Starting phenix.real_space_refine on Mon Apr 8 06:21:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bob_16140/04_2024/8bob_16140_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bob_16140/04_2024/8bob_16140.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bob_16140/04_2024/8bob_16140.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bob_16140/04_2024/8bob_16140.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bob_16140/04_2024/8bob_16140_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bob_16140/04_2024/8bob_16140_updated.pdb" } resolution = 2.94 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= 0.002 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 6 5.49 5 S 68 5.16 5 C 8058 2.51 5 N 2214 2.21 5 O 2366 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 12": "NH1" <-> "NH2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C GLU 115": "OE1" <-> "OE2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C GLU 299": "OE1" <-> "OE2" Residue "C GLU 302": "OE1" <-> "OE2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "C GLU 359": "OE1" <-> "OE2" Residue "C GLU 416": "OE1" <-> "OE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 115": "OE1" <-> "OE2" Residue "D GLU 190": "OE1" <-> "OE2" Residue "D GLU 193": "OE1" <-> "OE2" Residue "D GLU 299": "OE1" <-> "OE2" Residue "D GLU 302": "OE1" <-> "OE2" Residue "D GLU 316": "OE1" <-> "OE2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "D GLU 359": "OE1" <-> "OE2" Residue "D GLU 416": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 12712 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3052 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 15, 'TRANS': 370} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3052 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 15, 'TRANS': 370} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3262 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Chain: "D" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3262 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.68, per 1000 atoms: 0.53 Number of scatterers: 12712 At special positions: 0 Unit cell: (130.503, 126.259, 82.758, 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 68 16.00 P 6 15.00 O 2366 8.00 N 2214 7.00 C 8058 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: 5.45 Conformation dependent library (CDL) restraints added in 2.3 seconds 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3028 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 82 helices and 10 sheets defined 51.9% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.804A pdb=" N HIS A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 81 Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 96 through 106 Processing helix chain 'A' and resid 122 through 130 removed outlier: 3.733A pdb=" N LYS A 126 " --> pdb=" O ASP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 217 through 220 No H-bonds generated for 'chain 'A' and resid 217 through 220' Processing helix chain 'A' and resid 232 through 235 No H-bonds generated for 'chain 'A' and resid 232 through 235' Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 271 through 283 Processing helix chain 'A' and resid 285 through 309 Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 372 through 389 removed outlier: 3.606A pdb=" N LYS A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 56 removed outlier: 3.804A pdb=" N HIS B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 81 Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 96 through 106 Processing helix chain 'B' and resid 122 through 130 removed outlier: 3.732A pdb=" N LYS B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 217 through 220 No H-bonds generated for 'chain 'B' and resid 217 through 220' Processing helix chain 'B' and resid 232 through 235 No H-bonds generated for 'chain 'B' and resid 232 through 235' Processing helix chain 'B' and resid 250 through 261 Processing helix chain 'B' and resid 271 through 283 Processing helix chain 'B' and resid 285 through 309 Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 372 through 389 removed outlier: 3.606A pdb=" N LYS B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 6 No H-bonds generated for 'chain 'C' and resid 4 through 6' Processing helix chain 'C' and resid 20 through 31 removed outlier: 3.792A pdb=" N LYS C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ALA C 29 " --> pdb=" O LYS C 25 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ASN C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 55 removed outlier: 4.232A pdb=" N GLY C 55 " --> pdb=" O GLN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 69 Processing helix chain 'C' and resid 71 through 86 Processing helix chain 'C' and resid 91 through 99 Processing helix chain 'C' and resid 105 through 118 removed outlier: 3.922A pdb=" N GLU C 118 " --> pdb=" O ILE C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 136 through 148 Processing helix chain 'C' and resid 167 through 172 Processing helix chain 'C' and resid 181 through 184 No H-bonds generated for 'chain 'C' and resid 181 through 184' Processing helix chain 'C' and resid 188 through 198 Processing helix chain 'C' and resid 205 through 214 Processing helix chain 'C' and resid 219 through 230 Processing helix chain 'C' and resid 236 through 243 Processing helix chain 'C' and resid 248 through 258 Processing helix chain 'C' and resid 265 through 276 removed outlier: 4.532A pdb=" N ILE C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 288 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 322 through 335 removed outlier: 3.867A pdb=" N TRP C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 354 Processing helix chain 'C' and resid 357 through 367 Processing helix chain 'C' and resid 370 through 386 removed outlier: 6.455A pdb=" N TRP C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N SER C 383 " --> pdb=" O ASN C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 398 Processing helix chain 'C' and resid 406 through 416 removed outlier: 4.886A pdb=" N ALA C 411 " --> pdb=" O ALA C 407 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ILE C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA C 413 " --> pdb=" O ALA C 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 6 No H-bonds generated for 'chain 'D' and resid 4 through 6' Processing helix chain 'D' and resid 20 through 31 removed outlier: 4.314A pdb=" N GLY D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ALA D 29 " --> pdb=" O LYS D 25 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ASN D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 53 Processing helix chain 'D' and resid 66 through 69 Processing helix chain 'D' and resid 71 through 86 Processing helix chain 'D' and resid 91 through 99 Processing helix chain 'D' and resid 105 through 118 removed outlier: 3.928A pdb=" N GLU D 118 " --> pdb=" O ILE D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 136 through 148 Processing helix chain 'D' and resid 167 through 172 Processing helix chain 'D' and resid 181 through 184 No H-bonds generated for 'chain 'D' and resid 181 through 184' Processing helix chain 'D' and resid 188 through 198 Processing helix chain 'D' and resid 205 through 214 Processing helix chain 'D' and resid 219 through 230 Processing helix chain 'D' and resid 236 through 243 Processing helix chain 'D' and resid 248 through 258 Processing helix chain 'D' and resid 265 through 276 removed outlier: 4.532A pdb=" N ILE D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 288 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 322 through 335 removed outlier: 3.867A pdb=" N TRP D 334 " --> pdb=" O GLN D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 354 Processing helix chain 'D' and resid 357 through 367 Processing helix chain 'D' and resid 370 through 386 removed outlier: 6.454A pdb=" N TRP D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER D 383 " --> pdb=" O ASN D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 398 removed outlier: 3.682A pdb=" N LYS D 398 " --> pdb=" O GLU D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 416 Processing sheet with id= A, first strand: chain 'A' and resid 31 through 33 Processing sheet with id= B, first strand: chain 'A' and resid 90 through 93 removed outlier: 6.621A pdb=" N VAL A 198 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LEU A 228 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER A 200 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N GLY A 113 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N MET A 166 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL A 115 " --> pdb=" O MET A 166 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N LEU A 168 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N HIS A 117 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR A 134 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE A 116 " --> pdb=" O THR A 134 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N MET A 136 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N THR A 118 " --> pdb=" O MET A 136 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL A 138 " --> pdb=" O THR A 118 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 323 through 327 Processing sheet with id= D, first strand: chain 'B' and resid 31 through 33 Processing sheet with id= E, first strand: chain 'B' and resid 90 through 93 removed outlier: 6.621A pdb=" N VAL B 198 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LEU B 228 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER B 200 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLY B 113 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N MET B 166 " --> pdb=" O GLY B 113 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL B 115 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N LEU B 168 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N HIS B 117 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR B 134 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE B 116 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N MET B 136 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N THR B 118 " --> pdb=" O MET B 136 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL B 138 " --> pdb=" O THR B 118 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 323 through 327 Processing sheet with id= G, first strand: chain 'C' and resid 176 through 179 removed outlier: 6.386A pdb=" N LEU C 34 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ILE C 179 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU C 36 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N ALA C 35 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU C 155 " --> pdb=" O ALA C 35 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE C 37 " --> pdb=" O LEU C 155 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL C 157 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU C 123 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL C 156 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU C 125 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU C 158 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE C 127 " --> pdb=" O LEU C 158 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 308 through 310 Processing sheet with id= I, first strand: chain 'D' and resid 176 through 179 removed outlier: 6.385A pdb=" N LEU D 34 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ILE D 179 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU D 36 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N ALA D 35 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU D 155 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE D 37 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL D 157 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU D 123 " --> pdb=" O THR D 154 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N VAL D 156 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU D 125 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU D 158 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE D 127 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 308 through 310 534 hydrogen bonds defined for protein. 1584 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: 3.73 Time building geometry restraints manager: 5.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2904 1.33 - 1.45: 2849 1.45 - 1.57: 7139 1.57 - 1.69: 8 1.69 - 1.81: 108 Bond restraints: 13008 Sorted by residual: bond pdb=" N ILE B 215 " pdb=" CA ILE B 215 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.01e-02 9.80e+03 1.01e+01 bond pdb=" N ILE C 410 " pdb=" CA ILE C 410 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.00e+01 bond pdb=" N VAL A 220 " pdb=" CA VAL A 220 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.29e-02 6.01e+03 9.17e+00 bond pdb=" N ARG B 222 " pdb=" CA ARG B 222 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.26e-02 6.30e+03 8.80e+00 bond pdb=" N VAL B 220 " pdb=" CA VAL B 220 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.29e-02 6.01e+03 8.72e+00 ... (remaining 13003 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.87: 401 106.87 - 114.09: 7565 114.09 - 121.30: 6632 121.30 - 128.52: 2938 128.52 - 135.73: 156 Bond angle restraints: 17692 Sorted by residual: angle pdb=" CA ALA C 409 " pdb=" C ALA C 409 " pdb=" O ALA C 409 " ideal model delta sigma weight residual 120.55 115.67 4.88 1.06e+00 8.90e-01 2.12e+01 angle pdb=" N PRO D 406 " pdb=" CA PRO D 406 " pdb=" C PRO D 406 " ideal model delta sigma weight residual 113.53 107.60 5.93 1.39e+00 5.18e-01 1.82e+01 angle pdb=" N ALA C 408 " pdb=" CA ALA C 408 " pdb=" C ALA C 408 " ideal model delta sigma weight residual 111.28 106.94 4.34 1.09e+00 8.42e-01 1.58e+01 angle pdb=" N ILE D 414 " pdb=" CA ILE D 414 " pdb=" C ILE D 414 " ideal model delta sigma weight residual 110.62 106.60 4.02 1.02e+00 9.61e-01 1.55e+01 angle pdb=" N ILE C 114 " pdb=" CA ILE C 114 " pdb=" C ILE C 114 " ideal model delta sigma weight residual 110.23 106.22 4.01 1.04e+00 9.25e-01 1.49e+01 ... (remaining 17687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.21: 7540 35.21 - 70.41: 154 70.41 - 105.62: 8 105.62 - 140.83: 4 140.83 - 176.04: 2 Dihedral angle restraints: 7708 sinusoidal: 3036 harmonic: 4672 Sorted by residual: dihedral pdb=" O1B ADP C 501 " pdb=" O3A ADP C 501 " pdb=" PB ADP C 501 " pdb=" PA ADP C 501 " ideal model delta sinusoidal sigma weight residual 300.00 123.96 176.04 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual 300.00 124.00 175.99 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP C 501 " pdb=" O5' ADP C 501 " pdb=" PA ADP C 501 " pdb=" O2A ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 57.75 -117.75 1 2.00e+01 2.50e-03 3.52e+01 ... (remaining 7705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1437 0.056 - 0.113: 437 0.113 - 0.169: 59 0.169 - 0.225: 14 0.225 - 0.281: 9 Chirality restraints: 1956 Sorted by residual: chirality pdb=" CA TYR C 43 " pdb=" N TYR C 43 " pdb=" C TYR C 43 " pdb=" CB TYR C 43 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA TYR D 43 " pdb=" N TYR D 43 " pdb=" C TYR D 43 " pdb=" CB TYR D 43 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA ILE C 114 " pdb=" N ILE C 114 " pdb=" C ILE C 114 " pdb=" CB ILE C 114 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1953 not shown) Planarity restraints: 2272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 14 " 0.028 2.00e-02 2.50e+03 1.91e-02 9.16e+00 pdb=" CG TRP A 14 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 14 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 14 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 14 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 14 " 0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP A 14 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 14 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 14 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 14 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 14 " 0.028 2.00e-02 2.50e+03 1.91e-02 9.11e+00 pdb=" CG TRP B 14 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B 14 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 14 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 14 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 14 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP B 14 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 14 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 14 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 14 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 409 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.94e+00 pdb=" C ALA C 409 " -0.049 2.00e-02 2.50e+03 pdb=" O ALA C 409 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE C 410 " 0.017 2.00e-02 2.50e+03 ... (remaining 2269 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1994 2.75 - 3.28: 12917 3.28 - 3.82: 21733 3.82 - 4.36: 26320 4.36 - 4.90: 43497 Nonbonded interactions: 106461 Sorted by model distance: nonbonded pdb=" OG SER D 8 " pdb=" O MET D 311 " model vdw 2.208 2.440 nonbonded pdb=" OG SER C 8 " pdb=" O MET C 311 " model vdw 2.208 2.440 nonbonded pdb=" NH1 ARG C 242 " pdb=" OE2 GLU C 258 " model vdw 2.210 2.520 nonbonded pdb=" NH1 ARG D 242 " pdb=" OE2 GLU D 258 " model vdw 2.210 2.520 nonbonded pdb=" OE1 GLU D 291 " pdb=" N ASN D 293 " model vdw 2.215 2.520 ... (remaining 106456 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 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: 0.020 Extract box with map and model: 5.090 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 36.250 Find NCS groups from input model: 0.750 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:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 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 0.074 13008 Z= 0.608 Angle : 0.870 10.090 17692 Z= 0.544 Chirality : 0.056 0.281 1956 Planarity : 0.004 0.046 2272 Dihedral : 15.310 176.037 4680 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.21 % Favored : 95.48 % Rotamer: Outliers : 3.17 % Allowed : 4.75 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % 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: -1.98 (0.19), residues: 1592 helix: -0.78 (0.16), residues: 860 sheet: -1.78 (0.37), residues: 194 loop : -1.74 (0.24), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 14 HIS 0.004 0.001 HIS D 344 PHE 0.020 0.002 PHE A 77 TYR 0.031 0.002 TYR D 43 ARG 0.005 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 117 time to evaluate : 1.499 Fit side-chains revert: symmetry clash REVERT: A 351 MET cc_start: 0.8384 (tpp) cc_final: 0.8115 (tpt) REVERT: B 351 MET cc_start: 0.8486 (tpp) cc_final: 0.8227 (tpt) REVERT: C 1 MET cc_start: 0.6596 (ttt) cc_final: 0.6299 (mpp) REVERT: C 273 LYS cc_start: 0.9123 (mttt) cc_final: 0.8718 (mtpp) REVERT: C 280 MET cc_start: 0.7896 (mtm) cc_final: 0.7684 (ptp) REVERT: D 1 MET cc_start: 0.6777 (ttt) cc_final: 0.6500 (mpp) REVERT: D 280 MET cc_start: 0.7843 (mtm) cc_final: 0.7486 (ptp) outliers start: 42 outliers final: 6 residues processed: 148 average time/residue: 1.3625 time to fit residues: 219.5112 Evaluate side-chains 75 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 259 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.0970 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 125 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 145 optimal weight: 7.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN A 56 HIS A 75 HIS A 219 ASN A 282 GLN A 298 ASN A 336 ASN B 17 GLN B 56 HIS B 75 HIS B 219 ASN B 282 GLN B 298 ASN B 336 ASN C 30 ASN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 HIS C 262 ASN C 269 HIS C 405 ASN D 30 ASN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 HIS D 262 ASN D 269 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13008 Z= 0.164 Angle : 0.548 7.776 17692 Z= 0.274 Chirality : 0.041 0.250 1956 Planarity : 0.004 0.038 2272 Dihedral : 8.589 148.381 1772 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.49 % Allowed : 7.54 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % 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: -0.42 (0.21), residues: 1592 helix: 0.59 (0.17), residues: 888 sheet: -1.31 (0.38), residues: 206 loop : -1.22 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 14 HIS 0.005 0.001 HIS C 237 PHE 0.014 0.001 PHE D 194 TYR 0.019 0.001 TYR C 254 ARG 0.009 0.001 ARG D 242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 95 time to evaluate : 1.575 Fit side-chains REVERT: A 351 MET cc_start: 0.8388 (tpp) cc_final: 0.8105 (tpt) REVERT: B 351 MET cc_start: 0.8435 (tpp) cc_final: 0.8161 (tpt) REVERT: C 311 MET cc_start: 0.8386 (mmp) cc_final: 0.8111 (mmm) REVERT: D 238 LYS cc_start: 0.6968 (ttpt) cc_final: 0.5159 (ttpt) REVERT: D 378 LEU cc_start: 0.5060 (OUTLIER) cc_final: 0.4716 (mm) outliers start: 33 outliers final: 9 residues processed: 122 average time/residue: 1.2765 time to fit residues: 170.5986 Evaluate side-chains 76 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 332 CYS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 332 CYS Chi-restraints excluded: chain D residue 378 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 120 optimal weight: 0.0670 chunk 98 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 157 optimal weight: 20.0000 chunk 129 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 overall best weight: 1.1120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN A 249 ASN B 219 ASN B 249 ASN C 169 ASN D 169 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13008 Z= 0.211 Angle : 0.544 7.280 17692 Z= 0.269 Chirality : 0.041 0.213 1956 Planarity : 0.004 0.047 2272 Dihedral : 7.515 123.280 1765 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.58 % Allowed : 10.86 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % 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: 0.27 (0.21), residues: 1592 helix: 1.10 (0.18), residues: 860 sheet: -1.05 (0.39), residues: 208 loop : -0.72 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 14 HIS 0.003 0.001 HIS D 15 PHE 0.012 0.001 PHE C 194 TYR 0.011 0.001 TYR A 98 ARG 0.009 0.000 ARG C 241 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 75 time to evaluate : 1.394 Fit side-chains REVERT: A 351 MET cc_start: 0.8372 (tpp) cc_final: 0.8120 (tpt) REVERT: B 351 MET cc_start: 0.8399 (tpp) cc_final: 0.8153 (tpt) REVERT: C 311 MET cc_start: 0.8310 (mmp) cc_final: 0.8060 (mmm) REVERT: D 376 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8427 (tp) REVERT: D 378 LEU cc_start: 0.5122 (OUTLIER) cc_final: 0.4763 (mm) outliers start: 21 outliers final: 8 residues processed: 92 average time/residue: 1.1803 time to fit residues: 120.2805 Evaluate side-chains 75 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 332 CYS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 378 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 146 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 169 ASN D 169 ASN D 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13008 Z= 0.353 Angle : 0.599 8.347 17692 Z= 0.298 Chirality : 0.044 0.240 1956 Planarity : 0.004 0.035 2272 Dihedral : 7.791 131.179 1765 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.70 % Favored : 97.17 % Rotamer: Outliers : 1.96 % Allowed : 13.05 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % 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: 0.37 (0.22), residues: 1592 helix: 1.19 (0.18), residues: 858 sheet: -1.06 (0.39), residues: 208 loop : -0.64 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 14 HIS 0.009 0.001 HIS D 380 PHE 0.013 0.001 PHE D 194 TYR 0.013 0.002 TYR A 98 ARG 0.006 0.001 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 70 time to evaluate : 1.361 Fit side-chains REVERT: A 351 MET cc_start: 0.8363 (tpp) cc_final: 0.8117 (tpt) REVERT: B 351 MET cc_start: 0.8370 (tpp) cc_final: 0.8110 (tpt) REVERT: B 390 ARG cc_start: 0.7368 (ttt90) cc_final: 0.7131 (tpt-90) REVERT: C 273 LYS cc_start: 0.9077 (mttt) cc_final: 0.8588 (mtpp) REVERT: D 378 LEU cc_start: 0.5043 (OUTLIER) cc_final: 0.4799 (mm) outliers start: 26 outliers final: 10 residues processed: 91 average time/residue: 1.3261 time to fit residues: 133.0077 Evaluate side-chains 76 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 332 CYS Chi-restraints excluded: chain D residue 378 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 131 optimal weight: 0.0870 chunk 106 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 138 optimal weight: 8.9990 chunk 39 optimal weight: 0.3980 overall best weight: 1.8964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN B 219 ASN C 188 HIS C 234 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13008 Z= 0.307 Angle : 0.574 9.056 17692 Z= 0.284 Chirality : 0.043 0.291 1956 Planarity : 0.004 0.033 2272 Dihedral : 7.543 125.782 1764 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.89 % Allowed : 13.20 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % 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 (0.22), residues: 1592 helix: 1.28 (0.18), residues: 858 sheet: -0.99 (0.39), residues: 208 loop : -0.60 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 325 HIS 0.010 0.001 HIS D 380 PHE 0.013 0.001 PHE C 194 TYR 0.012 0.001 TYR A 98 ARG 0.006 0.000 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 72 time to evaluate : 1.447 Fit side-chains REVERT: A 351 MET cc_start: 0.8356 (tpp) cc_final: 0.8099 (tpt) REVERT: B 351 MET cc_start: 0.8362 (tpp) cc_final: 0.8109 (tpt) REVERT: B 390 ARG cc_start: 0.7321 (ttt90) cc_final: 0.7086 (tpt-90) REVERT: C 273 LYS cc_start: 0.9051 (mttt) cc_final: 0.8625 (mtpp) REVERT: D 378 LEU cc_start: 0.4957 (OUTLIER) cc_final: 0.4710 (mm) outliers start: 25 outliers final: 13 residues processed: 90 average time/residue: 1.2394 time to fit residues: 122.9634 Evaluate side-chains 80 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 66 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 237 HIS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 332 CYS Chi-restraints excluded: chain D residue 378 LEU 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: 8.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 0.0870 chunk 38 optimal weight: 0.7980 chunk 154 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 234 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13008 Z= 0.184 Angle : 0.527 9.928 17692 Z= 0.257 Chirality : 0.040 0.132 1956 Planarity : 0.003 0.031 2272 Dihedral : 7.107 119.737 1764 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.89 % Allowed : 13.57 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.22), residues: 1592 helix: 1.49 (0.18), residues: 858 sheet: -0.65 (0.40), residues: 204 loop : -0.47 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 325 HIS 0.007 0.001 HIS D 380 PHE 0.012 0.001 PHE C 194 TYR 0.008 0.001 TYR A 98 ARG 0.008 0.000 ARG D 198 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 72 time to evaluate : 1.544 Fit side-chains REVERT: A 351 MET cc_start: 0.8369 (tpp) cc_final: 0.8124 (tpt) REVERT: B 351 MET cc_start: 0.8372 (tpp) cc_final: 0.8117 (tpt) outliers start: 25 outliers final: 13 residues processed: 88 average time/residue: 1.2858 time to fit residues: 124.4978 Evaluate side-chains 79 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 332 CYS Chi-restraints excluded: chain D residue 372 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 6.9990 chunk 17 optimal weight: 0.0570 chunk 88 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 234 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13008 Z= 0.270 Angle : 0.565 10.779 17692 Z= 0.276 Chirality : 0.042 0.135 1956 Planarity : 0.004 0.032 2272 Dihedral : 7.225 122.251 1763 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.73 % Allowed : 14.40 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % 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: 0.79 (0.22), residues: 1592 helix: 1.48 (0.18), residues: 858 sheet: -0.73 (0.39), residues: 214 loop : -0.42 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 325 HIS 0.006 0.001 HIS D 380 PHE 0.013 0.001 PHE D 194 TYR 0.011 0.001 TYR B 98 ARG 0.007 0.000 ARG D 198 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 66 time to evaluate : 1.394 Fit side-chains REVERT: A 351 MET cc_start: 0.8338 (tpp) cc_final: 0.8085 (tpt) REVERT: B 351 MET cc_start: 0.8340 (tpp) cc_final: 0.8080 (tpt) outliers start: 23 outliers final: 14 residues processed: 82 average time/residue: 1.2029 time to fit residues: 109.3609 Evaluate side-chains 78 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 332 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 98 optimal weight: 0.0770 chunk 105 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 234 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13008 Z= 0.183 Angle : 0.529 11.472 17692 Z= 0.256 Chirality : 0.040 0.130 1956 Planarity : 0.003 0.032 2272 Dihedral : 6.872 116.736 1762 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.28 % Allowed : 14.93 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % 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: 0.93 (0.22), residues: 1592 helix: 1.60 (0.18), residues: 856 sheet: -0.56 (0.40), residues: 212 loop : -0.40 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 325 HIS 0.005 0.001 HIS D 380 PHE 0.014 0.001 PHE D 194 TYR 0.011 0.001 TYR D 254 ARG 0.007 0.000 ARG D 374 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 72 time to evaluate : 1.364 Fit side-chains revert: symmetry clash REVERT: A 351 MET cc_start: 0.8358 (tpp) cc_final: 0.8098 (tpt) REVERT: B 351 MET cc_start: 0.8340 (tpp) cc_final: 0.8085 (tpt) REVERT: C 391 SER cc_start: 0.7913 (m) cc_final: 0.7484 (t) outliers start: 17 outliers final: 11 residues processed: 87 average time/residue: 1.1704 time to fit residues: 113.0734 Evaluate side-chains 80 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 332 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 7.9990 chunk 147 optimal weight: 0.0570 chunk 134 optimal weight: 0.6980 chunk 143 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 250 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13008 Z= 0.234 Angle : 0.549 12.078 17692 Z= 0.266 Chirality : 0.041 0.134 1956 Planarity : 0.003 0.032 2272 Dihedral : 6.932 117.504 1762 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.13 % Allowed : 15.23 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.13 % 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: 0.91 (0.22), residues: 1592 helix: 1.57 (0.18), residues: 856 sheet: -0.59 (0.40), residues: 212 loop : -0.39 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 382 HIS 0.013 0.001 HIS D 250 PHE 0.015 0.001 PHE D 194 TYR 0.018 0.001 TYR C 254 ARG 0.007 0.000 ARG D 374 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 66 time to evaluate : 1.397 Fit side-chains REVERT: A 351 MET cc_start: 0.8309 (tpp) cc_final: 0.8061 (tpt) REVERT: B 351 MET cc_start: 0.8326 (tpp) cc_final: 0.8084 (tpt) REVERT: C 391 SER cc_start: 0.7809 (m) cc_final: 0.7499 (t) outliers start: 15 outliers final: 12 residues processed: 79 average time/residue: 1.1708 time to fit residues: 102.8541 Evaluate side-chains 77 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 332 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.3473 > 50: distance: 31 - 37: 14.628 distance: 37 - 38: 15.128 distance: 38 - 39: 35.058 distance: 38 - 41: 8.865 distance: 39 - 40: 19.439 distance: 39 - 43: 22.278 distance: 41 - 42: 5.485 distance: 43 - 44: 8.792 distance: 44 - 45: 29.435 distance: 44 - 47: 29.542 distance: 45 - 46: 12.978 distance: 45 - 49: 11.348 distance: 47 - 48: 7.303 distance: 49 - 50: 15.587 distance: 49 - 55: 31.431 distance: 50 - 51: 22.562 distance: 50 - 53: 30.965 distance: 51 - 52: 26.214 distance: 51 - 56: 19.685 distance: 53 - 54: 17.064 distance: 54 - 55: 32.114 distance: 56 - 57: 21.247 distance: 57 - 58: 14.279 distance: 57 - 60: 16.713 distance: 58 - 59: 35.844 distance: 58 - 64: 3.956 distance: 60 - 61: 23.628 distance: 60 - 62: 16.823 distance: 61 - 63: 45.993 distance: 64 - 65: 24.269 distance: 65 - 66: 18.495 distance: 65 - 68: 26.587 distance: 66 - 67: 35.295 distance: 66 - 73: 21.906 distance: 68 - 69: 20.507 distance: 69 - 70: 35.695 distance: 70 - 71: 31.056 distance: 70 - 72: 13.176 distance: 73 - 74: 8.217 distance: 74 - 75: 21.953 distance: 74 - 77: 33.164 distance: 75 - 76: 27.592 distance: 75 - 78: 19.205 distance: 76 - 98: 34.539 distance: 78 - 79: 37.256 distance: 79 - 80: 8.701 distance: 79 - 82: 29.885 distance: 80 - 81: 15.047 distance: 80 - 83: 30.933 distance: 81 - 104: 19.660 distance: 83 - 84: 12.999 distance: 84 - 85: 18.971 distance: 84 - 87: 9.825 distance: 85 - 86: 4.238 distance: 85 - 92: 4.561 distance: 86 - 112: 29.004 distance: 87 - 88: 19.905 distance: 88 - 89: 14.943 distance: 89 - 90: 12.004 distance: 89 - 91: 24.296 distance: 92 - 93: 16.011 distance: 93 - 94: 6.023 distance: 93 - 96: 10.773 distance: 94 - 95: 8.248 distance: 94 - 98: 6.436 distance: 95 - 120: 32.647 distance: 96 - 97: 27.277 distance: 98 - 99: 12.784 distance: 99 - 100: 4.481 distance: 99 - 102: 20.010 distance: 100 - 101: 13.733 distance: 100 - 104: 20.219 distance: 101 - 126: 26.553 distance: 102 - 103: 9.764