 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 217 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 151 time to evaluate : 1.417 Fit side-chains REVERT: A 77 LEU cc_start: 0.3081 (OUTLIER) cc_final: 0.2625 (tt) REVERT: A 203 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8119 (mp) REVERT: A 273 ARG cc_start: 0.7538 (ptm-80) cc_final: 0.7081 (mtm-85) REVERT: A 330 ARG cc_start: 0.7124 (mtt90) cc_final: 0.6669 (ttm-80) REVERT: A 333 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: B 77 LEU cc_start: 0.3089 (OUTLIER) cc_final: 0.2628 (tt) REVERT: B 203 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8117 (mp) REVERT: B 273 ARG cc_start: 0.7674 (ptt90) cc_final: 0.7112 (mtm-85) REVERT: B 330 ARG cc_start: 0.7125 (mtt90) cc_final: 0.6699 (ttm-80) REVERT: C 77 LEU cc_start: 0.3081 (OUTLIER) cc_final: 0.2619 (tt) REVERT: C 203 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8114 (mp) REVERT: C 273 ARG cc_start: 0.7654 (ptt90) cc_final: 0.7094 (mtm-85) REVERT: D 77 LEU cc_start: 0.2931 (OUTLIER) cc_final: 0.2460 (tt) REVERT: D 203 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8123 (mp) REVERT: D 273 ARG cc_start: 0.7670 (ptt90) cc_final: 0.7109 (mtm-85) REVERT: D 330 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.6846 (mtm-85) outliers start: 66 outliers final: 15 residues processed: 188 average time/residue: 1.2387 time to fit residues: 255.9662 Evaluate side-chains 167 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 1.600 ------------------------------------------------------------------------------- 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 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 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 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 244 SER Chi-restraints excluded: chain C residue 346 VAL 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 330 ARG 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: 2.9990 chunk 87 optimal weight: 0.5980 chunk 2 optimal weight: 0.0970 chunk 115 optimal weight: 7.9990 chunk 63 optimal weight: 0.2980 chunk 131 optimal weight: 0.2980 chunk 106 optimal weight: 0.2980 chunk 0 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN B 164 ASN C 164 ASN D 164 ASN D 253 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1825 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= 0.145 Angle : 0.597 7.967 18760 Z= 0.271 Chirality : 0.040 0.131 2148 Planarity : 0.004 0.047 2248 Dihedral : 15.751 160.891 2524 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.22 % Allowed : 16.13 % Favored : 79.65 % 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: 0.67 (0.23), residues: 1588 helix: 1.22 (0.18), residues: 996 sheet: 0.41 (0.64), residues: 88 loop : -1.08 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 264 HIS 0.001 0.000 HIS B 232 PHE 0.008 0.001 PHE D 40 TYR 0.006 0.001 TYR A 170 ARG 0.003 0.000 ARG B 233 *********************** 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: 58 poor density : 155 time to evaluate : 1.390 Fit side-chains REVERT: A 44 LEU cc_start: 0.6006 (OUTLIER) cc_final: 0.5742 (mm) REVERT: A 77 LEU cc_start: 0.2954 (OUTLIER) cc_final: 0.2525 (tt) REVERT: A 203 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8152 (mp) REVERT: A 273 ARG cc_start: 0.7492 (ptm-80) cc_final: 0.7069 (mtm-85) REVERT: A 330 ARG cc_start: 0.7111 (mtt90) cc_final: 0.6699 (ttm-80) REVERT: A 333 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: B 44 LEU cc_start: 0.6093 (OUTLIER) cc_final: 0.5843 (mm) REVERT: B 77 LEU cc_start: 0.2967 (OUTLIER) cc_final: 0.2531 (tt) REVERT: B 203 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8149 (mp) REVERT: B 273 ARG cc_start: 0.7655 (ptt90) cc_final: 0.7117 (mtm-85) REVERT: B 330 ARG cc_start: 0.7137 (mtt90) cc_final: 0.6843 (mtm-85) REVERT: C 44 LEU cc_start: 0.6086 (OUTLIER) cc_final: 0.5845 (mm) REVERT: C 77 LEU cc_start: 0.2958 (OUTLIER) cc_final: 0.2524 (tt) REVERT: C 203 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8150 (mp) REVERT: C 273 ARG cc_start: 0.7631 (ptt90) cc_final: 0.7107 (mtm-85) REVERT: C 330 ARG cc_start: 0.7131 (mtt90) cc_final: 0.6720 (ttm-80) REVERT: D 44 LEU cc_start: 0.5992 (OUTLIER) cc_final: 0.5738 (mm) REVERT: D 77 LEU cc_start: 0.3079 (OUTLIER) cc_final: 0.2664 (tt) REVERT: D 203 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8171 (mp) REVERT: D 273 ARG cc_start: 0.7637 (ptt90) cc_final: 0.7111 (mtm-85) REVERT: D 330 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6679 (mtm-85) outliers start: 58 outliers final: 12 residues processed: 183 average time/residue: 1.2262 time to fit residues: 246.5573 Evaluate side-chains 172 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 1.415 ------------------------------------------------------------------------------- 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 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 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 77 LEU Chi-restraints excluded: chain C residue 203 ILE 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 203 ILE Chi-restraints excluded: chain D residue 330 ARG 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: 2.9990 chunk 139 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 154 optimal weight: 0.2980 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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: 0.7630 moved from start: 0.1787 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= 0.212 Angle : 0.623 8.999 18760 Z= 0.287 Chirality : 0.041 0.125 2148 Planarity : 0.004 0.045 2248 Dihedral : 15.788 159.767 2524 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 4.29 % Allowed : 16.64 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.23), residues: 1588 helix: 1.47 (0.18), residues: 948 sheet: 0.28 (0.61), residues: 88 loop : -0.61 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 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 B 170 ARG 0.002 0.000 ARG C 356 *********************** 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: 59 poor density : 143 time to evaluate : 1.414 Fit side-chains REVERT: A 44 LEU cc_start: 0.6151 (OUTLIER) cc_final: 0.5946 (mm) REVERT: A 77 LEU cc_start: 0.2975 (OUTLIER) cc_final: 0.2564 (tt) REVERT: A 203 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8011 (mp) REVERT: A 273 ARG cc_start: 0.7527 (ptm-80) cc_final: 0.7073 (mtm-85) REVERT: A 313 ILE cc_start: 0.8202 (pt) cc_final: 0.7815 (mm) REVERT: A 330 ARG cc_start: 0.7118 (mtt90) cc_final: 0.6704 (ttm-80) REVERT: A 333 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: B 55 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7371 (tp) REVERT: B 77 LEU cc_start: 0.2984 (OUTLIER) cc_final: 0.2568 (tt) REVERT: B 203 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8012 (mp) REVERT: B 273 ARG cc_start: 0.7632 (ptt90) cc_final: 0.7099 (mtm-85) REVERT: B 313 ILE cc_start: 0.8175 (pt) cc_final: 0.7747 (mm) REVERT: B 330 ARG cc_start: 0.7079 (mtt90) cc_final: 0.6727 (ttm-80) REVERT: C 55 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7366 (tp) REVERT: C 77 LEU cc_start: 0.2976 (OUTLIER) cc_final: 0.2563 (tt) REVERT: C 203 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8011 (mp) REVERT: C 273 ARG cc_start: 0.7591 (ptt90) cc_final: 0.7077 (mtm-85) REVERT: C 313 ILE cc_start: 0.8215 (pt) cc_final: 0.7809 (mm) REVERT: C 330 ARG cc_start: 0.7207 (mtt90) cc_final: 0.6893 (ttm-80) REVERT: D 44 LEU cc_start: 0.6142 (OUTLIER) cc_final: 0.5915 (mm) REVERT: D 77 LEU cc_start: 0.2858 (OUTLIER) cc_final: 0.2457 (tt) REVERT: D 203 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8011 (mp) REVERT: D 273 ARG cc_start: 0.7626 (ptt90) cc_final: 0.7093 (mtm-85) REVERT: D 313 ILE cc_start: 0.8184 (pt) cc_final: 0.7837 (mm) REVERT: D 333 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7245 (mp0) outliers start: 59 outliers final: 19 residues processed: 183 average time/residue: 1.2143 time to fit residues: 245.1576 Evaluate side-chains 175 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 143 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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 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 224 LYS 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 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 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: 0.9990 chunk 17 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.7639 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13992 Z= 0.233 Angle : 0.632 8.864 18760 Z= 0.292 Chirality : 0.042 0.126 2148 Planarity : 0.004 0.046 2248 Dihedral : 15.588 159.705 2524 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 4.51 % Allowed : 17.81 % Favored : 77.69 % 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: 1.44 (0.18), residues: 944 sheet: 0.28 (0.61), residues: 88 loop : -0.83 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 264 HIS 0.002 0.001 HIS A 149 PHE 0.005 0.001 PHE D 40 TYR 0.010 0.001 TYR A 170 ARG 0.002 0.000 ARG D 235 *********************** 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: 62 poor density : 143 time to evaluate : 1.509 Fit side-chains REVERT: A 44 LEU cc_start: 0.6157 (OUTLIER) cc_final: 0.5935 (mm) REVERT: A 77 LEU cc_start: 0.2771 (OUTLIER) cc_final: 0.2358 (tt) REVERT: A 203 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8065 (mp) REVERT: A 273 ARG cc_start: 0.7532 (ptm-80) cc_final: 0.7062 (mtm-85) REVERT: A 330 ARG cc_start: 0.7137 (mtt90) cc_final: 0.6693 (ttm-80) REVERT: A 333 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: B 55 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7371 (tp) REVERT: B 77 LEU cc_start: 0.2783 (OUTLIER) cc_final: 0.2363 (tt) REVERT: B 203 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8064 (mp) REVERT: B 273 ARG cc_start: 0.7589 (ptt90) cc_final: 0.7039 (mtm-85) REVERT: B 330 ARG cc_start: 0.7046 (mtt90) cc_final: 0.6717 (mtm-85) REVERT: C 55 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7368 (tp) REVERT: C 77 LEU cc_start: 0.2776 (OUTLIER) cc_final: 0.2355 (tt) REVERT: C 203 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8066 (mp) REVERT: C 273 ARG cc_start: 0.7593 (ptt90) cc_final: 0.7063 (mtm-85) REVERT: C 330 ARG cc_start: 0.7131 (mtt90) cc_final: 0.6760 (ttm-80) REVERT: D 44 LEU cc_start: 0.6149 (OUTLIER) cc_final: 0.5931 (mm) REVERT: D 55 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7365 (tp) REVERT: D 77 LEU cc_start: 0.2693 (OUTLIER) cc_final: 0.2302 (tt) REVERT: D 203 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8067 (mp) REVERT: D 273 ARG cc_start: 0.7617 (ptt90) cc_final: 0.7084 (mtm-85) REVERT: D 313 ILE cc_start: 0.8223 (pt) cc_final: 0.7815 (mm) outliers start: 62 outliers final: 21 residues processed: 184 average time/residue: 1.1931 time to fit residues: 241.8926 Evaluate side-chains 176 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 141 time to evaluate : 1.400 ------------------------------------------------------------------------------- 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 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 224 LYS Chi-restraints excluded: chain B residue 337 ASP 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 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 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: 0.8980 chunk 46 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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: 0.7650 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13992 Z= 0.252 Angle : 0.642 10.131 18760 Z= 0.295 Chirality : 0.042 0.125 2148 Planarity : 0.004 0.046 2248 Dihedral : 15.753 159.325 2524 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 4.36 % Allowed : 17.95 % Favored : 77.69 % 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: 0.86 (0.23), residues: 1588 helix: 1.44 (0.18), residues: 944 sheet: 0.24 (0.60), residues: 88 loop : -0.84 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 264 HIS 0.002 0.001 HIS C 149 PHE 0.005 0.001 PHE C 260 TYR 0.010 0.001 TYR D 170 ARG 0.002 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 204 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 144 time to evaluate : 1.445 Fit side-chains REVERT: A 44 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.5956 (mm) REVERT: A 55 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7369 (tp) REVERT: A 77 LEU cc_start: 0.2745 (OUTLIER) cc_final: 0.2359 (tt) REVERT: A 273 ARG cc_start: 0.7529 (ptm-80) cc_final: 0.7060 (mtm-85) REVERT: A 318 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7223 (tp30) REVERT: A 330 ARG cc_start: 0.7147 (mtt90) cc_final: 0.6696 (mtm-85) REVERT: A 333 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: B 77 LEU cc_start: 0.2759 (OUTLIER) cc_final: 0.2364 (tt) REVERT: B 318 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7233 (tp30) REVERT: B 330 ARG cc_start: 0.7097 (mtt90) cc_final: 0.6723 (mtm-85) REVERT: C 77 LEU cc_start: 0.2754 (OUTLIER) cc_final: 0.2362 (tt) REVERT: C 273 ARG cc_start: 0.7579 (ptt90) cc_final: 0.7057 (mtm-85) REVERT: C 318 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7211 (tp30) REVERT: C 330 ARG cc_start: 0.7072 (mtt90) cc_final: 0.6629 (ttm-80) REVERT: D 44 LEU cc_start: 0.6236 (OUTLIER) cc_final: 0.5957 (mm) REVERT: D 55 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7368 (tp) REVERT: D 77 LEU cc_start: 0.2686 (OUTLIER) cc_final: 0.2319 (tt) REVERT: D 333 GLU cc_start: 0.7554 (mp0) cc_final: 0.6937 (mp0) outliers start: 60 outliers final: 25 residues processed: 189 average time/residue: 1.2946 time to fit residues: 268.4152 Evaluate side-chains 182 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 145 time to evaluate : 1.429 ------------------------------------------------------------------------------- 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 318 GLU 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 203 ILE Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 337 ASP 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.7980 chunk 147 optimal weight: 0.4980 chunk 134 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 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: 0.7623 moved from start: 0.1939 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= 0.187 Angle : 0.599 9.409 18760 Z= 0.276 Chirality : 0.041 0.122 2148 Planarity : 0.004 0.045 2248 Dihedral : 15.425 159.533 2524 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.49 % Allowed : 19.11 % Favored : 77.40 % 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: 1.00 (0.23), residues: 1588 helix: 1.52 (0.18), residues: 948 sheet: 0.30 (0.60), residues: 88 loop : -0.76 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 264 HIS 0.002 0.001 HIS A 149 PHE 0.007 0.001 PHE D 40 TYR 0.008 0.001 TYR A 170 ARG 0.001 0.000 ARG C 356 *********************** 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 195 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 147 time to evaluate : 1.488 Fit side-chains REVERT: A 44 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5929 (mm) REVERT: A 77 LEU cc_start: 0.2699 (OUTLIER) cc_final: 0.2334 (tt) REVERT: A 203 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8110 (mp) REVERT: A 273 ARG cc_start: 0.7496 (ptm-80) cc_final: 0.7032 (mtm-85) REVERT: A 313 ILE cc_start: 0.8178 (pt) cc_final: 0.7826 (mm) REVERT: A 330 ARG cc_start: 0.7123 (mtt90) cc_final: 0.6684 (mtm-85) REVERT: A 333 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7070 (mp0) REVERT: B 77 LEU cc_start: 0.2710 (OUTLIER) cc_final: 0.2342 (tt) REVERT: B 203 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8108 (mp) REVERT: B 273 ARG cc_start: 0.7467 (ptt90) cc_final: 0.6996 (mtm-85) REVERT: B 313 ILE cc_start: 0.8199 (pt) cc_final: 0.7823 (mm) REVERT: B 330 ARG cc_start: 0.7069 (mtt90) cc_final: 0.6559 (mtm-85) REVERT: C 77 LEU cc_start: 0.2706 (OUTLIER) cc_final: 0.2343 (tt) REVERT: C 203 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8112 (mp) REVERT: C 273 ARG cc_start: 0.7561 (ptt90) cc_final: 0.7050 (mtm-85) REVERT: C 313 ILE cc_start: 0.8180 (pt) cc_final: 0.7815 (mm) REVERT: D 44 LEU cc_start: 0.6157 (OUTLIER) cc_final: 0.5925 (mm) REVERT: D 77 LEU cc_start: 0.2658 (OUTLIER) cc_final: 0.2303 (tt) REVERT: D 203 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8114 (mp) REVERT: D 273 ARG cc_start: 0.7475 (ptt90) cc_final: 0.7001 (mtm-85) REVERT: D 313 ILE cc_start: 0.8162 (pt) cc_final: 0.7840 (mm) REVERT: D 330 ARG cc_start: 0.7048 (mtt90) cc_final: 0.6602 (ttm-80) REVERT: D 333 GLU cc_start: 0.7390 (mp0) cc_final: 0.6688 (mp0) outliers start: 48 outliers final: 20 residues processed: 181 average time/residue: 1.2397 time to fit residues: 246.5872 Evaluate side-chains 175 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 144 time to evaluate : 1.543 ------------------------------------------------------------------------------- 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 77 LEU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 337 ASP 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.2980 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 126 optimal weight: 0.1980 chunk 13 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7606 moved from start: 0.2078 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= 0.170 Angle : 0.622 13.125 18760 Z= 0.279 Chirality : 0.040 0.121 2148 Planarity : 0.004 0.045 2248 Dihedral : 15.196 160.170 2524 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.05 % Allowed : 19.55 % Favored : 77.40 % 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: 1.04 (0.23), residues: 1588 helix: 1.54 (0.18), residues: 956 sheet: 0.29 (0.61), residues: 88 loop : -0.73 (0.29), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 264 HIS 0.002 0.001 HIS C 232 PHE 0.007 0.001 PHE C 40 TYR 0.007 0.001 TYR C 170 ARG 0.001 0.000 ARG B 330 ********************** REFINEMENT MACRO_CYCLE 10 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 184 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 142 time to evaluate : 1.269 Fit side-chains REVERT: A 77 LEU cc_start: 0.2755 (OUTLIER) cc_final: 0.2420 (tt) REVERT: A 203 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8120 (mp) REVERT: A 273 ARG cc_start: 0.7485 (ptm-80) cc_final: 0.7032 (mtm-85) REVERT: A 313 ILE cc_start: 0.8157 (pt) cc_final: 0.7824 (mm) REVERT: A 330 ARG cc_start: 0.7071 (mtt90) cc_final: 0.6637 (mtm-85) REVERT: A 333 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: A 369 MET cc_start: 0.7351 (ppp) cc_final: 0.7031 (mtt) REVERT: B 55 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7282 (tp) REVERT: B 77 LEU cc_start: 0.2786 (OUTLIER) cc_final: 0.2443 (tt) REVERT: B 203 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8116 (mp) REVERT: B 273 ARG cc_start: 0.7442 (ptt90) cc_final: 0.6986 (mtm-85) REVERT: B 313 ILE cc_start: 0.8186 (pt) cc_final: 0.7830 (mm) REVERT: B 318 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7189 (tp30) REVERT: B 330 ARG cc_start: 0.7098 (mtt90) cc_final: 0.6834 (ttm-80) REVERT: B 333 GLU cc_start: 0.7517 (mp0) cc_final: 0.7290 (mm-30) REVERT: C 55 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7286 (tp) REVERT: C 77 LEU cc_start: 0.2785 (OUTLIER) cc_final: 0.2443 (tt) REVERT: C 203 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8118 (mp) REVERT: C 273 ARG cc_start: 0.7497 (ptt90) cc_final: 0.7024 (mtm-85) REVERT: C 313 ILE cc_start: 0.8160 (pt) cc_final: 0.7826 (mm) REVERT: C 318 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7190 (tp30) REVERT: D 77 LEU cc_start: 0.2733 (OUTLIER) cc_final: 0.2401 (tt) REVERT: D 203 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8123 (mp) REVERT: D 273 ARG cc_start: 0.7475 (ptt90) cc_final: 0.7007 (mtm-85) REVERT: D 313 ILE cc_start: 0.8123 (pt) cc_final: 0.7815 (mm) REVERT: D 330 ARG cc_start: 0.7044 (mtt90) cc_final: 0.6759 (ttm-80) outliers start: 42 outliers final: 18 residues processed: 170 average time/residue: 0.9970 time to fit residues: 186.3392 Evaluate side-chains 168 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 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 203 ILE Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 337 ASP 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 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 77 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 117 optimal weight: 0.0870 chunk 18 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.185407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.147914 restraints weight = 14633.402| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.84 r_work: 0.3130 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2118 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= 0.181 Angle : 0.623 11.505 18760 Z= 0.280 Chirality : 0.041 0.158 2148 Planarity : 0.004 0.045 2248 Dihedral : 15.137 160.810 2524 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.12 % Allowed : 19.55 % Favored : 77.33 % 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: 1.05 (0.23), residues: 1588 helix: 1.54 (0.18), residues: 956 sheet: 0.22 (0.61), residues: 88 loop : -0.71 (0.29), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 264 HIS 0.002 0.001 HIS D 232 PHE 0.006 0.001 PHE C 40 TYR 0.008 0.001 TYR B 170 ARG 0.001 0.000 ARG C 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4649.71 seconds wall clock time: 86 minutes 48.25 seconds (5208.25 seconds total)