Starting phenix.real_space_refine on Thu Feb 15 03:49:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xld_22240/02_2024/6xld_22240_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xld_22240/02_2024/6xld_22240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xld_22240/02_2024/6xld_22240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xld_22240/02_2024/6xld_22240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xld_22240/02_2024/6xld_22240_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xld_22240/02_2024/6xld_22240_updated.pdb" } resolution = 3.66 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= 0.004 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 P 6 5.49 5 Mg 2 5.21 5 S 20 5.16 5 C 7020 2.51 5 N 1804 2.21 5 O 2140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "A ARG 595": "NH1" <-> "NH2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A GLU 620": "OE1" <-> "OE2" Residue "A GLU 644": "OE1" <-> "OE2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 133": "NH1" <-> "NH2" Residue "B TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 343": "NH1" <-> "NH2" Residue "B GLU 349": "OE1" <-> "OE2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B ARG 389": "NH1" <-> "NH2" Residue "B GLU 408": "OE1" <-> "OE2" Residue "B PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 462": "OE1" <-> "OE2" Residue "B TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 502": "OD1" <-> "OD2" Residue "B PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 536": "NH1" <-> "NH2" Residue "B GLU 537": "OE1" <-> "OE2" Residue "B TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 544": "OE1" <-> "OE2" Residue "B TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 587": "NH1" <-> "NH2" Residue "B ARG 595": "NH1" <-> "NH2" Residue "B PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "B GLU 644": "OE1" <-> "OE2" Residue "B PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 259": "OE1" <-> "OE2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 304": "OE1" <-> "OE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C GLU 325": "OE1" <-> "OE2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10992 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4897 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 20, 'TRANS': 585} Chain breaks: 3 Chain: "B" Number of atoms: 4879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4879 Classifications: {'peptide': 604} Link IDs: {'PTRANS': 19, 'TRANS': 584} Chain breaks: 3 Chain: "C" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1152 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.95, per 1000 atoms: 0.54 Number of scatterers: 10992 At special positions: 0 Unit cell: (99.546, 91.074, 133.434, 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) S 20 16.00 P 6 15.00 Mg 2 11.99 O 2140 8.00 N 1804 7.00 C 7020 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: 4.20 Conformation dependent library (CDL) restraints added in 2.1 seconds 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2584 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 9 sheets defined 36.0% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 12 through 18 removed outlier: 4.460A pdb=" N SER A 17 " --> pdb=" O THR A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.690A pdb=" N LEU A 31 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A 35 " --> pdb=" O ARG A 32 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP A 40 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A 41 " --> pdb=" O ALA A 38 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 45 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 56 Processing helix chain 'A' and resid 88 through 91 No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.512A pdb=" N LEU A 127 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 128 " --> pdb=" O TYR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 185 removed outlier: 3.771A pdb=" N LEU A 182 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU A 183 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR A 184 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 282 through 292 removed outlier: 3.667A pdb=" N SER A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 404 removed outlier: 3.508A pdb=" N GLU A 398 " --> pdb=" O LYS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.652A pdb=" N VAL A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 438 removed outlier: 3.906A pdb=" N LYS A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.544A pdb=" N VAL A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 453 through 458' Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 502 through 509 removed outlier: 3.844A pdb=" N GLN A 508 " --> pdb=" O TYR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 540 removed outlier: 3.535A pdb=" N ALA A 534 " --> pdb=" O ASP A 530 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU A 535 " --> pdb=" O GLU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 557 removed outlier: 3.503A pdb=" N ILE A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASP A 556 " --> pdb=" O ASP A 552 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N GLN A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 591 removed outlier: 3.831A pdb=" N ARG A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 591 " --> pdb=" O ARG A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 626 removed outlier: 3.830A pdb=" N LYS A 623 " --> pdb=" O LYS A 619 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 624 " --> pdb=" O GLU A 620 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 625 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A 626 " --> pdb=" O LYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 650 removed outlier: 3.896A pdb=" N ASP A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 638 " --> pdb=" O THR A 634 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 648 " --> pdb=" O GLU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 671 Processing helix chain 'B' and resid 12 through 21 removed outlier: 4.529A pdb=" N SER B 17 " --> pdb=" O THR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 49 removed outlier: 3.678A pdb=" N LEU B 31 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU B 33 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN B 37 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP B 40 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE B 45 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 46 " --> pdb=" O ASP B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 56 Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 124 through 129 removed outlier: 3.569A pdb=" N LEU B 127 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 128 " --> pdb=" O TYR B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 185 Processing helix chain 'B' and resid 187 through 197 Processing helix chain 'B' and resid 277 through 279 No H-bonds generated for 'chain 'B' and resid 277 through 279' Processing helix chain 'B' and resid 282 through 292 Processing helix chain 'B' and resid 384 through 404 Processing helix chain 'B' and resid 408 through 416 removed outlier: 3.877A pdb=" N LYS B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 427 removed outlier: 3.723A pdb=" N VAL B 425 " --> pdb=" O ILE B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 438 removed outlier: 3.795A pdb=" N LYS B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.538A pdb=" N VAL B 457 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 453 through 458' Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'B' and resid 502 through 509 removed outlier: 4.224A pdb=" N GLN B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 540 removed outlier: 3.699A pdb=" N LYS B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU B 539 " --> pdb=" O GLU B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 557 removed outlier: 3.644A pdb=" N ASP B 552 " --> pdb=" O LYS B 548 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASP B 556 " --> pdb=" O ASP B 552 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N GLN B 557 " --> pdb=" O ILE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 591 removed outlier: 3.895A pdb=" N ARG B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 591 " --> pdb=" O ARG B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 626 removed outlier: 3.765A pdb=" N LYS B 623 " --> pdb=" O LYS B 619 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 625 " --> pdb=" O LEU B 621 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP B 626 " --> pdb=" O LYS B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 650 removed outlier: 3.688A pdb=" N ASP B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU B 638 " --> pdb=" O THR B 634 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU B 641 " --> pdb=" O ASP B 637 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 648 " --> pdb=" O GLU B 644 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B 649 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 671 Processing helix chain 'C' and resid 226 through 232 removed outlier: 4.101A pdb=" N GLU C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 243 removed outlier: 4.028A pdb=" N ALA C 241 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRP C 242 " --> pdb=" O ARG C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 335 removed outlier: 3.678A pdb=" N GLU C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU C 334 " --> pdb=" O ALA C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing sheet with id= A, first strand: chain 'A' and resid 262 through 265 removed outlier: 6.013A pdb=" N ILE A 64 " --> pdb=" O GLN A 206 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LEU A 208 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ILE A 66 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG A 133 " --> pdb=" O PHE A 176 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 301 through 308 removed outlier: 3.515A pdb=" N TYR A 301 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 516 through 519 Processing sheet with id= D, first strand: chain 'A' and resid 561 through 563 removed outlier: 6.415A pdb=" N PHE A 609 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 262 through 265 removed outlier: 6.264A pdb=" N ILE B 64 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU B 208 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE B 66 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG B 174 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG B 133 " --> pdb=" O PHE B 176 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 301 through 307 removed outlier: 3.538A pdb=" N TYR B 301 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR B 347 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL B 341 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N PHE B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 516 through 519 Processing sheet with id= H, first strand: chain 'B' and resid 561 through 564 removed outlier: 9.111A pdb=" N VAL B 562 " --> pdb=" O LYS B 607 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE B 609 " --> pdb=" O VAL B 562 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N SER B 564 " --> pdb=" O PHE B 609 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE B 611 " --> pdb=" O SER B 564 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 246 through 248 removed outlier: 3.630A pdb=" N GLU C 259 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL C 282 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N CYS C 275 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LYS C 280 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N THR C 214 " --> pdb=" O GLY C 319 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 963 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: 3.15 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3567 1.34 - 1.46: 2402 1.46 - 1.58: 5167 1.58 - 1.69: 10 1.69 - 1.81: 40 Bond restraints: 11186 Sorted by residual: bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" O5' ANP B 801 " pdb=" PA ANP B 801 " ideal model delta sigma weight residual 1.655 1.581 0.074 2.00e-02 2.50e+03 1.38e+01 ... (remaining 11181 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.15: 242 107.15 - 113.86: 6338 113.86 - 120.58: 4606 120.58 - 127.30: 3833 127.30 - 134.02: 79 Bond angle restraints: 15098 Sorted by residual: angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 109.74 17.21 3.00e+00 1.11e-01 3.29e+01 angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 109.86 17.09 3.00e+00 1.11e-01 3.25e+01 angle pdb=" O1B ANP B 801 " pdb=" PB ANP B 801 " pdb=" O2B ANP B 801 " ideal model delta sigma weight residual 120.08 109.52 10.56 3.00e+00 1.11e-01 1.24e+01 angle pdb=" O1B ANP A 801 " pdb=" PB ANP A 801 " pdb=" O2B ANP A 801 " ideal model delta sigma weight residual 120.08 109.55 10.53 3.00e+00 1.11e-01 1.23e+01 angle pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " pdb=" O2G ANP B 801 " ideal model delta sigma weight residual 101.05 109.64 -8.59 3.00e+00 1.11e-01 8.20e+00 ... (remaining 15093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 6638 17.67 - 35.34: 172 35.34 - 53.01: 31 53.01 - 70.67: 17 70.67 - 88.34: 17 Dihedral angle restraints: 6875 sinusoidal: 2911 harmonic: 3964 Sorted by residual: dihedral pdb=" CB GLU C 304 " pdb=" CG GLU C 304 " pdb=" CD GLU C 304 " pdb=" OE1 GLU C 304 " ideal model delta sinusoidal sigma weight residual 0.00 -88.34 88.34 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU B 351 " pdb=" CG GLU B 351 " pdb=" CD GLU B 351 " pdb=" OE1 GLU B 351 " ideal model delta sinusoidal sigma weight residual 0.00 87.70 -87.70 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU B 462 " pdb=" CG GLU B 462 " pdb=" CD GLU B 462 " pdb=" OE1 GLU B 462 " ideal model delta sinusoidal sigma weight residual 0.00 -86.37 86.37 1 3.00e+01 1.11e-03 9.99e+00 ... (remaining 6872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1486 0.055 - 0.109: 194 0.109 - 0.164: 19 0.164 - 0.218: 0 0.218 - 0.273: 2 Chirality restraints: 1701 Sorted by residual: chirality pdb=" C3' ANP A 801 " pdb=" C2' ANP A 801 " pdb=" C4' ANP A 801 " pdb=" O3' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C3' ANP B 801 " pdb=" C2' ANP B 801 " pdb=" C4' ANP B 801 " pdb=" O3' ANP B 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA ILE B 64 " pdb=" N ILE B 64 " pdb=" C ILE B 64 " pdb=" CB ILE B 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 1698 not shown) Planarity restraints: 1923 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 354 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO A 355 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 570 " -0.016 5.00e-02 4.00e+02 2.45e-02 9.62e-01 pdb=" N PRO B 571 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO B 571 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 571 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 544 " 0.016 5.00e-02 4.00e+02 2.36e-02 8.94e-01 pdb=" N PRO A 545 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 545 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 545 " 0.013 5.00e-02 4.00e+02 ... (remaining 1920 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 139 2.63 - 3.20: 9509 3.20 - 3.76: 16819 3.76 - 4.33: 24653 4.33 - 4.90: 39673 Nonbonded interactions: 90793 Sorted by model distance: nonbonded pdb=" O1B ANP A 801 " pdb="MG MG A 802 " model vdw 2.061 2.170 nonbonded pdb=" O1B ANP B 801 " pdb="MG MG B 802 " model vdw 2.107 2.170 nonbonded pdb=" OD1 ASN B 37 " pdb="MG MG B 802 " model vdw 2.131 2.170 nonbonded pdb=" O1A ANP B 801 " pdb="MG MG B 802 " model vdw 2.141 2.170 nonbonded pdb=" OD1 ASN A 37 " pdb="MG MG A 802 " model vdw 2.166 2.170 ... (remaining 90788 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 323 or resid 335 through 675 or resid 801 throug \ h 802)) selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.870 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 31.330 Find NCS groups from input model: 0.580 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: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 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 : 0.003 0.143 11186 Z= 0.191 Angle : 0.507 17.210 15098 Z= 0.243 Chirality : 0.039 0.273 1701 Planarity : 0.003 0.034 1923 Dihedral : 10.186 88.343 4291 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.58 % Allowed : 3.31 % Favored : 96.11 % 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: -3.76 (0.19), residues: 1331 helix: -3.74 (0.12), residues: 513 sheet: -1.24 (0.31), residues: 272 loop : -1.60 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 273 HIS 0.001 0.000 HIS A 463 PHE 0.004 0.001 PHE A 609 TYR 0.005 0.001 TYR B 285 ARG 0.001 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 294 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LEU cc_start: 0.8068 (tp) cc_final: 0.7805 (tp) REVERT: C 223 ASN cc_start: 0.7570 (t0) cc_final: 0.7337 (p0) outliers start: 7 outliers final: 1 residues processed: 299 average time/residue: 0.2987 time to fit residues: 117.2606 Evaluate side-chains 124 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.3980 chunk 100 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 120 optimal weight: 0.0670 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 92 ASN A 261 GLN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS A 431 ASN A 640 ASN B 9 GLN B 55 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 HIS B 304 HIS B 442 ASN B 557 GLN B 640 ASN C 237 GLN C 284 HIS ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11186 Z= 0.143 Angle : 0.513 7.547 15098 Z= 0.259 Chirality : 0.042 0.163 1701 Planarity : 0.004 0.035 1923 Dihedral : 5.539 69.055 1505 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.90 % Allowed : 10.01 % Favored : 88.09 % 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: -2.19 (0.21), residues: 1331 helix: -1.95 (0.19), residues: 531 sheet: -0.95 (0.29), residues: 268 loop : -0.89 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 148 HIS 0.004 0.001 HIS B 197 PHE 0.018 0.001 PHE A 660 TYR 0.017 0.001 TYR A 441 ARG 0.005 0.000 ARG C 238 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 137 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.5195 (mtp) cc_final: 0.4992 (mtm) REVERT: B 84 MET cc_start: 0.7958 (mtp) cc_final: 0.7565 (mtp) REVERT: B 408 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7435 (pp20) REVERT: B 650 SER cc_start: 0.8489 (m) cc_final: 0.8265 (p) outliers start: 23 outliers final: 8 residues processed: 158 average time/residue: 0.2316 time to fit residues: 52.2581 Evaluate side-chains 109 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 637 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 82 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11186 Z= 0.276 Angle : 0.575 7.447 15098 Z= 0.297 Chirality : 0.044 0.251 1701 Planarity : 0.004 0.037 1923 Dihedral : 6.212 80.330 1504 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.07 % Allowed : 11.91 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.22), residues: 1331 helix: -0.95 (0.22), residues: 522 sheet: -0.80 (0.30), residues: 259 loop : -0.63 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 296 HIS 0.005 0.001 HIS A 426 PHE 0.016 0.002 PHE B 8 TYR 0.015 0.002 TYR A 125 ARG 0.005 0.001 ARG C 238 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.6010 (mtp) cc_final: 0.5789 (mtm) REVERT: B 84 MET cc_start: 0.8125 (mtp) cc_final: 0.7597 (mtp) REVERT: B 381 GLN cc_start: 0.6829 (mp10) cc_final: 0.6505 (mp10) REVERT: B 644 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6901 (mt-10) outliers start: 25 outliers final: 12 residues processed: 128 average time/residue: 0.2451 time to fit residues: 45.2491 Evaluate side-chains 90 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain C residue 224 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 121 optimal weight: 8.9990 chunk 128 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 11186 Z= 0.199 Angle : 0.500 8.000 15098 Z= 0.253 Chirality : 0.042 0.181 1701 Planarity : 0.003 0.040 1923 Dihedral : 5.920 77.316 1504 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.57 % Allowed : 13.56 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.23), residues: 1331 helix: -0.41 (0.23), residues: 526 sheet: -0.76 (0.31), residues: 263 loop : -0.37 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 148 HIS 0.003 0.001 HIS A 426 PHE 0.013 0.001 PHE A 660 TYR 0.012 0.001 TYR B 289 ARG 0.004 0.000 ARG C 238 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8810 (mt) REVERT: B 84 MET cc_start: 0.7826 (mtp) cc_final: 0.7372 (mtp) REVERT: B 381 GLN cc_start: 0.6864 (mp10) cc_final: 0.6580 (mp10) REVERT: B 385 MET cc_start: 0.6997 (tpp) cc_final: 0.6742 (ptt) REVERT: B 408 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7638 (pp20) REVERT: B 650 SER cc_start: 0.8685 (m) cc_final: 0.8198 (t) outliers start: 19 outliers final: 10 residues processed: 111 average time/residue: 0.1907 time to fit residues: 31.7658 Evaluate side-chains 90 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 637 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 1 optimal weight: 0.2980 chunk 95 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11186 Z= 0.160 Angle : 0.475 8.236 15098 Z= 0.241 Chirality : 0.042 0.176 1701 Planarity : 0.003 0.052 1923 Dihedral : 5.803 76.129 1504 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.07 % Allowed : 14.47 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.23), residues: 1331 helix: -0.12 (0.24), residues: 528 sheet: -0.70 (0.31), residues: 269 loop : -0.27 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 148 HIS 0.002 0.000 HIS A 426 PHE 0.017 0.001 PHE A 512 TYR 0.014 0.001 TYR B 289 ARG 0.003 0.000 ARG A 536 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 90 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8773 (mt) REVERT: A 586 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6774 (mp0) REVERT: B 84 MET cc_start: 0.7981 (mtp) cc_final: 0.7674 (mtp) REVERT: B 381 GLN cc_start: 0.6795 (mp10) cc_final: 0.6531 (mp10) REVERT: B 408 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7713 (pp20) REVERT: B 650 SER cc_start: 0.8641 (m) cc_final: 0.8175 (t) outliers start: 25 outliers final: 12 residues processed: 112 average time/residue: 0.2175 time to fit residues: 36.5925 Evaluate side-chains 91 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 255 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 426 HIS ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.5823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 11186 Z= 0.411 Angle : 0.657 9.564 15098 Z= 0.333 Chirality : 0.046 0.213 1701 Planarity : 0.004 0.043 1923 Dihedral : 6.531 72.632 1504 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.56 % Allowed : 14.97 % Favored : 82.46 % 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: -0.79 (0.23), residues: 1331 helix: -0.20 (0.23), residues: 519 sheet: -1.01 (0.31), residues: 266 loop : -0.34 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 148 HIS 0.003 0.001 HIS C 284 PHE 0.015 0.002 PHE B 8 TYR 0.016 0.002 TYR B 289 ARG 0.005 0.001 ARG A 536 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 83 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: B 84 MET cc_start: 0.8192 (mtp) cc_final: 0.7946 (mtp) REVERT: B 180 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7252 (p0) REVERT: B 381 GLN cc_start: 0.6942 (mp10) cc_final: 0.6474 (mp10) REVERT: B 650 SER cc_start: 0.8819 (m) cc_final: 0.8326 (t) REVERT: C 271 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7402 (pt0) outliers start: 31 outliers final: 18 residues processed: 111 average time/residue: 0.2136 time to fit residues: 35.2818 Evaluate side-chains 94 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 73 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 349 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN B 373 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 11186 Z= 0.245 Angle : 0.547 8.798 15098 Z= 0.276 Chirality : 0.043 0.157 1701 Planarity : 0.004 0.043 1923 Dihedral : 6.190 71.611 1504 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.90 % Allowed : 16.13 % Favored : 81.97 % 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: -0.60 (0.23), residues: 1331 helix: -0.03 (0.23), residues: 526 sheet: -0.94 (0.32), residues: 265 loop : -0.23 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 148 HIS 0.001 0.000 HIS B 463 PHE 0.012 0.001 PHE B 579 TYR 0.010 0.001 TYR B 289 ARG 0.005 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.7746 (mmm) cc_final: 0.7530 (mmm) REVERT: A 396 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8809 (mt) REVERT: A 586 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: B 84 MET cc_start: 0.8111 (mtp) cc_final: 0.7905 (mtp) REVERT: B 180 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7243 (p0) REVERT: B 649 THR cc_start: 0.8656 (p) cc_final: 0.8349 (t) REVERT: B 650 SER cc_start: 0.8833 (m) cc_final: 0.8557 (p) outliers start: 23 outliers final: 15 residues processed: 101 average time/residue: 0.2089 time to fit residues: 32.1910 Evaluate side-chains 90 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 349 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 0.1980 chunk 51 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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: 0.8088 moved from start: 0.5963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11186 Z= 0.204 Angle : 0.527 9.116 15098 Z= 0.264 Chirality : 0.042 0.141 1701 Planarity : 0.003 0.042 1923 Dihedral : 6.083 71.590 1504 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.23 % Allowed : 15.72 % Favored : 82.05 % 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: -0.51 (0.23), residues: 1331 helix: 0.09 (0.24), residues: 521 sheet: -0.86 (0.32), residues: 270 loop : -0.25 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 148 HIS 0.002 0.001 HIS C 284 PHE 0.010 0.001 PHE B 579 TYR 0.019 0.001 TYR B 289 ARG 0.005 0.000 ARG C 329 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 82 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8802 (mt) REVERT: A 586 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: A 589 MET cc_start: 0.8485 (mmm) cc_final: 0.8265 (mmm) REVERT: B 180 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7186 (p0) REVERT: B 649 THR cc_start: 0.8663 (p) cc_final: 0.8355 (t) REVERT: B 650 SER cc_start: 0.8834 (m) cc_final: 0.8554 (p) outliers start: 27 outliers final: 15 residues processed: 105 average time/residue: 0.2178 time to fit residues: 34.5829 Evaluate side-chains 94 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 76 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 349 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 0.1980 chunk 122 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 71 optimal weight: 0.0270 chunk 52 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 overall best weight: 1.4444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.6044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11186 Z= 0.187 Angle : 0.521 8.777 15098 Z= 0.262 Chirality : 0.042 0.196 1701 Planarity : 0.003 0.042 1923 Dihedral : 6.043 70.956 1504 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.82 % Allowed : 15.55 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.23), residues: 1331 helix: 0.14 (0.24), residues: 524 sheet: -0.84 (0.33), residues: 261 loop : -0.20 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 148 HIS 0.012 0.001 HIS C 284 PHE 0.011 0.001 PHE A 6 TYR 0.015 0.001 TYR B 289 ARG 0.005 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 383 LYS cc_start: 0.6889 (mmpt) cc_final: 0.6478 (mmtp) REVERT: A 396 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8788 (mt) REVERT: A 586 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: A 589 MET cc_start: 0.8474 (mmm) cc_final: 0.8251 (mmm) REVERT: B 180 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.7117 (p0) REVERT: B 649 THR cc_start: 0.8668 (p) cc_final: 0.8346 (t) REVERT: B 650 SER cc_start: 0.8850 (m) cc_final: 0.8586 (p) outliers start: 22 outliers final: 16 residues processed: 103 average time/residue: 0.1953 time to fit residues: 31.0598 Evaluate side-chains 97 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 349 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 121 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 81 optimal weight: 0.1980 chunk 64 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.6078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11186 Z= 0.173 Angle : 0.533 9.263 15098 Z= 0.268 Chirality : 0.043 0.237 1701 Planarity : 0.003 0.050 1923 Dihedral : 6.025 70.529 1504 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.32 % Allowed : 16.38 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.23), residues: 1331 helix: 0.18 (0.24), residues: 517 sheet: -0.78 (0.32), residues: 273 loop : -0.11 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 148 HIS 0.009 0.001 HIS C 284 PHE 0.013 0.001 PHE A 6 TYR 0.014 0.001 TYR B 289 ARG 0.005 0.000 ARG A 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 1.382 Fit side-chains revert: symmetry clash REVERT: A 383 LYS cc_start: 0.6720 (mmpt) cc_final: 0.6337 (mmtp) REVERT: A 396 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8785 (mt) REVERT: A 586 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: A 589 MET cc_start: 0.8470 (mmm) cc_final: 0.8247 (mmm) REVERT: B 180 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7097 (p0) REVERT: B 649 THR cc_start: 0.8664 (p) cc_final: 0.8339 (t) REVERT: B 650 SER cc_start: 0.8915 (m) cc_final: 0.8601 (p) outliers start: 16 outliers final: 13 residues processed: 98 average time/residue: 0.2088 time to fit residues: 31.5434 Evaluate side-chains 91 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 349 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.080461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.070278 restraints weight = 35150.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.072108 restraints weight = 20083.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.073387 restraints weight = 13672.298| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.6142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11186 Z= 0.179 Angle : 0.540 11.005 15098 Z= 0.270 Chirality : 0.043 0.226 1701 Planarity : 0.004 0.050 1923 Dihedral : 6.014 70.582 1504 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.65 % Allowed : 16.38 % Favored : 81.97 % 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: -0.36 (0.23), residues: 1331 helix: 0.13 (0.24), residues: 523 sheet: -0.73 (0.33), residues: 260 loop : -0.12 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP B 148 HIS 0.009 0.001 HIS C 284 PHE 0.014 0.001 PHE A 6 TYR 0.014 0.001 TYR B 289 ARG 0.004 0.000 ARG A 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1956.67 seconds wall clock time: 38 minutes 27.07 seconds (2307.07 seconds total)