Starting phenix.real_space_refine on Thu Feb 15 21:35:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtf_24681/02_2024/7rtf_24681_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtf_24681/02_2024/7rtf_24681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtf_24681/02_2024/7rtf_24681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtf_24681/02_2024/7rtf_24681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtf_24681/02_2024/7rtf_24681_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtf_24681/02_2024/7rtf_24681_updated.pdb" } resolution = 2.9 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= 0.007 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 9052 2.51 5 N 2088 2.21 5 O 2284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 92": "OD1" <-> "OD2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A GLU 271": "OE1" <-> "OE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A ASP 388": "OD1" <-> "OD2" Residue "A ASP 393": "OD1" <-> "OD2" Residue "B TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 92": "OD1" <-> "OD2" Residue "B ASP 261": "OD1" <-> "OD2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B ASP 337": "OD1" <-> "OD2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "B ASP 388": "OD1" <-> "OD2" Residue "B ASP 393": "OD1" <-> "OD2" Residue "C TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 92": "OD1" <-> "OD2" Residue "C ASP 261": "OD1" <-> "OD2" Residue "C GLU 271": "OE1" <-> "OE2" Residue "C GLU 272": "OE1" <-> "OE2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "C ASP 337": "OD1" <-> "OD2" Residue "C GLU 347": "OE1" <-> "OE2" Residue "C GLU 368": "OE1" <-> "OE2" Residue "C ASP 388": "OD1" <-> "OD2" Residue "C ASP 393": "OD1" <-> "OD2" Residue "D TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 92": "OD1" <-> "OD2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D GLU 271": "OE1" <-> "OE2" Residue "D GLU 272": "OE1" <-> "OE2" Residue "D GLU 318": "OE1" <-> "OE2" Residue "D ASP 337": "OD1" <-> "OD2" Residue "D GLU 347": "OE1" <-> "OE2" Residue "D GLU 368": "OE1" <-> "OE2" Residue "D ASP 388": "OD1" <-> "OD2" Residue "D ASP 393": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13460 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3134 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 24, 'TRANS': 370} Chain breaks: 1 Chain: "B" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3134 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 24, 'TRANS': 370} Chain breaks: 1 Chain: "C" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3134 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 24, 'TRANS': 370} Chain breaks: 1 Chain: "D" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3134 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 24, 'TRANS': 370} Chain breaks: 1 Chain: "A" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 231 Unusual residues: {'PGW': 12} Classifications: {'RNA': 1, 'undetermined': 12} Modifications used: {'rna3p': 1} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 403 Unresolved non-hydrogen angles: 478 Unresolved non-hydrogen dihedrals: 406 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'PGW:plan-1': 10, 'PGW:plan-2': 10, 'PGW:plan-3': 5} Unresolved non-hydrogen planarities: 95 Chain: "B" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 231 Unusual residues: {'PGW': 12} Classifications: {'RNA': 1, 'undetermined': 12} Modifications used: {'rna3p': 1} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 403 Unresolved non-hydrogen angles: 478 Unresolved non-hydrogen dihedrals: 406 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'PGW:plan-1': 10, 'PGW:plan-2': 10, 'PGW:plan-3': 5} Unresolved non-hydrogen planarities: 95 Chain: "C" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 231 Unusual residues: {'PGW': 12} Classifications: {'RNA': 1, 'undetermined': 12} Modifications used: {'rna3p': 1} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 403 Unresolved non-hydrogen angles: 478 Unresolved non-hydrogen dihedrals: 406 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'PGW:plan-1': 10, 'PGW:plan-2': 10, 'PGW:plan-3': 5} Unresolved non-hydrogen planarities: 95 Chain: "D" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 231 Unusual residues: {'PGW': 12} Classifications: {'RNA': 1, 'undetermined': 12} Modifications used: {'rna3p': 1} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 403 Unresolved non-hydrogen angles: 478 Unresolved non-hydrogen dihedrals: 406 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'PGW:plan-1': 10, 'PGW:plan-2': 10, 'PGW:plan-3': 5} Unresolved non-hydrogen planarities: 95 Time building chain proxies: 7.88, per 1000 atoms: 0.59 Number of scatterers: 13460 At special positions: 0 Unit cell: (105.827, 105.827, 120.01, 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 2284 8.00 N 2088 7.00 C 9052 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: 5.25 Conformation dependent library (CDL) restraints added in 2.2 seconds 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3000 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 8 sheets defined 58.7% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'A' and resid 11 through 35 removed outlier: 3.511A pdb=" N TRP A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Proline residue: A 31 - end of helix removed outlier: 3.505A pdb=" N VAL A 35 " --> pdb=" O PRO A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.539A pdb=" N LEU A 49 " --> pdb=" O PRO A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 82 through 86 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 105 through 125 removed outlier: 3.568A pdb=" N LEU A 109 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR A 123 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE A 125 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 157 removed outlier: 3.647A pdb=" N ARG A 136 " --> pdb=" O PRO A 132 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 181 Processing helix chain 'A' and resid 194 through 224 removed outlier: 3.873A pdb=" N LYS A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 245 removed outlier: 3.639A pdb=" N TYR A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 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 291 Processing helix chain 'A' and resid 295 through 298 removed outlier: 3.739A pdb=" N LYS A 298 " --> pdb=" O VAL A 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 295 through 298' Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.848A pdb=" N LEU A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N HIS A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.650A pdb=" N LEU A 371 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 372 " --> pdb=" O MET A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 372' Processing helix chain 'A' and resid 395 through 401 Processing helix chain 'A' and resid 405 through 414 Processing helix chain 'B' and resid 11 through 35 removed outlier: 3.510A pdb=" N TRP B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Proline residue: B 31 - end of helix removed outlier: 3.506A pdb=" N VAL B 35 " --> pdb=" O PRO B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 55 removed outlier: 3.538A pdb=" N LEU B 49 " --> pdb=" O PRO B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 82 through 86 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 105 through 125 removed outlier: 3.568A pdb=" N LEU B 109 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR B 123 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE B 125 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 157 removed outlier: 3.647A pdb=" N ARG B 136 " --> pdb=" O PRO B 132 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 181 Processing helix chain 'B' and resid 194 through 224 removed outlier: 3.873A pdb=" N LYS B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 245 removed outlier: 3.639A pdb=" N TYR B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 267 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 291 Processing helix chain 'B' and resid 295 through 298 removed outlier: 3.739A pdb=" N LYS B 298 " --> pdb=" O VAL B 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 295 through 298' Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.849A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N HIS B 316 " --> pdb=" O ASP B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.651A pdb=" N LEU B 371 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 372 " --> pdb=" O MET B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 372' Processing helix chain 'B' and resid 395 through 401 Processing helix chain 'B' and resid 405 through 414 Processing helix chain 'C' and resid 11 through 35 removed outlier: 3.511A pdb=" N TRP C 18 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE C 28 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Proline residue: C 31 - end of helix removed outlier: 3.505A pdb=" N VAL C 35 " --> pdb=" O PRO C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 55 removed outlier: 3.538A pdb=" N LEU C 49 " --> pdb=" O PRO C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 82 through 86 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 105 through 125 removed outlier: 3.568A pdb=" N LEU C 109 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR C 123 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE C 125 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 157 removed outlier: 3.646A pdb=" N ARG C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 181 Processing helix chain 'C' and resid 194 through 224 removed outlier: 3.873A pdb=" N LYS C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 245 removed outlier: 3.639A pdb=" N TYR C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 267 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 291 Processing helix chain 'C' and resid 295 through 298 removed outlier: 3.739A pdb=" N LYS C 298 " --> pdb=" O VAL C 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 295 through 298' Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.848A pdb=" N LEU C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N HIS C 316 " --> pdb=" O ASP C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 372 removed outlier: 3.650A pdb=" N LEU C 371 " --> pdb=" O GLU C 368 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 372 " --> pdb=" O MET C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 372' Processing helix chain 'C' and resid 395 through 401 Processing helix chain 'C' and resid 405 through 414 Processing helix chain 'D' and resid 11 through 35 removed outlier: 3.510A pdb=" N TRP D 18 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) Proline residue: D 31 - end of helix removed outlier: 3.505A pdb=" N VAL D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 55 removed outlier: 3.538A pdb=" N LEU D 49 " --> pdb=" O PRO D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 62 Processing helix chain 'D' and resid 82 through 86 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 105 through 125 removed outlier: 3.568A pdb=" N LEU D 109 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR D 123 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE D 125 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 157 removed outlier: 3.646A pdb=" N ARG D 136 " --> pdb=" O PRO D 132 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 181 Processing helix chain 'D' and resid 194 through 224 removed outlier: 3.873A pdb=" N LYS D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 245 removed outlier: 3.640A pdb=" N TYR D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 267 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 291 Processing helix chain 'D' and resid 295 through 298 removed outlier: 3.740A pdb=" N LYS D 298 " --> pdb=" O VAL D 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 295 through 298' Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.847A pdb=" N LEU D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N HIS D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 372 removed outlier: 3.649A pdb=" N LEU D 371 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE D 372 " --> pdb=" O MET D 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 368 through 372' Processing helix chain 'D' and resid 395 through 401 Processing helix chain 'D' and resid 405 through 414 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: 3.702A 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: 3.701A 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: 3.701A 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: 3.702A pdb=" N ALA D 358 " --> pdb=" O VAL D 348 " (cutoff:3.500A) 628 hydrogen bonds defined for protein. 1656 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: 3.68 Time building geometry restraints manager: 5.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3774 1.34 - 1.46: 1908 1.46 - 1.57: 7966 1.57 - 1.69: 12 1.69 - 1.81: 52 Bond restraints: 13712 Sorted by residual: bond pdb=" C10 PGW B 507 " pdb=" C9 PGW B 507 " ideal model delta sigma weight residual 1.333 1.524 -0.191 2.00e-02 2.50e+03 9.10e+01 bond pdb=" C10 PGW C 507 " pdb=" C9 PGW C 507 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.01e+01 bond pdb=" C10 PGW A 507 " pdb=" C9 PGW A 507 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.01e+01 bond pdb=" C10 PGW A 513 " pdb=" C9 PGW A 513 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.00e+01 bond pdb=" C10 PGW D 513 " pdb=" C9 PGW D 513 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 8.98e+01 ... (remaining 13707 not shown) Histogram of bond angle deviations from ideal: 100.50 - 107.62: 588 107.62 - 114.75: 8242 114.75 - 121.87: 7123 121.87 - 129.00: 2363 129.00 - 136.12: 100 Bond angle restraints: 18416 Sorted by residual: angle pdb=" C06 PGW C 504 " pdb=" C10 PGW C 504 " pdb=" C9 PGW C 504 " ideal model delta sigma weight residual 126.92 109.71 17.21 3.00e+00 1.11e-01 3.29e+01 angle pdb=" C06 PGW A 504 " pdb=" C10 PGW A 504 " pdb=" C9 PGW A 504 " ideal model delta sigma weight residual 126.92 109.75 17.17 3.00e+00 1.11e-01 3.28e+01 angle pdb=" C06 PGW B 504 " pdb=" C10 PGW B 504 " pdb=" C9 PGW B 504 " ideal model delta sigma weight residual 126.92 109.76 17.16 3.00e+00 1.11e-01 3.27e+01 angle pdb=" C06 PGW D 504 " pdb=" C10 PGW D 504 " pdb=" C9 PGW D 504 " ideal model delta sigma weight residual 126.92 109.77 17.15 3.00e+00 1.11e-01 3.27e+01 angle pdb=" C06 PGW D 509 " pdb=" C10 PGW D 509 " pdb=" C9 PGW D 509 " ideal model delta sigma weight residual 126.92 109.83 17.09 3.00e+00 1.11e-01 3.24e+01 ... (remaining 18411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.49: 7960 33.49 - 66.98: 384 66.98 - 100.46: 32 100.46 - 133.95: 16 133.95 - 167.44: 24 Dihedral angle restraints: 8416 sinusoidal: 3768 harmonic: 4648 Sorted by residual: dihedral pdb=" C5' CMP D 501 " pdb=" O5' CMP D 501 " pdb=" P CMP D 501 " pdb=" O1P CMP D 501 " ideal model delta sinusoidal sigma weight residual 60.00 170.49 -110.49 1 2.00e+01 2.50e-03 3.24e+01 dihedral pdb=" C5' CMP C 501 " pdb=" O5' CMP C 501 " pdb=" P CMP C 501 " pdb=" O1P CMP C 501 " ideal model delta sinusoidal sigma weight residual 60.00 170.46 -110.46 1 2.00e+01 2.50e-03 3.24e+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 60.00 170.44 -110.44 1 2.00e+01 2.50e-03 3.24e+01 ... (remaining 8413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1653 0.060 - 0.119: 372 0.119 - 0.179: 83 0.179 - 0.238: 4 0.238 - 0.298: 4 Chirality restraints: 2116 Sorted by residual: chirality pdb=" CB ILE C 58 " pdb=" CA ILE C 58 " pdb=" CG1 ILE C 58 " pdb=" CG2 ILE C 58 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB ILE B 58 " pdb=" CA ILE B 58 " pdb=" CG1 ILE B 58 " pdb=" CG2 ILE B 58 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB ILE A 58 " pdb=" CA ILE A 58 " pdb=" CG1 ILE A 58 " pdb=" CG2 ILE A 58 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 2113 not shown) Planarity restraints: 2212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW A 509 " 0.161 2.00e-02 2.50e+03 1.62e-01 2.64e+02 pdb=" C10 PGW A 509 " -0.155 2.00e-02 2.50e+03 pdb=" C8 PGW A 509 " 0.164 2.00e-02 2.50e+03 pdb=" C9 PGW A 509 " -0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW D 509 " -0.161 2.00e-02 2.50e+03 1.62e-01 2.64e+02 pdb=" C10 PGW D 509 " 0.155 2.00e-02 2.50e+03 pdb=" C8 PGW D 509 " -0.164 2.00e-02 2.50e+03 pdb=" C9 PGW D 509 " 0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW C 509 " -0.161 2.00e-02 2.50e+03 1.62e-01 2.64e+02 pdb=" C10 PGW C 509 " 0.155 2.00e-02 2.50e+03 pdb=" C8 PGW C 509 " -0.164 2.00e-02 2.50e+03 pdb=" C9 PGW C 509 " 0.170 2.00e-02 2.50e+03 ... (remaining 2209 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3227 2.80 - 3.33: 11945 3.33 - 3.85: 20630 3.85 - 4.38: 24434 4.38 - 4.90: 42200 Nonbonded interactions: 102436 Sorted by model distance: nonbonded pdb=" OH TYR A 186 " pdb=" OG1 THR B 180 " model vdw 2.280 2.440 nonbonded pdb=" OH TYR C 186 " pdb=" OG1 THR D 180 " model vdw 2.297 2.440 nonbonded pdb=" OG1 THR A 180 " pdb=" OH TYR D 186 " model vdw 2.304 2.440 nonbonded pdb=" OH TYR B 186 " pdb=" OG1 THR C 180 " model vdw 2.306 2.440 nonbonded pdb=" OH TYR D 327 " pdb=" OE2 GLU D 353 " model vdw 2.307 2.440 ... (remaining 102431 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.810 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: 3.690 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 37.770 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 0.191 13712 Z= 0.565 Angle : 1.354 17.206 18416 Z= 0.550 Chirality : 0.053 0.298 2116 Planarity : 0.013 0.162 2212 Dihedral : 21.044 167.438 5416 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 1.41 % Allowed : 7.94 % Favored : 90.65 % 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: -0.52 (0.22), residues: 1564 helix: 0.21 (0.18), residues: 952 sheet: -0.45 (0.53), residues: 88 loop : -1.19 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 264 HIS 0.002 0.000 HIS D 316 PHE 0.007 0.001 PHE D 40 TYR 0.013 0.001 TYR D 199 ARG 0.005 0.001 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 1.431 Fit side-chains REVERT: B 334 MET cc_start: 0.7348 (mmp) cc_final: 0.7090 (mmt) REVERT: C 334 MET cc_start: 0.7328 (mmp) cc_final: 0.7063 (mmt) outliers start: 19 outliers final: 4 residues processed: 150 average time/residue: 1.4171 time to fit residues: 230.8874 Evaluate side-chains 145 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 314 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 47 optimal weight: 0.0370 chunk 74 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.0462 ------------------------------------------------------------------------------- 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: 0.7823 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13712 Z= 0.228 Angle : 0.687 8.709 18416 Z= 0.320 Chirality : 0.045 0.189 2116 Planarity : 0.005 0.043 2212 Dihedral : 20.526 168.607 2464 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.11 % Allowed : 12.98 % Favored : 85.91 % 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: 0.13 (0.22), residues: 1564 helix: 0.75 (0.18), residues: 940 sheet: -0.11 (0.59), residues: 88 loop : -0.96 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 176 HIS 0.002 0.001 HIS B 292 PHE 0.006 0.001 PHE A 397 TYR 0.009 0.001 TYR A 199 ARG 0.007 0.001 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 1.492 Fit side-chains outliers start: 15 outliers final: 13 residues processed: 135 average time/residue: 1.2783 time to fit residues: 189.2275 Evaluate side-chains 143 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 314 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 141 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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: 0.7840 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 13712 Z= 0.235 Angle : 0.645 7.186 18416 Z= 0.306 Chirality : 0.044 0.201 2116 Planarity : 0.004 0.041 2212 Dihedral : 18.288 151.801 2464 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.82 % Allowed : 13.95 % Favored : 83.23 % 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: 0.43 (0.23), residues: 1564 helix: 1.06 (0.18), residues: 944 sheet: -0.05 (0.58), residues: 88 loop : -0.97 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 176 HIS 0.002 0.001 HIS A 292 PHE 0.004 0.001 PHE A 397 TYR 0.011 0.001 TYR C 199 ARG 0.002 0.000 ARG A 254 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 145 time to evaluate : 1.530 Fit side-chains outliers start: 38 outliers final: 18 residues processed: 169 average time/residue: 1.2858 time to fit residues: 237.8823 Evaluate side-chains 158 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 140 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 67 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 74 optimal weight: 0.0000 chunk 134 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN D 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13712 Z= 0.197 Angle : 0.610 7.808 18416 Z= 0.289 Chirality : 0.043 0.195 2116 Planarity : 0.004 0.036 2212 Dihedral : 17.395 145.205 2464 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.97 % Allowed : 16.17 % Favored : 80.86 % 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: 0.70 (0.23), residues: 1564 helix: 1.23 (0.18), residues: 952 sheet: -0.02 (0.57), residues: 88 loop : -0.79 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 176 HIS 0.002 0.001 HIS A 292 PHE 0.004 0.001 PHE A 242 TYR 0.013 0.001 TYR D 199 ARG 0.002 0.000 ARG D 382 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 141 time to evaluate : 1.598 Fit side-chains REVERT: A 414 LEU cc_start: 0.4572 (OUTLIER) cc_final: 0.4339 (tm) REVERT: B 414 LEU cc_start: 0.4620 (OUTLIER) cc_final: 0.4356 (tm) REVERT: C 414 LEU cc_start: 0.4512 (OUTLIER) cc_final: 0.4271 (tm) REVERT: D 414 LEU cc_start: 0.4510 (OUTLIER) cc_final: 0.4297 (tm) outliers start: 40 outliers final: 21 residues processed: 169 average time/residue: 1.2509 time to fit residues: 232.0853 Evaluate side-chains 158 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 414 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.0970 chunk 85 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 104 optimal weight: 0.0000 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13712 Z= 0.162 Angle : 0.570 8.047 18416 Z= 0.271 Chirality : 0.042 0.218 2116 Planarity : 0.004 0.032 2212 Dihedral : 16.109 132.063 2464 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.60 % Allowed : 16.99 % Favored : 80.42 % 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: 0.95 (0.23), residues: 1564 helix: 1.46 (0.18), residues: 948 sheet: -0.01 (0.55), residues: 88 loop : -0.72 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 264 HIS 0.001 0.000 HIS C 292 PHE 0.004 0.001 PHE D 40 TYR 0.015 0.001 TYR D 199 ARG 0.003 0.000 ARG D 391 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 154 time to evaluate : 1.351 Fit side-chains REVERT: A 388 ASP cc_start: 0.8037 (t70) cc_final: 0.7724 (t0) REVERT: A 391 ARG cc_start: 0.8696 (ttp80) cc_final: 0.8423 (ttp80) REVERT: A 414 LEU cc_start: 0.4499 (OUTLIER) cc_final: 0.4289 (tm) REVERT: B 388 ASP cc_start: 0.8005 (t70) cc_final: 0.7724 (t0) REVERT: B 414 LEU cc_start: 0.4497 (OUTLIER) cc_final: 0.4244 (tm) REVERT: C 388 ASP cc_start: 0.7990 (t70) cc_final: 0.7706 (t0) REVERT: C 414 LEU cc_start: 0.4464 (OUTLIER) cc_final: 0.4237 (tm) REVERT: D 388 ASP cc_start: 0.8050 (t70) cc_final: 0.7745 (t0) REVERT: D 391 ARG cc_start: 0.8682 (ttp80) cc_final: 0.8408 (ttp80) REVERT: D 414 LEU cc_start: 0.4519 (OUTLIER) cc_final: 0.4259 (tm) outliers start: 35 outliers final: 22 residues processed: 182 average time/residue: 1.1258 time to fit residues: 226.1861 Evaluate side-chains 170 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 144 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 414 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 88 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 150 optimal weight: 0.0570 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN D 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13712 Z= 0.162 Angle : 0.580 8.286 18416 Z= 0.271 Chirality : 0.042 0.218 2116 Planarity : 0.004 0.034 2212 Dihedral : 15.354 130.314 2464 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.19 % Allowed : 16.69 % Favored : 80.12 % 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: 1.11 (0.23), residues: 1564 helix: 1.57 (0.18), residues: 948 sheet: 0.13 (0.56), residues: 88 loop : -0.64 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 264 HIS 0.001 0.000 HIS C 292 PHE 0.004 0.001 PHE C 40 TYR 0.015 0.001 TYR D 199 ARG 0.003 0.000 ARG D 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 149 time to evaluate : 1.598 Fit side-chains REVERT: A 388 ASP cc_start: 0.7939 (t70) cc_final: 0.7712 (t0) REVERT: A 414 LEU cc_start: 0.4599 (OUTLIER) cc_final: 0.4340 (tm) REVERT: B 388 ASP cc_start: 0.7962 (t70) cc_final: 0.7751 (t0) REVERT: C 388 ASP cc_start: 0.7943 (t70) cc_final: 0.7743 (t0) REVERT: D 388 ASP cc_start: 0.7954 (t70) cc_final: 0.7726 (t0) outliers start: 43 outliers final: 25 residues processed: 178 average time/residue: 1.1227 time to fit residues: 220.4955 Evaluate side-chains 160 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 6.9990 chunk 17 optimal weight: 0.0270 chunk 85 optimal weight: 0.0570 chunk 110 optimal weight: 0.9980 chunk 127 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 chunk 150 optimal weight: 0.0870 chunk 94 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.2534 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13712 Z= 0.139 Angle : 0.564 8.217 18416 Z= 0.262 Chirality : 0.041 0.224 2116 Planarity : 0.004 0.032 2212 Dihedral : 14.180 130.368 2464 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.93 % Allowed : 19.14 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.23), residues: 1564 helix: 1.81 (0.18), residues: 940 sheet: 0.20 (0.55), residues: 88 loop : -0.61 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 264 HIS 0.001 0.000 HIS A 292 PHE 0.005 0.001 PHE B 40 TYR 0.017 0.001 TYR C 199 ARG 0.004 0.000 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 144 time to evaluate : 1.450 Fit side-chains REVERT: B 277 LYS cc_start: 0.8126 (mtmp) cc_final: 0.7837 (mtmt) REVERT: B 384 ARG cc_start: 0.7884 (mtm-85) cc_final: 0.7657 (mtp85) REVERT: C 277 LYS cc_start: 0.8148 (mtmp) cc_final: 0.7878 (mtmt) REVERT: C 384 ARG cc_start: 0.7898 (mtm-85) cc_final: 0.7665 (mtp85) REVERT: D 384 ARG cc_start: 0.7767 (mtm-85) cc_final: 0.7511 (mtp85) outliers start: 26 outliers final: 11 residues processed: 157 average time/residue: 1.3275 time to fit residues: 227.1488 Evaluate side-chains 148 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 314 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 95 optimal weight: 0.0070 chunk 102 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 14 optimal weight: 0.0370 chunk 118 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- 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: 0.7779 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13712 Z= 0.150 Angle : 0.581 8.356 18416 Z= 0.270 Chirality : 0.042 0.219 2116 Planarity : 0.004 0.036 2212 Dihedral : 13.628 130.247 2464 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.30 % Allowed : 18.10 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.23), residues: 1564 helix: 1.83 (0.18), residues: 940 sheet: 0.39 (0.56), residues: 88 loop : -0.55 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 264 HIS 0.001 0.000 HIS D 292 PHE 0.006 0.001 PHE A 397 TYR 0.007 0.001 TYR D 170 ARG 0.010 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 1.609 Fit side-chains REVERT: A 277 LYS cc_start: 0.8129 (mtmp) cc_final: 0.7851 (mtmt) REVERT: B 277 LYS cc_start: 0.8108 (mtmp) cc_final: 0.7830 (mtmt) REVERT: B 384 ARG cc_start: 0.7887 (mtm-85) cc_final: 0.7654 (mtp85) REVERT: C 277 LYS cc_start: 0.8107 (mtmp) cc_final: 0.7836 (mtmt) REVERT: C 384 ARG cc_start: 0.7910 (mtm-85) cc_final: 0.7671 (mtp85) REVERT: D 277 LYS cc_start: 0.8032 (mtmp) cc_final: 0.7783 (mtmt) REVERT: D 384 ARG cc_start: 0.7779 (mtm-85) cc_final: 0.7563 (mtp85) outliers start: 31 outliers final: 20 residues processed: 157 average time/residue: 1.2688 time to fit residues: 218.0843 Evaluate side-chains 149 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.0060 chunk 140 optimal weight: 0.4980 chunk 144 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 chunk 126 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 139 optimal weight: 0.0970 chunk 92 optimal weight: 0.0980 overall best weight: 0.2194 ------------------------------------------------------------------------------- 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: 0.7744 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13712 Z= 0.137 Angle : 0.566 8.266 18416 Z= 0.265 Chirality : 0.040 0.118 2116 Planarity : 0.004 0.049 2212 Dihedral : 12.592 130.406 2464 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.00 % Allowed : 18.69 % Favored : 79.30 % 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: 1.53 (0.23), residues: 1564 helix: 1.91 (0.18), residues: 940 sheet: 0.48 (0.56), residues: 88 loop : -0.47 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 264 HIS 0.001 0.000 HIS B 292 PHE 0.005 0.001 PHE B 40 TYR 0.007 0.001 TYR A 170 ARG 0.012 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 1.433 Fit side-chains REVERT: A 277 LYS cc_start: 0.8101 (mtmp) cc_final: 0.7786 (mtmt) REVERT: A 311 ARG cc_start: 0.7884 (ttm170) cc_final: 0.7362 (ttm-80) REVERT: B 277 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7755 (mtmt) REVERT: B 384 ARG cc_start: 0.7800 (mtm-85) cc_final: 0.7575 (mtp85) REVERT: C 277 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7735 (mtmt) REVERT: C 384 ARG cc_start: 0.7830 (mtm-85) cc_final: 0.7600 (mtp85) REVERT: D 277 LYS cc_start: 0.7989 (mtmp) cc_final: 0.7757 (mtmt) outliers start: 27 outliers final: 11 residues processed: 154 average time/residue: 1.3307 time to fit residues: 223.7919 Evaluate side-chains 147 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 277 LYS Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 102 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 123 optimal weight: 0.0870 chunk 12 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- 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: 0.7810 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13712 Z= 0.190 Angle : 0.616 8.523 18416 Z= 0.290 Chirality : 0.042 0.125 2116 Planarity : 0.004 0.030 2212 Dihedral : 12.856 130.048 2464 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.71 % Allowed : 18.92 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.23), residues: 1564 helix: 1.85 (0.18), residues: 940 sheet: 0.55 (0.57), residues: 88 loop : -0.55 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 176 HIS 0.002 0.001 HIS C 292 PHE 0.005 0.001 PHE C 174 TYR 0.008 0.001 TYR A 170 ARG 0.011 0.000 ARG B 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 1.374 Fit side-chains REVERT: A 277 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7915 (mtmt) REVERT: B 277 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7895 (mtmt) REVERT: B 384 ARG cc_start: 0.7916 (mtm-85) cc_final: 0.7681 (mtp85) REVERT: C 277 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7908 (mtmt) REVERT: C 384 ARG cc_start: 0.7924 (mtm-85) cc_final: 0.7689 (mtp85) REVERT: D 277 LYS cc_start: 0.8120 (mtmp) cc_final: 0.7889 (mtmt) outliers start: 23 outliers final: 13 residues processed: 143 average time/residue: 1.3761 time to fit residues: 214.2368 Evaluate side-chains 144 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 277 LYS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.0040 chunk 37 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.187946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.150432 restraints weight = 12818.546| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.20 r_work: 0.3321 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13712 Z= 0.170 Angle : 0.600 8.458 18416 Z= 0.281 Chirality : 0.041 0.149 2116 Planarity : 0.004 0.057 2212 Dihedral : 12.500 130.190 2464 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.71 % Allowed : 18.92 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.23), residues: 1564 helix: 1.87 (0.18), residues: 940 sheet: 0.56 (0.57), residues: 88 loop : -0.53 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 176 HIS 0.001 0.001 HIS C 292 PHE 0.004 0.001 PHE D 366 TYR 0.008 0.001 TYR A 170 ARG 0.016 0.000 ARG A 399 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4244.81 seconds wall clock time: 76 minutes 33.81 seconds (4593.81 seconds total)