Starting phenix.real_space_refine on Tue Jul 23 01:22:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekp_28209/07_2024/8ekp_28209.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekp_28209/07_2024/8ekp_28209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekp_28209/07_2024/8ekp_28209.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekp_28209/07_2024/8ekp_28209.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekp_28209/07_2024/8ekp_28209.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekp_28209/07_2024/8ekp_28209.cif" } resolution = 2.75 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= 1.000 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 112 5.16 5 C 13368 2.51 5 N 3404 2.21 5 O 3556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 113": "OE1" <-> "OE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C GLU 240": "OE1" <-> "OE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "D GLU 240": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 20448 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5042 Classifications: {'peptide': 622} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 599} Chain breaks: 4 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'TRP:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 5042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5042 Classifications: {'peptide': 622} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 599} Chain breaks: 4 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'TRP:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 5042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5042 Classifications: {'peptide': 622} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 599} Chain breaks: 4 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'TRP:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 5042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5042 Classifications: {'peptide': 622} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 599} Chain breaks: 4 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'TRP:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'PEX': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'PEX': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'PEX': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'PEX': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.05, per 1000 atoms: 0.64 Number of scatterers: 20448 At special positions: 0 Unit cell: (137.97, 137.97, 112.42, 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 112 16.00 P 8 15.00 O 3556 8.00 N 3404 7.00 C 13368 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: 8.59 Conformation dependent library (CDL) restraints added in 3.4 seconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4704 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 62.2% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.833A pdb=" N THR A 93 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 135 through 146 removed outlier: 3.644A pdb=" N LEU A 140 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN A 141 " --> pdb=" O MET A 137 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 142 " --> pdb=" O PRO A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 176 through 186 removed outlier: 3.529A pdb=" N VAL A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 297 through 305 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.955A pdb=" N VAL A 374 " --> pdb=" O HIS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 413 removed outlier: 5.217A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 466 through 492 removed outlier: 7.391A pdb=" N PHE A 472 " --> pdb=" O MET A 468 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU A 473 " --> pdb=" O ASP A 469 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 510 removed outlier: 3.687A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 518 removed outlier: 3.691A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 529 Processing helix chain 'A' and resid 533 through 538 Processing helix chain 'A' and resid 539 through 559 removed outlier: 4.081A pdb=" N VAL A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 557 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 Processing helix chain 'A' and resid 619 through 649 Processing helix chain 'A' and resid 655 through 672 Processing helix chain 'A' and resid 711 through 718 removed outlier: 3.549A pdb=" N TRP A 715 " --> pdb=" O ASN A 711 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 87 Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.833A pdb=" N THR B 93 " --> pdb=" O GLU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 135 through 146 removed outlier: 3.644A pdb=" N LEU B 140 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN B 141 " --> pdb=" O MET B 137 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 142 " --> pdb=" O PRO B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 176 through 186 removed outlier: 3.529A pdb=" N VAL B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 260 through 282 Processing helix chain 'B' and resid 297 through 305 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 323 through 327 Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.955A pdb=" N VAL B 374 " --> pdb=" O HIS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 413 removed outlier: 5.217A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 466 through 492 removed outlier: 7.391A pdb=" N PHE B 472 " --> pdb=" O MET B 468 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU B 473 " --> pdb=" O ASP B 469 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 510 removed outlier: 3.687A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 518 removed outlier: 3.691A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 529 Processing helix chain 'B' and resid 533 through 538 Processing helix chain 'B' and resid 539 through 559 removed outlier: 4.081A pdb=" N VAL B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 557 " --> pdb=" O VAL B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 Processing helix chain 'B' and resid 619 through 649 Processing helix chain 'B' and resid 655 through 672 Processing helix chain 'B' and resid 711 through 718 removed outlier: 3.549A pdb=" N TRP B 715 " --> pdb=" O ASN B 711 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 717 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR B 718 " --> pdb=" O ALA B 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.833A pdb=" N THR C 93 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 103 Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 135 through 146 removed outlier: 3.644A pdb=" N LEU C 140 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN C 141 " --> pdb=" O MET C 137 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 142 " --> pdb=" O PRO C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 174 Processing helix chain 'C' and resid 176 through 186 removed outlier: 3.529A pdb=" N VAL C 184 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 282 Processing helix chain 'C' and resid 297 through 305 Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 323 through 327 Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.955A pdb=" N VAL C 374 " --> pdb=" O HIS C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 413 removed outlier: 5.217A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 466 through 492 removed outlier: 7.391A pdb=" N PHE C 472 " --> pdb=" O MET C 468 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU C 473 " --> pdb=" O ASP C 469 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 510 removed outlier: 3.687A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 518 removed outlier: 3.691A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 529 Processing helix chain 'C' and resid 533 through 538 Processing helix chain 'C' and resid 539 through 559 removed outlier: 4.081A pdb=" N VAL C 543 " --> pdb=" O ARG C 539 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER C 557 " --> pdb=" O VAL C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 602 Processing helix chain 'C' and resid 619 through 649 Processing helix chain 'C' and resid 655 through 672 Processing helix chain 'C' and resid 711 through 718 removed outlier: 3.549A pdb=" N TRP C 715 " --> pdb=" O ASN C 711 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS C 717 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 87 Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.833A pdb=" N THR D 93 " --> pdb=" O GLU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 135 through 146 removed outlier: 3.644A pdb=" N LEU D 140 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN D 141 " --> pdb=" O MET D 137 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE D 142 " --> pdb=" O PRO D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 174 Processing helix chain 'D' and resid 176 through 186 removed outlier: 3.529A pdb=" N VAL D 184 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 282 Processing helix chain 'D' and resid 297 through 305 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 355 through 363 Processing helix chain 'D' and resid 368 through 374 removed outlier: 3.955A pdb=" N VAL D 374 " --> pdb=" O HIS D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 413 removed outlier: 5.217A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 466 through 492 removed outlier: 7.391A pdb=" N PHE D 472 " --> pdb=" O MET D 468 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU D 473 " --> pdb=" O ASP D 469 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE D 474 " --> pdb=" O SER D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 510 removed outlier: 3.687A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 518 removed outlier: 3.691A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 529 Processing helix chain 'D' and resid 533 through 538 Processing helix chain 'D' and resid 539 through 559 removed outlier: 4.080A pdb=" N VAL D 543 " --> pdb=" O ARG D 539 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 557 " --> pdb=" O VAL D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 602 Processing helix chain 'D' and resid 619 through 649 Processing helix chain 'D' and resid 655 through 672 Processing helix chain 'D' and resid 711 through 718 removed outlier: 3.549A pdb=" N TRP D 715 " --> pdb=" O ASN D 711 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS D 717 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR D 718 " --> pdb=" O ALA D 714 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 335 removed outlier: 6.986A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASP A 700 " --> pdb=" O VAL A 691 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 335 removed outlier: 6.986A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASP B 700 " --> pdb=" O VAL B 691 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 335 removed outlier: 6.986A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASP C 700 " --> pdb=" O VAL C 691 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 335 removed outlier: 6.986A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASP D 700 " --> pdb=" O VAL D 691 " (cutoff:3.500A) 1080 hydrogen bonds defined for protein. 3120 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: 6.10 Time building geometry restraints manager: 9.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3160 1.31 - 1.43: 5844 1.43 - 1.56: 11736 1.56 - 1.69: 20 1.69 - 1.81: 172 Bond restraints: 20932 Sorted by residual: bond pdb=" C4 PEX D 802 " pdb=" O4 PEX D 802 " ideal model delta sigma weight residual 1.327 1.402 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C4 PEX C 802 " pdb=" O4 PEX C 802 " ideal model delta sigma weight residual 1.327 1.402 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C4 PEX B 802 " pdb=" O4 PEX B 802 " ideal model delta sigma weight residual 1.327 1.402 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C4 PEX A 802 " pdb=" O4 PEX A 802 " ideal model delta sigma weight residual 1.327 1.402 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C4 PEX A 801 " pdb=" O4 PEX A 801 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.31e+01 ... (remaining 20927 not shown) Histogram of bond angle deviations from ideal: 100.20 - 106.97: 556 106.97 - 113.75: 11508 113.75 - 120.53: 8517 120.53 - 127.31: 7486 127.31 - 134.09: 245 Bond angle restraints: 28312 Sorted by residual: angle pdb=" O3 PEX A 802 " pdb=" P1 PEX A 802 " pdb=" O8 PEX A 802 " ideal model delta sigma weight residual 93.74 109.87 -16.13 3.00e+00 1.11e-01 2.89e+01 angle pdb=" O3 PEX B 802 " pdb=" P1 PEX B 802 " pdb=" O8 PEX B 802 " ideal model delta sigma weight residual 93.74 109.87 -16.13 3.00e+00 1.11e-01 2.89e+01 angle pdb=" O3 PEX C 802 " pdb=" P1 PEX C 802 " pdb=" O8 PEX C 802 " ideal model delta sigma weight residual 93.74 109.87 -16.13 3.00e+00 1.11e-01 2.89e+01 angle pdb=" O3 PEX D 802 " pdb=" P1 PEX D 802 " pdb=" O8 PEX D 802 " ideal model delta sigma weight residual 93.74 109.87 -16.13 3.00e+00 1.11e-01 2.89e+01 angle pdb=" O3 PEX B 801 " pdb=" P1 PEX B 801 " pdb=" O8 PEX B 801 " ideal model delta sigma weight residual 93.74 109.48 -15.74 3.00e+00 1.11e-01 2.75e+01 ... (remaining 28307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.87: 12052 30.87 - 61.73: 360 61.73 - 92.60: 20 92.60 - 123.47: 0 123.47 - 154.33: 4 Dihedral angle restraints: 12436 sinusoidal: 5164 harmonic: 7272 Sorted by residual: dihedral pdb=" CA ARG A 539 " pdb=" C ARG A 539 " pdb=" N PHE A 540 " pdb=" CA PHE A 540 " ideal model delta harmonic sigma weight residual 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA ARG B 539 " pdb=" C ARG B 539 " pdb=" N PHE B 540 " pdb=" CA PHE B 540 " ideal model delta harmonic sigma weight residual 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA ARG C 539 " pdb=" C ARG C 539 " pdb=" N PHE C 540 " pdb=" CA PHE C 540 " ideal model delta harmonic sigma weight residual 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 12433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2350 0.045 - 0.090: 646 0.090 - 0.134: 132 0.134 - 0.179: 12 0.179 - 0.224: 20 Chirality restraints: 3160 Sorted by residual: chirality pdb=" CG LEU B 636 " pdb=" CB LEU B 636 " pdb=" CD1 LEU B 636 " pdb=" CD2 LEU B 636 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU C 636 " pdb=" CB LEU C 636 " pdb=" CD1 LEU C 636 " pdb=" CD2 LEU C 636 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CG LEU A 636 " pdb=" CB LEU A 636 " pdb=" CD1 LEU A 636 " pdb=" CD2 LEU A 636 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 3157 not shown) Planarity restraints: 3492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 530 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.21e+00 pdb=" CD GLN B 530 " 0.043 2.00e-02 2.50e+03 pdb=" OE1 GLN B 530 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 GLN B 530 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 530 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.21e+00 pdb=" CD GLN C 530 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLN C 530 " 0.016 2.00e-02 2.50e+03 pdb=" NE2 GLN C 530 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 530 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.21e+00 pdb=" CD GLN A 530 " 0.043 2.00e-02 2.50e+03 pdb=" OE1 GLN A 530 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 GLN A 530 " -0.014 2.00e-02 2.50e+03 ... (remaining 3489 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5224 2.80 - 3.32: 17880 3.32 - 3.85: 33952 3.85 - 4.37: 41364 4.37 - 4.90: 69132 Nonbonded interactions: 167552 Sorted by model distance: nonbonded pdb=" O GLY D 131 " pdb=" OG SER D 176 " model vdw 2.269 2.440 nonbonded pdb=" O GLY A 131 " pdb=" OG SER A 176 " model vdw 2.269 2.440 nonbonded pdb=" O GLY B 131 " pdb=" OG SER B 176 " model vdw 2.269 2.440 nonbonded pdb=" O GLY C 131 " pdb=" OG SER C 176 " model vdw 2.269 2.440 nonbonded pdb=" O MET C 468 " pdb=" N1 PEX C 801 " model vdw 2.415 2.520 ... (remaining 167547 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: 6.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 56.430 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 20932 Z= 0.258 Angle : 0.874 16.126 28312 Z= 0.417 Chirality : 0.044 0.224 3160 Planarity : 0.007 0.093 3492 Dihedral : 14.700 154.331 7732 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.14), residues: 2448 helix: -2.37 (0.09), residues: 1424 sheet: 1.00 (0.52), residues: 112 loop : -1.28 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 333 HIS 0.005 0.001 HIS C 251 PHE 0.014 0.001 PHE D 161 TYR 0.022 0.001 TYR B 544 ARG 0.017 0.001 ARG C 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 2.197 Fit side-chains REVERT: A 76 ASP cc_start: 0.7519 (t0) cc_final: 0.7085 (t0) REVERT: A 617 ARG cc_start: 0.7042 (ttm170) cc_final: 0.6836 (ttm-80) REVERT: A 654 ASP cc_start: 0.6134 (t70) cc_final: 0.5786 (t70) REVERT: A 701 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7385 (mt-10) REVERT: B 76 ASP cc_start: 0.7524 (t0) cc_final: 0.6384 (p0) REVERT: B 617 ARG cc_start: 0.7050 (ttm170) cc_final: 0.6844 (ttm-80) REVERT: B 654 ASP cc_start: 0.6138 (t70) cc_final: 0.5792 (t70) REVERT: B 701 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7399 (mt-10) REVERT: C 76 ASP cc_start: 0.7525 (t0) cc_final: 0.7094 (t0) REVERT: C 617 ARG cc_start: 0.7037 (ttm170) cc_final: 0.6830 (ttm-80) REVERT: C 654 ASP cc_start: 0.6129 (t70) cc_final: 0.5776 (t70) REVERT: C 701 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7397 (mt-10) REVERT: D 76 ASP cc_start: 0.7519 (t0) cc_final: 0.7087 (t0) REVERT: D 617 ARG cc_start: 0.7049 (ttm170) cc_final: 0.6844 (ttm-80) REVERT: D 654 ASP cc_start: 0.6138 (t70) cc_final: 0.5788 (t70) REVERT: D 701 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7402 (mt-10) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 1.1868 time to fit residues: 513.3490 Evaluate side-chains 311 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 chunk 225 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 186 ASN A 234 HIS A 235 GLN A 354 ASN A 383 GLN A 487 GLN A 673 ASN B 165 HIS B 186 ASN B 235 GLN B 354 ASN B 383 GLN B 487 GLN B 673 ASN C 165 HIS C 186 ASN C 235 GLN C 354 ASN C 383 GLN C 487 GLN C 673 ASN D 165 HIS D 186 ASN D 234 HIS D 235 GLN D 354 ASN D 383 GLN D 487 GLN D 673 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 20932 Z= 0.535 Angle : 0.740 9.618 28312 Z= 0.374 Chirality : 0.049 0.161 3160 Planarity : 0.007 0.068 3492 Dihedral : 11.365 149.560 2960 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.97 % Allowed : 6.91 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.50 (0.16), residues: 2448 helix: 0.01 (0.13), residues: 1476 sheet: 1.13 (0.50), residues: 112 loop : -0.96 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 509 HIS 0.006 0.002 HIS D 521 PHE 0.030 0.003 PHE D 407 TYR 0.024 0.003 TYR B 515 ARG 0.005 0.001 ARG B 317 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 349 time to evaluate : 2.238 Fit side-chains REVERT: A 197 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7426 (ttm170) REVERT: A 372 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8523 (mtp) REVERT: A 647 GLU cc_start: 0.7481 (tt0) cc_final: 0.7245 (tt0) REVERT: A 683 HIS cc_start: 0.7563 (t-90) cc_final: 0.7125 (t-90) REVERT: B 197 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7439 (ttm170) REVERT: B 647 GLU cc_start: 0.7484 (tt0) cc_final: 0.7252 (tt0) REVERT: B 683 HIS cc_start: 0.7564 (t-90) cc_final: 0.7124 (t-90) REVERT: C 197 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7435 (ttm170) REVERT: C 372 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8522 (mtp) REVERT: C 647 GLU cc_start: 0.7486 (tt0) cc_final: 0.7255 (tt0) REVERT: C 683 HIS cc_start: 0.7568 (t-90) cc_final: 0.7132 (t-90) REVERT: D 197 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7432 (ttm170) REVERT: D 372 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8522 (mtp) REVERT: D 683 HIS cc_start: 0.7559 (t-90) cc_final: 0.7124 (t-90) outliers start: 43 outliers final: 20 residues processed: 364 average time/residue: 1.2274 time to fit residues: 509.4127 Evaluate side-chains 337 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 310 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 416 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 225 optimal weight: 0.9990 chunk 243 optimal weight: 0.7980 chunk 200 optimal weight: 0.6980 chunk 223 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 234 HIS A 235 GLN A 414 GLN B 186 ASN B 235 GLN B 452 GLN C 186 ASN C 235 GLN C 414 GLN D 186 ASN D 234 HIS D 235 GLN D 414 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20932 Z= 0.153 Angle : 0.482 7.657 28312 Z= 0.250 Chirality : 0.037 0.160 3160 Planarity : 0.004 0.055 3492 Dihedral : 10.357 142.707 2960 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.47 % Allowed : 10.21 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.60 (0.17), residues: 2448 helix: 1.12 (0.14), residues: 1476 sheet: 1.32 (0.52), residues: 112 loop : -0.94 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 333 HIS 0.002 0.001 HIS D 521 PHE 0.014 0.001 PHE B 540 TYR 0.012 0.001 TYR D 525 ARG 0.005 0.000 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 320 time to evaluate : 2.237 Fit side-chains REVERT: A 197 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7419 (ttm170) REVERT: A 234 HIS cc_start: 0.7498 (m-70) cc_final: 0.7183 (m170) REVERT: A 647 GLU cc_start: 0.7347 (tt0) cc_final: 0.7013 (mp0) REVERT: B 197 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7422 (ttm170) REVERT: B 647 GLU cc_start: 0.7341 (tt0) cc_final: 0.7108 (tt0) REVERT: C 197 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7453 (ttm170) REVERT: C 647 GLU cc_start: 0.7355 (tt0) cc_final: 0.7118 (tt0) REVERT: D 197 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7456 (ttm170) REVERT: D 234 HIS cc_start: 0.7477 (m-70) cc_final: 0.7163 (m170) REVERT: D 647 GLU cc_start: 0.7341 (tt0) cc_final: 0.7016 (mp0) outliers start: 54 outliers final: 28 residues processed: 345 average time/residue: 1.2502 time to fit residues: 491.4614 Evaluate side-chains 329 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 297 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 641 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 214 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 673 ASN B 186 ASN B 235 GLN B 673 ASN C 186 ASN C 452 GLN C 673 ASN D 186 ASN D 235 GLN D 673 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 20932 Z= 0.373 Angle : 0.605 9.279 28312 Z= 0.307 Chirality : 0.044 0.220 3160 Planarity : 0.005 0.058 3492 Dihedral : 10.745 146.949 2960 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.88 % Allowed : 12.00 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.55 (0.17), residues: 2448 helix: 1.10 (0.14), residues: 1476 sheet: 1.59 (0.59), residues: 88 loop : -0.99 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 333 HIS 0.004 0.001 HIS D 251 PHE 0.018 0.002 PHE D 407 TYR 0.018 0.002 TYR D 515 ARG 0.005 0.001 ARG D 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 329 time to evaluate : 2.240 Fit side-chains REVERT: A 197 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7341 (ttm170) REVERT: A 234 HIS cc_start: 0.7476 (m-70) cc_final: 0.7244 (m170) REVERT: A 647 GLU cc_start: 0.7533 (tt0) cc_final: 0.7292 (tt0) REVERT: B 197 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7345 (ttm170) REVERT: B 647 GLU cc_start: 0.7554 (tt0) cc_final: 0.7301 (tt0) REVERT: C 197 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7361 (ttm170) REVERT: D 197 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7356 (ttm170) REVERT: D 234 HIS cc_start: 0.7482 (m-70) cc_final: 0.7251 (m170) outliers start: 63 outliers final: 36 residues processed: 353 average time/residue: 1.1436 time to fit residues: 462.7191 Evaluate side-chains 356 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 316 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 641 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 0.6980 chunk 136 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 204 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 235 GLN A 452 GLN B 186 ASN B 235 GLN C 186 ASN C 235 GLN D 186 ASN D 235 GLN D 452 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20932 Z= 0.269 Angle : 0.545 9.086 28312 Z= 0.278 Chirality : 0.041 0.177 3160 Planarity : 0.004 0.054 3492 Dihedral : 10.436 144.541 2960 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.93 % Allowed : 13.46 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.17), residues: 2448 helix: 1.31 (0.14), residues: 1468 sheet: 1.65 (0.59), residues: 88 loop : -0.92 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 333 HIS 0.003 0.001 HIS D 202 PHE 0.019 0.002 PHE B 540 TYR 0.014 0.002 TYR D 515 ARG 0.005 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 318 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7362 (ttm170) REVERT: A 645 MET cc_start: 0.7841 (mtm) cc_final: 0.7545 (mtm) REVERT: B 197 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7365 (ttm170) REVERT: C 197 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7381 (ttm170) REVERT: C 645 MET cc_start: 0.7856 (mtm) cc_final: 0.7550 (mtm) REVERT: D 197 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7373 (ttm170) outliers start: 64 outliers final: 43 residues processed: 350 average time/residue: 1.1993 time to fit residues: 479.9072 Evaluate side-chains 363 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 316 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 535 ARG Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 641 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 7.9990 chunk 215 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 239 optimal weight: 0.9980 chunk 199 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 19 optimal weight: 0.0470 chunk 79 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 235 GLN B 186 ASN B 235 GLN C 186 ASN C 235 GLN D 186 ASN D 235 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20932 Z= 0.181 Angle : 0.491 9.319 28312 Z= 0.252 Chirality : 0.039 0.180 3160 Planarity : 0.004 0.049 3492 Dihedral : 9.853 141.235 2960 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.47 % Allowed : 14.15 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.08 (0.17), residues: 2448 helix: 1.58 (0.14), residues: 1468 sheet: 1.77 (0.59), residues: 88 loop : -0.86 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 333 HIS 0.002 0.001 HIS A 251 PHE 0.014 0.001 PHE B 405 TYR 0.010 0.001 TYR B 515 ARG 0.006 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 326 time to evaluate : 2.246 Fit side-chains REVERT: A 197 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7365 (ttm170) REVERT: A 645 MET cc_start: 0.7821 (mtm) cc_final: 0.7463 (mtm) REVERT: B 197 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7368 (ttm170) REVERT: C 197 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7378 (ttm170) REVERT: C 645 MET cc_start: 0.7819 (mtm) cc_final: 0.7520 (mtm) REVERT: D 197 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7409 (ttm170) outliers start: 54 outliers final: 38 residues processed: 352 average time/residue: 1.2227 time to fit residues: 491.6351 Evaluate side-chains 354 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 312 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 641 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 133 optimal weight: 0.2980 chunk 239 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 235 GLN A 530 GLN B 186 ASN B 235 GLN B 530 GLN C 186 ASN C 235 GLN C 530 GLN D 186 ASN D 235 GLN D 530 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20932 Z= 0.161 Angle : 0.481 10.125 28312 Z= 0.244 Chirality : 0.038 0.199 3160 Planarity : 0.003 0.048 3492 Dihedral : 9.469 137.554 2960 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.93 % Allowed : 13.92 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.23 (0.17), residues: 2448 helix: 1.67 (0.14), residues: 1476 sheet: 1.86 (0.60), residues: 88 loop : -0.76 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 333 HIS 0.002 0.001 HIS D 251 PHE 0.020 0.001 PHE C 540 TYR 0.011 0.001 TYR D 471 ARG 0.006 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 322 time to evaluate : 2.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7380 (ttm170) REVERT: B 197 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7382 (ttm170) REVERT: C 197 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7408 (ttm170) REVERT: D 197 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7409 (ttm170) outliers start: 64 outliers final: 34 residues processed: 364 average time/residue: 1.2060 time to fit residues: 502.7615 Evaluate side-chains 342 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 304 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 535 ARG Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 641 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.6381 > 50: distance: 85 - 90: 4.355 distance: 90 - 91: 5.808 distance: 91 - 92: 7.620 distance: 91 - 94: 3.650 distance: 92 - 93: 6.408 distance: 92 - 98: 7.837 distance: 93 - 130: 5.143 distance: 94 - 95: 4.448 distance: 95 - 96: 3.387 distance: 95 - 97: 14.151 distance: 98 - 99: 6.149 distance: 99 - 100: 24.409 distance: 99 - 102: 8.714 distance: 100 - 101: 11.114 distance: 100 - 109: 20.010 distance: 101 - 138: 13.862 distance: 102 - 103: 7.901 distance: 103 - 104: 4.830 distance: 104 - 105: 4.379 distance: 105 - 106: 5.147 distance: 106 - 107: 4.423 distance: 106 - 108: 5.475 distance: 109 - 110: 12.406 distance: 110 - 111: 8.220 distance: 111 - 112: 11.709 distance: 111 - 119: 5.333 distance: 113 - 114: 11.940 distance: 114 - 115: 21.260 distance: 114 - 116: 19.426 distance: 115 - 117: 7.727 distance: 116 - 118: 16.791 distance: 117 - 118: 20.722 distance: 119 - 120: 15.035 distance: 120 - 121: 20.251 distance: 120 - 123: 15.312 distance: 121 - 122: 16.096 distance: 121 - 130: 19.358 distance: 123 - 124: 7.511 distance: 124 - 125: 3.941 distance: 125 - 126: 3.556 distance: 126 - 127: 4.298 distance: 127 - 128: 5.414 distance: 127 - 129: 3.686 distance: 130 - 131: 5.101 distance: 131 - 132: 8.834 distance: 131 - 134: 6.647 distance: 132 - 133: 12.701 distance: 132 - 138: 22.100 distance: 134 - 135: 6.056 distance: 135 - 136: 4.832 distance: 136 - 137: 10.211 distance: 138 - 139: 6.506 distance: 139 - 140: 30.642 distance: 139 - 142: 35.749 distance: 140 - 141: 27.412 distance: 140 - 145: 29.644 distance: 142 - 143: 16.042 distance: 142 - 144: 10.743 distance: 145 - 146: 14.279 distance: 146 - 147: 46.843 distance: 146 - 149: 15.428 distance: 147 - 148: 25.788 distance: 147 - 152: 35.350 distance: 149 - 150: 18.548 distance: 149 - 151: 23.684 distance: 152 - 153: 9.027 distance: 153 - 154: 22.555 distance: 153 - 156: 16.965 distance: 154 - 155: 4.853 distance: 154 - 160: 10.915 distance: 156 - 157: 7.690 distance: 157 - 158: 19.226 distance: 157 - 159: 25.255 distance: 160 - 161: 14.638 distance: 161 - 162: 24.752 distance: 161 - 164: 7.958 distance: 162 - 163: 15.508 distance: 162 - 169: 6.868 distance: 164 - 165: 14.179 distance: 165 - 166: 23.712 distance: 166 - 167: 13.416 distance: 166 - 168: 22.299 distance: 169 - 170: 6.818 distance: 169 - 175: 3.571 distance: 170 - 171: 36.293 distance: 170 - 173: 8.968 distance: 171 - 172: 8.110 distance: 171 - 176: 31.112 distance: 172 - 200: 26.905 distance: 173 - 174: 7.759 distance: 174 - 175: 14.273