Starting phenix.real_space_refine on Thu Feb 15 02:23:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7q_30300/02_2024/7c7q_30300_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7q_30300/02_2024/7c7q_30300.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7q_30300/02_2024/7c7q_30300_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7q_30300/02_2024/7c7q_30300_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7q_30300/02_2024/7c7q_30300_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7q_30300/02_2024/7c7q_30300.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7q_30300/02_2024/7c7q_30300.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7q_30300/02_2024/7c7q_30300_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7q_30300/02_2024/7c7q_30300_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 61 5.16 5 Cl 1 4.86 5 C 7057 2.51 5 N 1789 2.21 5 O 1983 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 168": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 236": "OD1" <-> "OD2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 528": "OD1" <-> "OD2" Residue "A TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 732": "OD1" <-> "OD2" Residue "A PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 744": "OE1" <-> "OE2" Residue "A GLU 745": "OE1" <-> "OE2" Residue "A ARG 764": "NH1" <-> "NH2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 214": "OD1" <-> "OD2" Residue "B TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 256": "OD1" <-> "OD2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 339": "OE1" <-> "OE2" Residue "B PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 387": "OD1" <-> "OD2" Residue "B ASP 392": "OD1" <-> "OD2" Residue "B PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 421": "OE1" <-> "OE2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 454": "OD1" <-> "OD2" Residue "B PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 550": "OE1" <-> "OE2" Residue "B PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 577": "NH1" <-> "NH2" Residue "B GLU 626": "OE1" <-> "OE2" Residue "B TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 638": "OD1" <-> "OD2" Residue "B TYR 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 715": "OD1" <-> "OD2" Residue "B PHE 721": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10894 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5406 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 28, 'TRANS': 649} Chain breaks: 2 Chain: "B" Number of atoms: 5339 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 670, 5328 Classifications: {'peptide': 670} Link IDs: {'PTRANS': 27, 'TRANS': 642} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 670, 5328 Classifications: {'peptide': 670} Link IDs: {'PTRANS': 27, 'TRANS': 642} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 5433 Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 107 Unusual residues: {'2C0': 1, 'FN0': 1, 'NAG': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE B 572 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 572 " occ=0.50 Time building chain proxies: 8.57, per 1000 atoms: 0.79 Number of scatterers: 10894 At special positions: 0 Unit cell: (78.078, 100.386, 165.282, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 61 16.00 F 3 9.00 O 1983 8.00 N 1789 7.00 C 7057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 246 " distance=2.04 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 663 " - pdb=" SG CYS A 761 " distance=1.88 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 266 " distance=2.03 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 648 " distance=2.03 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 Atom "HETATM10799 O5 NAG A1004 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1001 " - " ASN A 409 " " NAG A1002 " - " ASN A 440 " " NAG A1003 " - " ASN A 482 " " NAG A1004 " - " ASN A 502 " " NAG A1005 " - " ASN A 514 " " NAG B1001 " - " ASN B 389 " " NAG B1002 " - " ASN B 404 " " NAG B1003 " - " ASN B 453 " Time building additional restraints: 4.61 Conformation dependent library (CDL) restraints added in 2.8 seconds 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2524 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 9 sheets defined 50.5% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'A' and resid 184 through 201 removed outlier: 3.882A pdb=" N CYS A 188 " --> pdb=" O GLY A 185 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLN A 189 " --> pdb=" O GLN A 186 " (cutoff:3.500A) Proline residue: A 190 - end of helix removed outlier: 3.794A pdb=" N GLU A 193 " --> pdb=" O PRO A 190 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET A 194 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU A 196 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP A 198 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 199 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER A 201 " --> pdb=" O ASP A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.666A pdb=" N LYS A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 259 removed outlier: 4.672A pdb=" N ARG A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N MET A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 275 Processing helix chain 'A' and resid 290 through 303 removed outlier: 3.654A pdb=" N ASN A 294 " --> pdb=" O THR A 291 " (cutoff:3.500A) Proline residue: A 295 - end of helix removed outlier: 3.733A pdb=" N LYS A 303 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 333 Processing helix chain 'A' and resid 348 through 357 Processing helix chain 'A' and resid 368 through 381 removed outlier: 4.092A pdb=" N LYS A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 418 removed outlier: 4.154A pdb=" N GLU A 417 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 453 Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 467 through 483 removed outlier: 3.660A pdb=" N ILE A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 514 Processing helix chain 'A' and resid 589 through 615 Processing helix chain 'A' and resid 621 through 623 No H-bonds generated for 'chain 'A' and resid 621 through 623' Processing helix chain 'A' and resid 627 through 648 removed outlier: 4.583A pdb=" N VAL A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N PHE A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 659 through 691 removed outlier: 3.839A pdb=" N CYS A 663 " --> pdb=" O PRO A 660 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 664 " --> pdb=" O PHE A 661 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N TRP A 668 " --> pdb=" O ALA A 665 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 669 " --> pdb=" O ARG A 666 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 670 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 672 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 676 " --> pdb=" O GLY A 673 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLY A 679 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N SER A 680 " --> pdb=" O GLY A 677 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR A 683 " --> pdb=" O SER A 680 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS A 684 " --> pdb=" O MET A 681 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 691 " --> pdb=" O VAL A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 731 removed outlier: 3.949A pdb=" N VAL A 714 " --> pdb=" O LEU A 710 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TRP A 728 " --> pdb=" O THR A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 790 Processing helix chain 'A' and resid 802 through 825 Proline residue: A 821 - end of helix removed outlier: 3.604A pdb=" N MET A 824 " --> pdb=" O ALA A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 860 removed outlier: 3.884A pdb=" N ALA A 840 " --> pdb=" O PHE A 836 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER A 844 " --> pdb=" O ALA A 840 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) Proline residue: A 855 - end of helix Processing helix chain 'B' and resid 70 through 91 removed outlier: 4.200A pdb=" N ARG B 75 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU B 78 " --> pdb=" O ARG B 75 " (cutoff:3.500A) Proline residue: B 79 - end of helix removed outlier: 4.149A pdb=" N GLU B 82 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU B 86 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 89 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU B 91 " --> pdb=" O ILE B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 123 removed outlier: 3.783A pdb=" N LEU B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 148 removed outlier: 3.671A pdb=" N ILE B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER B 145 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 146 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLN B 147 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N GLY B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 164 Processing helix chain 'B' and resid 179 through 192 removed outlier: 3.805A pdb=" N VAL B 182 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN B 183 " --> pdb=" O ASN B 180 " (cutoff:3.500A) Proline residue: B 184 - end of helix removed outlier: 3.571A pdb=" N LEU B 187 " --> pdb=" O PRO B 184 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS B 191 " --> pdb=" O LYS B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 218 removed outlier: 3.631A pdb=" N GLY B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 246 Processing helix chain 'B' and resid 257 through 267 removed outlier: 3.933A pdb=" N ALA B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 291 No H-bonds generated for 'chain 'B' and resid 289 through 291' Processing helix chain 'B' and resid 304 through 311 Processing helix chain 'B' and resid 335 through 345 Processing helix chain 'B' and resid 355 through 375 Processing helix chain 'B' and resid 393 through 404 Processing helix chain 'B' and resid 479 through 505 removed outlier: 3.664A pdb=" N LEU B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 513 No H-bonds generated for 'chain 'B' and resid 510 through 513' Processing helix chain 'B' and resid 517 through 537 removed outlier: 3.694A pdb=" N ILE B 523 " --> pdb=" O MET B 519 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B 532 " --> pdb=" O MET B 528 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N PHE B 535 " --> pdb=" O TYR B 531 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE B 537 " --> pdb=" O SER B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 582 removed outlier: 3.997A pdb=" N THR B 554 " --> pdb=" O GLU B 550 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR B 557 " --> pdb=" O CYS B 553 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET B 571 " --> pdb=" O ALA B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 618 removed outlier: 3.921A pdb=" N ILE B 600 " --> pdb=" O LYS B 596 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL B 601 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 618 " --> pdb=" O CYS B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 679 removed outlier: 3.652A pdb=" N LEU B 674 " --> pdb=" O PHE B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 710 removed outlier: 3.729A pdb=" N ILE B 704 " --> pdb=" O GLY B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 747 removed outlier: 3.536A pdb=" N LEU B 726 " --> pdb=" O CYS B 722 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE B 728 " --> pdb=" O VAL B 724 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU B 736 " --> pdb=" O SER B 732 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL B 739 " --> pdb=" O THR B 735 " (cutoff:3.500A) Proline residue: B 742 - end of helix removed outlier: 3.853A pdb=" N THR B 746 " --> pdb=" O PRO B 742 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 209 through 216 removed outlier: 6.220A pdb=" N ARG A 168 " --> pdb=" O GLU A 210 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LYS A 212 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL A 170 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE A 214 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE A 172 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N HIS A 216 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA A 174 " --> pdb=" O HIS A 216 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 264 through 266 Processing sheet with id= C, first strand: chain 'A' and resid 559 through 562 removed outlier: 6.877A pdb=" N ILE A 539 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR A 552 " --> pdb=" O THR A 537 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR A 537 " --> pdb=" O TYR A 552 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR A 425 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE A 393 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LYS A 308 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N VAL A 363 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA A 310 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N LEU A 365 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE A 312 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLU A 336 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N THR A 311 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N THR A 338 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 13.091A pdb=" N GLN A 313 " --> pdb=" O THR A 338 " (cutoff:3.500A) removed outlier: 9.923A pdb=" N ARG A 340 " --> pdb=" O GLN A 313 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 517 through 520 Processing sheet with id= E, first strand: chain 'A' and resid 581 through 584 Processing sheet with id= F, first strand: chain 'B' and resid 98 through 105 removed outlier: 7.420A pdb=" N MET B 59 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N VAL B 130 " --> pdb=" O MET B 59 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU B 61 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLY B 132 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL B 152 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLY B 132 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N LEU B 154 " --> pdb=" O GLY B 132 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.353A pdb=" N THR B 200 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N PHE B 232 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR B 202 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLN B 278 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N GLY B 253 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE B 280 " --> pdb=" O GLY B 253 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE B 315 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY B 440 " --> pdb=" O PHE B 428 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLN B 430 " --> pdb=" O LYS B 438 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LYS B 438 " --> pdb=" O GLN B 430 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLN B 432 " --> pdb=" O GLU B 436 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLU B 436 " --> pdb=" O GLN B 432 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 407 through 410 Processing sheet with id= I, first strand: chain 'B' and resid 470 through 474 removed outlier: 6.898A pdb=" N SER B 640 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N GLN B 473 " --> pdb=" O SER B 640 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ARG B 642 " --> pdb=" O GLN B 473 " (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1315 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: 3.32 Time building geometry restraints manager: 4.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2454 1.33 - 1.45: 2440 1.45 - 1.57: 6158 1.57 - 1.69: 0 1.69 - 1.81: 98 Bond restraints: 11150 Sorted by residual: bond pdb=" C6 FN0 A1006 " pdb=" O1 FN0 A1006 " ideal model delta sigma weight residual 1.514 1.383 0.131 2.00e-02 2.50e+03 4.31e+01 bond pdb=" C17 FN0 A1006 " pdb=" F1 FN0 A1006 " ideal model delta sigma weight residual 1.365 1.290 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C13 FN0 A1006 " pdb=" O3 FN0 A1006 " ideal model delta sigma weight residual 1.185 1.259 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C13 FN0 A1006 " pdb=" O1 FN0 A1006 " ideal model delta sigma weight residual 1.422 1.353 0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C13 FN0 A1006 " pdb=" C7 FN0 A1006 " ideal model delta sigma weight residual 1.467 1.521 -0.054 2.00e-02 2.50e+03 7.34e+00 ... (remaining 11145 not shown) Histogram of bond angle deviations from ideal: 98.07 - 105.26: 218 105.26 - 112.46: 5676 112.46 - 119.65: 3826 119.65 - 126.85: 5250 126.85 - 134.05: 163 Bond angle restraints: 15133 Sorted by residual: angle pdb=" N THR B 238 " pdb=" CA THR B 238 " pdb=" C THR B 238 " ideal model delta sigma weight residual 113.38 99.51 13.87 1.23e+00 6.61e-01 1.27e+02 angle pdb=" N ASN A 409 " pdb=" CA ASN A 409 " pdb=" C ASN A 409 " ideal model delta sigma weight residual 111.36 121.71 -10.35 1.09e+00 8.42e-01 9.02e+01 angle pdb=" C ILE B 534 " pdb=" CA ILE B 534 " pdb=" CB ILE B 534 " ideal model delta sigma weight residual 112.14 106.19 5.95 1.35e+00 5.49e-01 1.94e+01 angle pdb=" N ASP B 454 " pdb=" CA ASP B 454 " pdb=" CB ASP B 454 " ideal model delta sigma weight residual 114.17 109.36 4.81 1.14e+00 7.69e-01 1.78e+01 angle pdb=" C17 FN0 A1006 " pdb=" C7 FN0 A1006 " pdb=" C5 FN0 A1006 " ideal model delta sigma weight residual 109.63 121.99 -12.36 3.00e+00 1.11e-01 1.70e+01 ... (remaining 15128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 6244 17.37 - 34.75: 378 34.75 - 52.12: 86 52.12 - 69.49: 9 69.49 - 86.86: 5 Dihedral angle restraints: 6722 sinusoidal: 2800 harmonic: 3922 Sorted by residual: dihedral pdb=" CB CYS B 553 " pdb=" SG CYS B 553 " pdb=" SG CYS B 648 " pdb=" CB CYS B 648 " ideal model delta sinusoidal sigma weight residual 93.00 166.99 -73.99 1 1.00e+01 1.00e-02 6.95e+01 dihedral pdb=" CB CYS A 663 " pdb=" SG CYS A 663 " pdb=" SG CYS A 761 " pdb=" CB CYS A 761 " ideal model delta sinusoidal sigma weight residual -86.00 -25.51 -60.49 1 1.00e+01 1.00e-02 4.87e+01 dihedral pdb=" CB CYS B 237 " pdb=" SG CYS B 237 " pdb=" SG CYS B 266 " pdb=" CB CYS B 266 " ideal model delta sinusoidal sigma weight residual -86.00 -29.81 -56.19 1 1.00e+01 1.00e-02 4.26e+01 ... (remaining 6719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.098: 1726 1.098 - 2.196: 1 2.196 - 3.295: 0 3.295 - 4.393: 0 4.393 - 5.491: 1 Chirality restraints: 1728 Sorted by residual: chirality pdb=" C7 FN0 A1006 " pdb=" C13 FN0 A1006 " pdb=" C17 FN0 A1006 " pdb=" C5 FN0 A1006 " both_signs ideal model delta sigma weight residual False -2.69 2.80 -5.49 2.00e-01 2.50e+01 7.54e+02 chirality pdb=" C1 NAG A1005 " pdb=" ND2 ASN A 514 " pdb=" C2 NAG A1005 " pdb=" O5 NAG A1005 " both_signs ideal model delta sigma weight residual False -2.40 -1.13 -1.27 2.00e-01 2.50e+01 4.06e+01 chirality pdb=" C1 NAG B1003 " pdb=" ND2 ASN B 453 " pdb=" C2 NAG B1003 " pdb=" O5 NAG B1003 " both_signs ideal model delta sigma weight residual False -2.40 -1.35 -1.05 2.00e-01 2.50e+01 2.74e+01 ... (remaining 1725 not shown) Planarity restraints: 1887 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 502 " -0.028 2.00e-02 2.50e+03 2.85e-01 1.02e+03 pdb=" CG ASN A 502 " 0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN A 502 " -0.212 2.00e-02 2.50e+03 pdb=" ND2 ASN A 502 " 0.494 2.00e-02 2.50e+03 pdb=" C1 NAG A1004 " -0.333 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1001 " -0.305 2.00e-02 2.50e+03 2.57e-01 8.28e+02 pdb=" C7 NAG A1001 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG A1001 " -0.187 2.00e-02 2.50e+03 pdb=" N2 NAG A1001 " 0.443 2.00e-02 2.50e+03 pdb=" O7 NAG A1001 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 409 " 0.208 2.00e-02 2.50e+03 2.56e-01 8.17e+02 pdb=" CG ASN A 409 " -0.086 2.00e-02 2.50e+03 pdb=" OD1 ASN A 409 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN A 409 " -0.420 2.00e-02 2.50e+03 pdb=" C1 NAG A1001 " 0.315 2.00e-02 2.50e+03 ... (remaining 1884 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 205 2.69 - 3.25: 10921 3.25 - 3.80: 16794 3.80 - 4.35: 22380 4.35 - 4.90: 36807 Nonbonded interactions: 87107 Sorted by model distance: nonbonded pdb=" O3 NAG A1003 " pdb=" O7 NAG A1003 " model vdw 2.144 2.440 nonbonded pdb=" O PHE A 366 " pdb=" OH TYR A 396 " model vdw 2.178 2.440 nonbonded pdb=" CG ASN A 502 " pdb=" O5 NAG A1004 " model vdw 2.205 2.616 nonbonded pdb=" OD2 ASP B 360 " pdb=" OG1 THR B 412 " model vdw 2.217 2.440 nonbonded pdb=" O ASN A 409 " pdb=" OD1 ASN A 409 " model vdw 2.220 3.040 ... (remaining 87102 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 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: 2.900 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: 6.670 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 35.850 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 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:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 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 0.131 11150 Z= 0.276 Angle : 0.745 13.869 15133 Z= 0.433 Chirality : 0.148 5.491 1728 Planarity : 0.009 0.257 1879 Dihedral : 11.722 86.863 4177 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: -2.81 (0.20), residues: 1337 helix: -1.57 (0.17), residues: 696 sheet: -1.85 (0.31), residues: 212 loop : -1.99 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 576 HIS 0.006 0.001 HIS B 647 PHE 0.012 0.001 PHE A 366 TYR 0.010 0.001 TYR B 314 ARG 0.004 0.000 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.7955 (m-30) cc_final: 0.7703 (m-30) REVERT: A 209 TYR cc_start: 0.8512 (m-80) cc_final: 0.8253 (m-80) REVERT: A 336 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7208 (mm-30) REVERT: A 352 LYS cc_start: 0.8499 (mttp) cc_final: 0.8214 (mtmt) REVERT: A 358 ASP cc_start: 0.6641 (t70) cc_final: 0.6148 (t70) REVERT: A 536 TRP cc_start: 0.8433 (m100) cc_final: 0.8222 (m100) REVERT: A 734 LEU cc_start: 0.7129 (mp) cc_final: 0.6850 (pt) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 1.1759 time to fit residues: 242.0789 Evaluate side-chains 133 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 56 optimal weight: 0.3980 chunk 34 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 ASN B 246 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11150 Z= 0.223 Angle : 0.773 26.651 15133 Z= 0.354 Chirality : 0.071 1.986 1728 Planarity : 0.004 0.037 1879 Dihedral : 8.342 107.056 1641 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.21 % Allowed : 10.30 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.68 (0.22), residues: 1337 helix: -0.54 (0.19), residues: 690 sheet: -1.45 (0.32), residues: 216 loop : -1.62 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 558 HIS 0.005 0.001 HIS B 647 PHE 0.024 0.001 PHE A 773 TYR 0.015 0.001 TYR A 776 ARG 0.006 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.7994 (m-30) cc_final: 0.7721 (m-30) REVERT: A 209 TYR cc_start: 0.8514 (m-80) cc_final: 0.8306 (m-80) REVERT: A 336 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7214 (mm-30) REVERT: A 352 LYS cc_start: 0.8430 (mttp) cc_final: 0.8162 (mtmt) REVERT: A 358 ASP cc_start: 0.6578 (t70) cc_final: 0.6122 (t70) REVERT: A 456 ARG cc_start: 0.7641 (mtm-85) cc_final: 0.7424 (mpp80) REVERT: A 536 TRP cc_start: 0.8409 (m100) cc_final: 0.8207 (m100) REVERT: B 102 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7011 (mtm180) REVERT: B 341 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.6189 (mt-10) REVERT: B 441 GLU cc_start: 0.6887 (pp20) cc_final: 0.6579 (pp20) outliers start: 26 outliers final: 13 residues processed: 154 average time/residue: 1.2068 time to fit residues: 201.3459 Evaluate side-chains 146 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 761 CYS Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 657 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 120 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7265 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11150 Z= 0.222 Angle : 0.736 26.251 15133 Z= 0.338 Chirality : 0.069 2.008 1728 Planarity : 0.004 0.040 1879 Dihedral : 6.865 87.400 1641 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.72 % Allowed : 13.11 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.20 (0.22), residues: 1337 helix: -0.12 (0.19), residues: 691 sheet: -1.13 (0.33), residues: 214 loop : -1.50 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 576 HIS 0.006 0.001 HIS B 647 PHE 0.025 0.001 PHE A 773 TYR 0.017 0.001 TYR A 776 ARG 0.005 0.000 ARG B 637 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 1.272 Fit side-chains revert: symmetry clash REVERT: A 168 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7467 (ttm110) REVERT: A 198 ASP cc_start: 0.7994 (m-30) cc_final: 0.7787 (m-30) REVERT: A 209 TYR cc_start: 0.8465 (m-80) cc_final: 0.8257 (m-80) REVERT: A 336 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7219 (mm-30) REVERT: A 352 LYS cc_start: 0.8398 (mttp) cc_final: 0.8163 (mtmt) REVERT: A 358 ASP cc_start: 0.6561 (t70) cc_final: 0.6120 (t70) REVERT: A 536 TRP cc_start: 0.8400 (m100) cc_final: 0.8194 (m100) REVERT: B 102 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7024 (mtm180) REVERT: B 341 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6283 (mt-10) REVERT: B 441 GLU cc_start: 0.6916 (pp20) cc_final: 0.6556 (pp20) REVERT: B 521 ASN cc_start: 0.7092 (t0) cc_final: 0.6871 (m110) outliers start: 32 outliers final: 16 residues processed: 151 average time/residue: 1.0584 time to fit residues: 172.7934 Evaluate side-chains 150 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 131 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 761 CYS Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 657 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 chunk 13 optimal weight: 0.0980 chunk 58 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 122 optimal weight: 0.3980 chunk 129 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11150 Z= 0.193 Angle : 0.715 26.334 15133 Z= 0.326 Chirality : 0.067 1.984 1728 Planarity : 0.004 0.042 1879 Dihedral : 6.744 87.130 1641 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.89 % Allowed : 15.15 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.23), residues: 1337 helix: 0.18 (0.20), residues: 691 sheet: -0.97 (0.34), residues: 214 loop : -1.36 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 576 HIS 0.004 0.001 HIS B 647 PHE 0.026 0.001 PHE A 773 TYR 0.018 0.001 TYR A 404 ARG 0.004 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 131 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 198 ASP cc_start: 0.7994 (m-30) cc_final: 0.7764 (m-30) REVERT: A 209 TYR cc_start: 0.8466 (m-80) cc_final: 0.8257 (m-80) REVERT: A 336 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7211 (mm-30) REVERT: A 352 LYS cc_start: 0.8422 (mttp) cc_final: 0.8160 (mtmt) REVERT: A 358 ASP cc_start: 0.6591 (t70) cc_final: 0.6167 (t70) REVERT: A 494 ARG cc_start: 0.5964 (OUTLIER) cc_final: 0.5430 (pmm150) REVERT: A 796 THR cc_start: 0.6639 (OUTLIER) cc_final: 0.6324 (m) REVERT: B 102 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.6952 (mtm180) REVERT: B 341 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.6334 (mt-10) REVERT: B 441 GLU cc_start: 0.6914 (pp20) cc_final: 0.6560 (pp20) outliers start: 34 outliers final: 18 residues processed: 147 average time/residue: 1.1980 time to fit residues: 189.8963 Evaluate side-chains 147 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 125 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 761 CYS Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 630 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 116 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN B 506 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11150 Z= 0.296 Angle : 0.751 26.299 15133 Z= 0.348 Chirality : 0.069 2.027 1728 Planarity : 0.004 0.043 1879 Dihedral : 6.866 87.158 1641 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.57 % Allowed : 16.09 % Favored : 80.34 % 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: -0.84 (0.23), residues: 1337 helix: 0.16 (0.20), residues: 692 sheet: -0.89 (0.34), residues: 212 loop : -1.36 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 576 HIS 0.007 0.001 HIS B 647 PHE 0.023 0.002 PHE A 773 TYR 0.019 0.002 TYR A 776 ARG 0.004 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 131 time to evaluate : 1.311 Fit side-chains revert: symmetry clash REVERT: A 198 ASP cc_start: 0.7995 (m-30) cc_final: 0.7758 (m-30) REVERT: A 209 TYR cc_start: 0.8454 (m-80) cc_final: 0.8225 (m-80) REVERT: A 336 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7214 (mm-30) REVERT: A 352 LYS cc_start: 0.8429 (mttp) cc_final: 0.8145 (mtmt) REVERT: A 494 ARG cc_start: 0.6110 (OUTLIER) cc_final: 0.5591 (pmm150) REVERT: A 691 VAL cc_start: 0.8756 (m) cc_final: 0.8504 (p) REVERT: B 102 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7008 (mtm180) REVERT: B 341 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6310 (mt-10) REVERT: B 441 GLU cc_start: 0.6951 (pp20) cc_final: 0.6596 (pp20) REVERT: B 581 ILE cc_start: 0.6995 (OUTLIER) cc_final: 0.6696 (tt) outliers start: 42 outliers final: 20 residues processed: 154 average time/residue: 1.2275 time to fit residues: 204.6059 Evaluate side-chains 149 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 761 CYS Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 630 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11150 Z= 0.295 Angle : 0.750 26.277 15133 Z= 0.349 Chirality : 0.069 2.037 1728 Planarity : 0.004 0.044 1879 Dihedral : 6.979 86.284 1641 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.32 % Allowed : 17.19 % Favored : 79.49 % 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: -0.81 (0.23), residues: 1337 helix: 0.17 (0.20), residues: 689 sheet: -0.94 (0.34), residues: 215 loop : -1.26 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 576 HIS 0.007 0.001 HIS B 647 PHE 0.028 0.002 PHE A 773 TYR 0.020 0.002 TYR A 776 ARG 0.004 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 129 time to evaluate : 1.244 Fit side-chains revert: symmetry clash REVERT: A 178 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7705 (mpt) REVERT: A 198 ASP cc_start: 0.7985 (m-30) cc_final: 0.7748 (m-30) REVERT: A 336 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7219 (mm-30) REVERT: A 352 LYS cc_start: 0.8424 (mttp) cc_final: 0.8157 (mtmt) REVERT: A 494 ARG cc_start: 0.6024 (OUTLIER) cc_final: 0.5609 (pmm150) REVERT: A 585 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6773 (mtt90) REVERT: B 102 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.6998 (mtm180) REVERT: B 341 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6305 (mt-10) REVERT: B 374 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7946 (pt0) REVERT: B 441 GLU cc_start: 0.6962 (pp20) cc_final: 0.6602 (pp20) REVERT: B 521 ASN cc_start: 0.7019 (t0) cc_final: 0.6812 (m110) REVERT: B 581 ILE cc_start: 0.7043 (OUTLIER) cc_final: 0.6753 (mp) REVERT: B 670 PHE cc_start: 0.7506 (OUTLIER) cc_final: 0.7302 (t80) outliers start: 39 outliers final: 22 residues processed: 149 average time/residue: 1.0108 time to fit residues: 162.7419 Evaluate side-chains 154 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 124 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 761 CYS Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 670 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11150 Z= 0.237 Angle : 0.734 26.335 15133 Z= 0.340 Chirality : 0.067 2.017 1728 Planarity : 0.004 0.044 1879 Dihedral : 6.824 85.511 1641 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.49 % Allowed : 17.79 % Favored : 78.72 % 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: -0.68 (0.23), residues: 1337 helix: 0.27 (0.20), residues: 689 sheet: -0.84 (0.34), residues: 215 loop : -1.22 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 576 HIS 0.005 0.001 HIS B 647 PHE 0.029 0.001 PHE A 773 TYR 0.018 0.001 TYR A 776 ARG 0.009 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 128 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 178 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7693 (mpt) REVERT: A 198 ASP cc_start: 0.7978 (m-30) cc_final: 0.7748 (m-30) REVERT: A 336 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7209 (mm-30) REVERT: A 352 LYS cc_start: 0.8436 (mttp) cc_final: 0.8172 (mtmt) REVERT: A 358 ASP cc_start: 0.6638 (t70) cc_final: 0.6180 (t70) REVERT: A 494 ARG cc_start: 0.6061 (OUTLIER) cc_final: 0.5667 (pmm150) REVERT: A 691 VAL cc_start: 0.8836 (m) cc_final: 0.8538 (p) REVERT: B 341 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6341 (mt-10) REVERT: B 374 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7949 (pt0) REVERT: B 441 GLU cc_start: 0.6951 (pp20) cc_final: 0.6594 (pp20) REVERT: B 521 ASN cc_start: 0.6988 (t0) cc_final: 0.6780 (m110) REVERT: B 581 ILE cc_start: 0.7025 (OUTLIER) cc_final: 0.6770 (mp) REVERT: B 670 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.7219 (t80) outliers start: 41 outliers final: 22 residues processed: 152 average time/residue: 1.0333 time to fit residues: 170.2111 Evaluate side-chains 156 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 761 CYS Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 670 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7277 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11150 Z= 0.226 Angle : 0.733 26.377 15133 Z= 0.338 Chirality : 0.067 2.001 1728 Planarity : 0.004 0.044 1879 Dihedral : 6.617 84.719 1641 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.06 % Allowed : 18.47 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.23), residues: 1337 helix: 0.33 (0.20), residues: 689 sheet: -0.73 (0.35), residues: 214 loop : -1.17 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 576 HIS 0.005 0.001 HIS B 647 PHE 0.026 0.001 PHE A 773 TYR 0.021 0.001 TYR A 404 ARG 0.006 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 131 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: A 168 ARG cc_start: 0.7894 (ttm110) cc_final: 0.7599 (ptp90) REVERT: A 178 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7687 (mpt) REVERT: A 198 ASP cc_start: 0.7981 (m-30) cc_final: 0.7746 (m-30) REVERT: A 336 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7205 (mm-30) REVERT: A 352 LYS cc_start: 0.8448 (mttp) cc_final: 0.8167 (mtmt) REVERT: A 358 ASP cc_start: 0.6654 (t70) cc_final: 0.6187 (t70) REVERT: A 691 VAL cc_start: 0.8819 (m) cc_final: 0.8555 (p) REVERT: B 341 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6371 (mt-10) REVERT: B 441 GLU cc_start: 0.6944 (pp20) cc_final: 0.6585 (pp20) REVERT: B 521 ASN cc_start: 0.6986 (t0) cc_final: 0.6750 (m110) REVERT: B 581 ILE cc_start: 0.7041 (OUTLIER) cc_final: 0.6816 (mp) REVERT: B 649 GLU cc_start: 0.6885 (mm-30) cc_final: 0.6659 (tp30) outliers start: 36 outliers final: 20 residues processed: 151 average time/residue: 0.9012 time to fit residues: 146.8157 Evaluate side-chains 150 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 761 CYS Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 581 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 0.4980 chunk 113 optimal weight: 0.0970 chunk 119 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 127 optimal weight: 0.0070 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 729 GLN B 326 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11150 Z= 0.163 Angle : 0.704 26.390 15133 Z= 0.321 Chirality : 0.065 1.960 1728 Planarity : 0.004 0.044 1879 Dihedral : 6.296 83.849 1641 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.45 % Allowed : 20.00 % Favored : 78.55 % 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: -0.35 (0.23), residues: 1337 helix: 0.54 (0.20), residues: 688 sheet: -0.59 (0.35), residues: 213 loop : -1.12 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 615 HIS 0.003 0.001 HIS A 287 PHE 0.031 0.001 PHE A 773 TYR 0.019 0.001 TYR A 776 ARG 0.006 0.000 ARG B 637 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 168 ARG cc_start: 0.7859 (ttm110) cc_final: 0.7653 (ptp90) REVERT: A 198 ASP cc_start: 0.8010 (m-30) cc_final: 0.7756 (m-30) REVERT: A 336 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7192 (mm-30) REVERT: A 352 LYS cc_start: 0.8398 (mttp) cc_final: 0.8135 (mtmt) REVERT: A 358 ASP cc_start: 0.6587 (t70) cc_final: 0.6149 (t70) REVERT: A 691 VAL cc_start: 0.8799 (m) cc_final: 0.8542 (p) REVERT: B 341 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6494 (mt-10) REVERT: B 441 GLU cc_start: 0.6913 (pp20) cc_final: 0.6555 (pp20) REVERT: B 501 PHE cc_start: 0.6337 (t80) cc_final: 0.5665 (m-10) REVERT: B 649 GLU cc_start: 0.6720 (mm-30) cc_final: 0.6510 (tp30) outliers start: 17 outliers final: 10 residues processed: 149 average time/residue: 1.0332 time to fit residues: 166.2888 Evaluate side-chains 141 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 761 CYS Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 525 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 113 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: