Starting phenix.real_space_refine on Mon Mar 18 02:42:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aa5_11690/03_2024/7aa5_11690_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aa5_11690/03_2024/7aa5_11690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aa5_11690/03_2024/7aa5_11690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aa5_11690/03_2024/7aa5_11690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aa5_11690/03_2024/7aa5_11690_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aa5_11690/03_2024/7aa5_11690_neut.pdb" } resolution = 4.18 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= 0.002 sd= 0.025 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 Ca 1 9.91 5 S 108 5.16 5 C 12804 2.51 5 N 3268 2.21 5 O 3516 1.98 5 H 8 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 208": "OD1" <-> "OD2" Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "A ASP 333": "OD1" <-> "OD2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 430": "OE1" <-> "OE2" Residue "A TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 510": "NH1" <-> "NH2" Residue "A PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 531": "OD1" <-> "OD2" Residue "A TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 616": "NH1" <-> "NH2" Residue "A TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 682": "OD1" <-> "OD2" Residue "A PHE 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 743": "OD1" <-> "OD2" Residue "A ARG 746": "NH1" <-> "NH2" Residue "A PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 208": "OD1" <-> "OD2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 315": "NH1" <-> "NH2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 391": "NH1" <-> "NH2" Residue "B GLU 397": "OE1" <-> "OE2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 430": "OE1" <-> "OE2" Residue "B TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 510": "NH1" <-> "NH2" Residue "B PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 531": "OD1" <-> "OD2" Residue "B TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 616": "NH1" <-> "NH2" Residue "B TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 682": "OD1" <-> "OD2" Residue "B PHE 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 743": "OD1" <-> "OD2" Residue "B ARG 746": "NH1" <-> "NH2" Residue "B PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 208": "OD1" <-> "OD2" Residue "C PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "C PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 315": "NH1" <-> "NH2" Residue "C ASP 333": "OD1" <-> "OD2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 391": "NH1" <-> "NH2" Residue "C GLU 397": "OE1" <-> "OE2" Residue "C ARG 400": "NH1" <-> "NH2" Residue "C PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 430": "OE1" <-> "OE2" Residue "C TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 510": "NH1" <-> "NH2" Residue "C PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 531": "OD1" <-> "OD2" Residue "C TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 616": "NH1" <-> "NH2" Residue "C TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 682": "OD1" <-> "OD2" Residue "C PHE 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 743": "OD1" <-> "OD2" Residue "C ARG 746": "NH1" <-> "NH2" Residue "C PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 208": "OD1" <-> "OD2" Residue "D PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 255": "OE1" <-> "OE2" Residue "D ARG 269": "NH1" <-> "NH2" Residue "D PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 315": "NH1" <-> "NH2" Residue "D ASP 333": "OD1" <-> "OD2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "D PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 391": "NH1" <-> "NH2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "D ARG 400": "NH1" <-> "NH2" Residue "D PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 430": "OE1" <-> "OE2" Residue "D TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 510": "NH1" <-> "NH2" Residue "D PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 531": "OD1" <-> "OD2" Residue "D TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 616": "NH1" <-> "NH2" Residue "D TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 682": "OD1" <-> "OD2" Residue "D PHE 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 743": "OD1" <-> "OD2" Residue "D ARG 746": "NH1" <-> "NH2" Residue "D PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19705 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4926 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 22, 'TRANS': 589} Chain breaks: 2 Chain: "B" Number of atoms: 4926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4926 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 22, 'TRANS': 589} Chain breaks: 2 Chain: "C" Number of atoms: 4926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4926 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 22, 'TRANS': 589} Chain breaks: 2 Chain: "D" Number of atoms: 4926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4926 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 22, 'TRANS': 589} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.35, per 1000 atoms: 0.53 Number of scatterers: 19705 At special positions: 0 Unit cell: (147.609, 147.609, 116.937, 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) Ca 1 19.99 S 108 16.00 O 3516 8.00 N 3268 7.00 C 12804 6.00 H 8 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.00 Conformation dependent library (CDL) restraints added in 3.6 seconds 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4632 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 61.4% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 150 through 161 removed outlier: 3.734A pdb=" N LEU A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 166 removed outlier: 3.999A pdb=" N ASP A 165 " --> pdb=" O SER A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 176 Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.699A pdb=" N ASN A 201 " --> pdb=" O LYS A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.939A pdb=" N ILE A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 323 through 331 Processing helix chain 'A' and resid 336 through 357 removed outlier: 3.736A pdb=" N PHE A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VAL A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 380 Processing helix chain 'A' and resid 382 through 392 removed outlier: 3.791A pdb=" N ARG A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.691A pdb=" N THR A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 400 " --> pdb=" O GLU A 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 396 through 400' Processing helix chain 'A' and resid 432 through 439 removed outlier: 3.515A pdb=" N ILE A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 450 removed outlier: 3.623A pdb=" N LEU A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 464 removed outlier: 4.119A pdb=" N LEU A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A 460 " --> pdb=" O ASN A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 491 removed outlier: 3.904A pdb=" N PHE A 471 " --> pdb=" O GLY A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 530 removed outlier: 3.554A pdb=" N ILE A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 570 removed outlier: 3.546A pdb=" N SER A 557 " --> pdb=" O TYR A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 593 removed outlier: 3.897A pdb=" N VAL A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU A 590 " --> pdb=" O TRP A 586 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR A 591 " --> pdb=" O MET A 587 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE A 592 " --> pdb=" O ASN A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 599 removed outlier: 3.625A pdb=" N LEU A 598 " --> pdb=" O GLY A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 610 removed outlier: 4.006A pdb=" N GLN A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS A 608 " --> pdb=" O ILE A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 635 Processing helix chain 'A' and resid 667 through 678 Processing helix chain 'A' and resid 693 through 709 removed outlier: 4.254A pdb=" N ILE A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 722 Processing helix chain 'A' and resid 723 through 725 No H-bonds generated for 'chain 'A' and resid 723 through 725' Processing helix chain 'A' and resid 729 through 748 removed outlier: 3.638A pdb=" N PHE A 748 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 161 removed outlier: 3.735A pdb=" N LEU B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 166 removed outlier: 4.000A pdb=" N ASP B 165 " --> pdb=" O SER B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 176 Processing helix chain 'B' and resid 193 through 201 removed outlier: 3.699A pdb=" N ASN B 201 " --> pdb=" O LYS B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 221 Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 240 through 249 removed outlier: 3.939A pdb=" N ILE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 261 Processing helix chain 'B' and resid 270 through 274 Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 323 through 331 Processing helix chain 'B' and resid 336 through 357 removed outlier: 3.735A pdb=" N PHE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N VAL B 342 " --> pdb=" O ASN B 338 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 380 Processing helix chain 'B' and resid 382 through 392 removed outlier: 3.791A pdb=" N ARG B 391 " --> pdb=" O GLN B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 400 removed outlier: 3.692A pdb=" N THR B 399 " --> pdb=" O ASP B 396 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 400 " --> pdb=" O GLU B 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 396 through 400' Processing helix chain 'B' and resid 432 through 439 removed outlier: 3.515A pdb=" N ILE B 436 " --> pdb=" O SER B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 450 removed outlier: 3.624A pdb=" N LEU B 450 " --> pdb=" O ARG B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 464 removed outlier: 4.120A pdb=" N LEU B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 491 removed outlier: 3.904A pdb=" N PHE B 471 " --> pdb=" O GLY B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 530 removed outlier: 3.554A pdb=" N ILE B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 570 removed outlier: 3.544A pdb=" N SER B 557 " --> pdb=" O TYR B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 593 removed outlier: 3.898A pdb=" N VAL B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU B 590 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR B 591 " --> pdb=" O MET B 587 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE B 592 " --> pdb=" O ASN B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 599 removed outlier: 3.626A pdb=" N LEU B 598 " --> pdb=" O GLY B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 610 removed outlier: 4.007A pdb=" N GLN B 607 " --> pdb=" O SER B 603 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS B 608 " --> pdb=" O ILE B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 635 Processing helix chain 'B' and resid 667 through 678 Processing helix chain 'B' and resid 693 through 709 removed outlier: 4.254A pdb=" N ILE B 697 " --> pdb=" O VAL B 693 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 722 Processing helix chain 'B' and resid 723 through 725 No H-bonds generated for 'chain 'B' and resid 723 through 725' Processing helix chain 'B' and resid 729 through 748 removed outlier: 3.639A pdb=" N PHE B 748 " --> pdb=" O ILE B 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 161 removed outlier: 3.734A pdb=" N LEU C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 166 removed outlier: 4.000A pdb=" N ASP C 165 " --> pdb=" O SER C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 176 Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.698A pdb=" N ASN C 201 " --> pdb=" O LYS C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 221 Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 240 through 249 removed outlier: 3.939A pdb=" N ILE C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 336 through 357 removed outlier: 3.735A pdb=" N PHE C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VAL C 342 " --> pdb=" O ASN C 338 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS C 344 " --> pdb=" O LYS C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 380 Processing helix chain 'C' and resid 382 through 392 removed outlier: 3.791A pdb=" N ARG C 391 " --> pdb=" O GLN C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 400 removed outlier: 3.691A pdb=" N THR C 399 " --> pdb=" O ASP C 396 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG C 400 " --> pdb=" O GLU C 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 396 through 400' Processing helix chain 'C' and resid 432 through 439 removed outlier: 3.514A pdb=" N ILE C 436 " --> pdb=" O SER C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 450 removed outlier: 3.624A pdb=" N LEU C 450 " --> pdb=" O ARG C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 464 removed outlier: 4.120A pdb=" N LEU C 458 " --> pdb=" O PRO C 454 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG C 460 " --> pdb=" O ASN C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 491 removed outlier: 3.904A pdb=" N PHE C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 530 removed outlier: 3.554A pdb=" N ILE C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 570 removed outlier: 3.545A pdb=" N SER C 557 " --> pdb=" O TYR C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 593 removed outlier: 3.898A pdb=" N VAL C 579 " --> pdb=" O LEU C 575 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU C 590 " --> pdb=" O TRP C 586 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR C 591 " --> pdb=" O MET C 587 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE C 592 " --> pdb=" O ASN C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 599 removed outlier: 3.626A pdb=" N LEU C 598 " --> pdb=" O GLY C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 610 removed outlier: 4.007A pdb=" N GLN C 607 " --> pdb=" O SER C 603 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS C 608 " --> pdb=" O ILE C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 635 Processing helix chain 'C' and resid 667 through 678 Processing helix chain 'C' and resid 693 through 709 removed outlier: 4.255A pdb=" N ILE C 697 " --> pdb=" O VAL C 693 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 698 " --> pdb=" O VAL C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 722 Processing helix chain 'C' and resid 723 through 725 No H-bonds generated for 'chain 'C' and resid 723 through 725' Processing helix chain 'C' and resid 729 through 748 removed outlier: 3.639A pdb=" N PHE C 748 " --> pdb=" O ILE C 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 161 removed outlier: 3.734A pdb=" N LEU D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 166 removed outlier: 4.000A pdb=" N ASP D 165 " --> pdb=" O SER D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 176 Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.699A pdb=" N ASN D 201 " --> pdb=" O LYS D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 221 Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'D' and resid 240 through 249 removed outlier: 3.939A pdb=" N ILE D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 323 through 331 Processing helix chain 'D' and resid 336 through 357 removed outlier: 3.735A pdb=" N PHE D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N VAL D 342 " --> pdb=" O ASN D 338 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 380 Processing helix chain 'D' and resid 382 through 392 removed outlier: 3.791A pdb=" N ARG D 391 " --> pdb=" O GLN D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 400 removed outlier: 3.691A pdb=" N THR D 399 " --> pdb=" O ASP D 396 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG D 400 " --> pdb=" O GLU D 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 396 through 400' Processing helix chain 'D' and resid 432 through 439 removed outlier: 3.514A pdb=" N ILE D 436 " --> pdb=" O SER D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 450 removed outlier: 3.623A pdb=" N LEU D 450 " --> pdb=" O ARG D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 464 removed outlier: 4.120A pdb=" N LEU D 458 " --> pdb=" O PRO D 454 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG D 460 " --> pdb=" O ASN D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 491 removed outlier: 3.904A pdb=" N PHE D 471 " --> pdb=" O GLY D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 530 removed outlier: 3.553A pdb=" N ILE D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 570 removed outlier: 3.544A pdb=" N SER D 557 " --> pdb=" O TYR D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 593 removed outlier: 3.898A pdb=" N VAL D 579 " --> pdb=" O LEU D 575 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU D 590 " --> pdb=" O TRP D 586 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR D 591 " --> pdb=" O MET D 587 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE D 592 " --> pdb=" O ASN D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 599 removed outlier: 3.626A pdb=" N LEU D 598 " --> pdb=" O GLY D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 610 removed outlier: 4.006A pdb=" N GLN D 607 " --> pdb=" O SER D 603 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS D 608 " --> pdb=" O ILE D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 635 Processing helix chain 'D' and resid 667 through 678 Processing helix chain 'D' and resid 693 through 709 removed outlier: 4.254A pdb=" N ILE D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 698 " --> pdb=" O VAL D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 722 Processing helix chain 'D' and resid 723 through 725 No H-bonds generated for 'chain 'D' and resid 723 through 725' Processing helix chain 'D' and resid 729 through 748 removed outlier: 3.639A pdb=" N PHE D 748 " --> pdb=" O ILE D 744 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 405 through 406 removed outlier: 3.651A pdb=" N LEU A 418 " --> pdb=" O PHE A 406 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 405 through 406 removed outlier: 3.652A pdb=" N LEU B 418 " --> pdb=" O PHE B 406 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 405 through 406 removed outlier: 3.651A pdb=" N LEU C 418 " --> pdb=" O PHE C 406 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 405 through 406 removed outlier: 3.651A pdb=" N LEU D 418 " --> pdb=" O PHE D 406 " (cutoff:3.500A) 944 hydrogen bonds defined for protein. 2784 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: 5.38 Time building geometry restraints manager: 8.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 8 1.17 - 1.33: 4161 1.33 - 1.49: 7284 1.49 - 1.65: 8513 1.65 - 1.81: 178 Bond restraints: 20144 Sorted by residual: bond pdb=" N PRO D 772 " pdb=" CD PRO D 772 " ideal model delta sigma weight residual 1.473 1.714 -0.241 1.40e-02 5.10e+03 2.96e+02 bond pdb=" N PRO B 772 " pdb=" CD PRO B 772 " ideal model delta sigma weight residual 1.473 1.714 -0.241 1.40e-02 5.10e+03 2.96e+02 bond pdb=" N PRO D 772 " pdb=" CA PRO D 772 " ideal model delta sigma weight residual 1.469 1.292 0.177 1.28e-02 6.10e+03 1.91e+02 bond pdb=" N PRO B 772 " pdb=" CA PRO B 772 " ideal model delta sigma weight residual 1.469 1.292 0.177 1.28e-02 6.10e+03 1.90e+02 bond pdb=" N PRO C 772 " pdb=" CD PRO C 772 " ideal model delta sigma weight residual 1.473 1.629 -0.156 1.40e-02 5.10e+03 1.25e+02 ... (remaining 20139 not shown) Histogram of bond angle deviations from ideal: 92.87 - 105.28: 354 105.28 - 117.70: 14468 117.70 - 130.11: 12352 130.11 - 142.52: 119 142.52 - 154.93: 3 Bond angle restraints: 27296 Sorted by residual: angle pdb=" C THR C 771 " pdb=" N PRO C 772 " pdb=" CA PRO C 772 " ideal model delta sigma weight residual 119.84 99.71 20.13 1.25e+00 6.40e-01 2.59e+02 angle pdb=" CA THR B 771 " pdb=" C THR B 771 " pdb=" O THR B 771 " ideal model delta sigma weight residual 120.16 100.91 19.25 1.37e+00 5.33e-01 1.97e+02 angle pdb=" CA THR D 771 " pdb=" C THR D 771 " pdb=" O THR D 771 " ideal model delta sigma weight residual 120.16 100.93 19.23 1.37e+00 5.33e-01 1.97e+02 angle pdb=" C THR D 771 " pdb=" N PRO D 772 " pdb=" CA PRO D 772 " ideal model delta sigma weight residual 119.84 102.33 17.51 1.25e+00 6.40e-01 1.96e+02 angle pdb=" C THR B 771 " pdb=" N PRO B 772 " pdb=" CA PRO B 772 " ideal model delta sigma weight residual 119.84 102.34 17.50 1.25e+00 6.40e-01 1.96e+02 ... (remaining 27291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 10620 17.58 - 35.16: 1116 35.16 - 52.73: 209 52.73 - 70.31: 46 70.31 - 87.89: 9 Dihedral angle restraints: 12000 sinusoidal: 4820 harmonic: 7180 Sorted by residual: dihedral pdb=" CA GLY C 770 " pdb=" C GLY C 770 " pdb=" N THR C 771 " pdb=" CA THR C 771 " ideal model delta harmonic sigma weight residual 180.00 106.78 73.22 0 5.00e+00 4.00e-02 2.14e+02 dihedral pdb=" CA GLY D 770 " pdb=" C GLY D 770 " pdb=" N THR D 771 " pdb=" CA THR D 771 " ideal model delta harmonic sigma weight residual 180.00 122.37 57.63 0 5.00e+00 4.00e-02 1.33e+02 dihedral pdb=" CA GLY B 770 " pdb=" C GLY B 770 " pdb=" N THR B 771 " pdb=" CA THR B 771 " ideal model delta harmonic sigma weight residual 180.00 122.41 57.59 0 5.00e+00 4.00e-02 1.33e+02 ... (remaining 11997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 3052 0.095 - 0.190: 78 0.190 - 0.286: 2 0.286 - 0.381: 1 0.381 - 0.476: 3 Chirality restraints: 3136 Sorted by residual: chirality pdb=" CA PRO B 772 " pdb=" N PRO B 772 " pdb=" C PRO B 772 " pdb=" CB PRO B 772 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" CA PRO D 772 " pdb=" N PRO D 772 " pdb=" C PRO D 772 " pdb=" CB PRO D 772 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" CB THR A 771 " pdb=" CA THR A 771 " pdb=" OG1 THR A 771 " pdb=" CG2 THR A 771 " both_signs ideal model delta sigma weight residual False 2.55 2.11 0.45 2.00e-01 2.50e+01 4.99e+00 ... (remaining 3133 not shown) Planarity restraints: 3408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 770 " 0.024 2.00e-02 2.50e+03 5.43e-02 2.95e+01 pdb=" C GLY A 770 " -0.094 2.00e-02 2.50e+03 pdb=" O GLY A 770 " 0.037 2.00e-02 2.50e+03 pdb=" N THR A 771 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 771 " -0.021 2.00e-02 2.50e+03 4.34e-02 1.88e+01 pdb=" C THR B 771 " 0.075 2.00e-02 2.50e+03 pdb=" O THR B 771 " -0.026 2.00e-02 2.50e+03 pdb=" N PRO B 772 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 771 " 0.021 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C THR D 771 " -0.075 2.00e-02 2.50e+03 pdb=" O THR D 771 " 0.026 2.00e-02 2.50e+03 pdb=" N PRO D 772 " 0.028 2.00e-02 2.50e+03 ... (remaining 3405 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.62: 403 2.62 - 3.11: 17172 3.11 - 3.61: 25393 3.61 - 4.10: 32478 4.10 - 4.60: 47585 Nonbonded interactions: 123031 Sorted by model distance: nonbonded pdb=" O THR A 339 " pdb=" OG1 THR A 343 " model vdw 2.119 2.200 nonbonded pdb=" O THR B 339 " pdb=" OG1 THR B 343 " model vdw 2.120 2.200 nonbonded pdb=" O THR C 339 " pdb=" OG1 THR C 343 " model vdw 2.120 2.200 nonbonded pdb=" O THR D 339 " pdb=" OG1 THR D 343 " model vdw 2.120 2.200 nonbonded pdb=" O ALA D 217 " pdb=" OG1 THR D 220 " model vdw 2.199 2.200 ... (remaining 123026 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 148 through 786) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 6.550 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: 0.480 Extract box with map and model: 27.840 Check model and map are aligned: 0.280 Set scattering table: 0.140 Process input model: 50.420 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 : 0.006 0.241 20136 Z= 0.392 Angle : 0.921 29.930 27288 Z= 0.544 Chirality : 0.045 0.476 3136 Planarity : 0.005 0.072 3408 Dihedral : 14.673 87.890 7360 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 21.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 15.06 % Favored : 84.74 % Rotamer: Outliers : 2.04 % Allowed : 4.72 % Favored : 93.24 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.34 % 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: -4.78 (0.13), residues: 2424 helix: -2.43 (0.11), residues: 1336 sheet: -1.80 (0.54), residues: 76 loop : -4.33 (0.15), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 733 HIS 0.004 0.001 HIS C 326 PHE 0.012 0.001 PHE B 756 TYR 0.012 0.001 TYR C 500 ARG 0.004 0.000 ARG A 757 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 288 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 244 time to evaluate : 2.112 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 223 MET cc_start: 0.7127 (mmm) cc_final: 0.6823 (mmm) REVERT: A 482 MET cc_start: 0.8206 (mmm) cc_final: 0.7707 (mmt) REVERT: A 578 MET cc_start: 0.6533 (mtp) cc_final: 0.6286 (tpp) REVERT: A 757 ARG cc_start: 0.8177 (ppt170) cc_final: 0.7956 (ppt170) REVERT: B 176 HIS cc_start: 0.8619 (t-170) cc_final: 0.8132 (m90) REVERT: B 482 MET cc_start: 0.7450 (mmm) cc_final: 0.6929 (mmt) REVERT: B 556 TYR cc_start: 0.9269 (t80) cc_final: 0.8726 (t80) REVERT: B 761 MET cc_start: 0.8316 (mmp) cc_final: 0.8035 (mmp) REVERT: C 223 MET cc_start: 0.7257 (mmm) cc_final: 0.6986 (mmm) REVERT: C 225 GLU cc_start: 0.7495 (tt0) cc_final: 0.7281 (tt0) REVERT: C 482 MET cc_start: 0.8305 (mmm) cc_final: 0.7802 (mmt) REVERT: D 223 MET cc_start: 0.7133 (mmm) cc_final: 0.6838 (mmm) REVERT: D 225 GLU cc_start: 0.7508 (tt0) cc_final: 0.7265 (tt0) REVERT: D 482 MET cc_start: 0.8211 (mmm) cc_final: 0.7717 (mmt) REVERT: D 713 MET cc_start: 0.9302 (OUTLIER) cc_final: 0.9099 (mmt) REVERT: D 757 ARG cc_start: 0.8230 (ppt170) cc_final: 0.7976 (ppt170) outliers start: 44 outliers final: 19 residues processed: 280 average time/residue: 0.2775 time to fit residues: 121.0600 Evaluate side-chains 205 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 185 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 221 optimal weight: 30.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN A 326 HIS ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 HIS ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN C 326 HIS ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 GLN D 326 HIS ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20136 Z= 0.342 Angle : 0.712 7.481 27288 Z= 0.370 Chirality : 0.039 0.170 3136 Planarity : 0.005 0.048 3408 Dihedral : 6.063 40.425 2692 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 63.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 16.21 % Favored : 83.62 % Rotamer: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.25 (0.15), residues: 2424 helix: -0.85 (0.13), residues: 1364 sheet: -1.80 (0.53), residues: 76 loop : -4.21 (0.16), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 586 HIS 0.007 0.001 HIS B 326 PHE 0.039 0.002 PHE B 615 TYR 0.017 0.002 TYR D 303 ARG 0.004 0.001 ARG D 179 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 2.342 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 HIS cc_start: 0.9058 (t-90) cc_final: 0.8856 (t-90) REVERT: A 482 MET cc_start: 0.8104 (mmm) cc_final: 0.7778 (mmt) REVERT: A 578 MET cc_start: 0.6604 (mtp) cc_final: 0.6319 (mtt) REVERT: A 587 MET cc_start: 0.8978 (mtm) cc_final: 0.8733 (mtp) REVERT: A 624 PHE cc_start: 0.9172 (m-80) cc_final: 0.8888 (m-80) REVERT: B 578 MET cc_start: 0.4553 (mtt) cc_final: 0.4326 (tpp) REVERT: B 587 MET cc_start: 0.8750 (mtm) cc_final: 0.8411 (mtp) REVERT: B 624 PHE cc_start: 0.9105 (m-80) cc_final: 0.8822 (m-80) REVERT: B 761 MET cc_start: 0.8505 (mmp) cc_final: 0.8016 (mmp) REVERT: C 176 HIS cc_start: 0.9098 (t-90) cc_final: 0.8886 (t-90) REVERT: C 587 MET cc_start: 0.8977 (mtm) cc_final: 0.8742 (mtp) REVERT: C 624 PHE cc_start: 0.9105 (m-80) cc_final: 0.8893 (m-80) REVERT: C 761 MET cc_start: 0.8396 (mmp) cc_final: 0.8145 (mmp) REVERT: D 761 MET cc_start: 0.8372 (mmp) cc_final: 0.8154 (mmp) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.3074 time to fit residues: 106.0577 Evaluate side-chains 185 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 221 optimal weight: 20.0000 chunk 239 optimal weight: 0.9980 chunk 197 optimal weight: 0.6980 chunk 220 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 chunk 178 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20136 Z= 0.153 Angle : 0.514 6.274 27288 Z= 0.275 Chirality : 0.035 0.140 3136 Planarity : 0.003 0.058 3408 Dihedral : 5.422 36.434 2692 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 56.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.21 % Favored : 87.62 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.28 (0.16), residues: 2424 helix: 0.02 (0.13), residues: 1396 sheet: -1.25 (0.55), residues: 76 loop : -4.04 (0.17), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 586 HIS 0.007 0.001 HIS A 731 PHE 0.022 0.001 PHE D 624 TYR 0.017 0.001 TYR D 621 ARG 0.005 0.000 ARG C 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 253 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 2.203 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 176 HIS cc_start: 0.9063 (t-90) cc_final: 0.8852 (t-90) REVERT: A 624 PHE cc_start: 0.9076 (m-80) cc_final: 0.8831 (m-80) REVERT: A 757 ARG cc_start: 0.8068 (ppt170) cc_final: 0.7807 (ppt170) REVERT: A 761 MET cc_start: 0.8330 (mmp) cc_final: 0.8114 (mmp) REVERT: B 578 MET cc_start: 0.4752 (mtt) cc_final: 0.4515 (tpp) REVERT: B 587 MET cc_start: 0.8768 (mtm) cc_final: 0.8481 (mtp) REVERT: B 624 PHE cc_start: 0.9008 (m-80) cc_final: 0.8775 (m-80) REVERT: B 778 PHE cc_start: 0.8057 (t80) cc_final: 0.7241 (t80) REVERT: C 176 HIS cc_start: 0.9079 (t-90) cc_final: 0.8848 (t-90) REVERT: D 587 MET cc_start: 0.8862 (mtm) cc_final: 0.8579 (mtp) REVERT: D 625 MET cc_start: 0.8937 (ptp) cc_final: 0.8552 (ptp) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.2830 time to fit residues: 113.2978 Evaluate side-chains 195 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 9.9990 chunk 166 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 105 optimal weight: 0.0870 chunk 149 optimal weight: 4.9990 chunk 222 optimal weight: 7.9990 chunk 235 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20136 Z= 0.145 Angle : 0.492 5.553 27288 Z= 0.262 Chirality : 0.035 0.135 3136 Planarity : 0.003 0.051 3408 Dihedral : 5.035 31.511 2692 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 61.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.20 % Favored : 86.63 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.55 (0.17), residues: 2424 helix: 0.71 (0.14), residues: 1372 sheet: -1.09 (0.56), residues: 76 loop : -3.79 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 586 HIS 0.010 0.001 HIS A 731 PHE 0.013 0.001 PHE B 624 TYR 0.012 0.001 TYR D 621 ARG 0.003 0.000 ARG C 391 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 239 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 2.129 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: symmetry clash REVERT: A 176 HIS cc_start: 0.9064 (t-90) cc_final: 0.8834 (t-90) REVERT: A 482 MET cc_start: 0.8145 (mmm) cc_final: 0.7561 (mmt) REVERT: A 622 LEU cc_start: 0.9248 (tp) cc_final: 0.8994 (tp) REVERT: B 578 MET cc_start: 0.4625 (mtt) cc_final: 0.4418 (tpp) REVERT: B 587 MET cc_start: 0.8751 (mtm) cc_final: 0.8480 (mtp) REVERT: B 622 LEU cc_start: 0.9285 (tp) cc_final: 0.9067 (tp) REVERT: B 624 PHE cc_start: 0.8988 (m-80) cc_final: 0.8767 (m-80) REVERT: B 710 LEU cc_start: 0.9829 (mm) cc_final: 0.9580 (mp) REVERT: B 761 MET cc_start: 0.8237 (mmp) cc_final: 0.7996 (mmp) REVERT: B 778 PHE cc_start: 0.8040 (t80) cc_final: 0.7122 (t80) REVERT: C 176 HIS cc_start: 0.9065 (t-90) cc_final: 0.8821 (t-90) REVERT: C 482 MET cc_start: 0.8191 (mmm) cc_final: 0.7680 (mmt) REVERT: C 622 LEU cc_start: 0.9105 (tp) cc_final: 0.8748 (tp) REVERT: D 482 MET cc_start: 0.8201 (mmm) cc_final: 0.7578 (mmt) REVERT: D 587 MET cc_start: 0.8864 (mtm) cc_final: 0.8595 (mtp) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.2881 time to fit residues: 109.4551 Evaluate side-chains 190 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 175 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 201 optimal weight: 6.9990 chunk 163 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 211 optimal weight: 0.3980 chunk 59 optimal weight: 20.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20136 Z= 0.192 Angle : 0.516 5.617 27288 Z= 0.273 Chirality : 0.035 0.145 3136 Planarity : 0.003 0.043 3408 Dihedral : 4.966 30.610 2692 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 66.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.86 % Favored : 85.97 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.36 (0.17), residues: 2424 helix: 0.87 (0.14), residues: 1380 sheet: -1.00 (0.56), residues: 76 loop : -3.75 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 586 HIS 0.005 0.001 HIS A 731 PHE 0.023 0.001 PHE D 624 TYR 0.012 0.001 TYR D 628 ARG 0.004 0.000 ARG C 757 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 2.282 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 176 HIS cc_start: 0.9070 (t-90) cc_final: 0.8824 (t-90) REVERT: A 482 MET cc_start: 0.8118 (mmm) cc_final: 0.7562 (mmt) REVERT: A 605 MET cc_start: 0.9450 (ptm) cc_final: 0.8995 (ptm) REVERT: A 622 LEU cc_start: 0.9187 (tp) cc_final: 0.8971 (tp) REVERT: A 761 MET cc_start: 0.8282 (mmp) cc_final: 0.7974 (mmp) REVERT: B 587 MET cc_start: 0.8738 (mtm) cc_final: 0.8510 (mtp) REVERT: B 710 LEU cc_start: 0.9823 (mm) cc_final: 0.9623 (mp) REVERT: B 761 MET cc_start: 0.8308 (mmp) cc_final: 0.8041 (mmp) REVERT: B 778 PHE cc_start: 0.8022 (t80) cc_final: 0.7078 (t80) REVERT: C 176 HIS cc_start: 0.9086 (t-90) cc_final: 0.8816 (t-90) REVERT: C 482 MET cc_start: 0.8176 (mmm) cc_final: 0.7678 (mmt) REVERT: C 622 LEU cc_start: 0.9130 (tp) cc_final: 0.8832 (tp) REVERT: C 713 MET cc_start: 0.9298 (tmm) cc_final: 0.9040 (tmm) REVERT: D 482 MET cc_start: 0.8168 (mmm) cc_final: 0.7592 (mmt) REVERT: D 587 MET cc_start: 0.8873 (mtm) cc_final: 0.8620 (mtp) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2795 time to fit residues: 102.8617 Evaluate side-chains 191 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 3.9990 chunk 212 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 236 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 109 optimal weight: 0.0370 chunk 19 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 GLN ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20136 Z= 0.128 Angle : 0.469 6.196 27288 Z= 0.249 Chirality : 0.034 0.114 3136 Planarity : 0.003 0.037 3408 Dihedral : 4.731 27.536 2692 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 63.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.95 % Favored : 86.88 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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: -0.90 (0.18), residues: 2424 helix: 1.29 (0.14), residues: 1376 sheet: -0.93 (0.57), residues: 76 loop : -3.61 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 733 HIS 0.004 0.001 HIS B 731 PHE 0.025 0.001 PHE C 615 TYR 0.011 0.001 TYR B 628 ARG 0.002 0.000 ARG C 594 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 239 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 2.283 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: symmetry clash REVERT: A 176 HIS cc_start: 0.9062 (t-90) cc_final: 0.8817 (t-90) REVERT: A 482 MET cc_start: 0.8150 (mmm) cc_final: 0.7586 (mmt) REVERT: A 605 MET cc_start: 0.9393 (ptm) cc_final: 0.9039 (ptm) REVERT: A 622 LEU cc_start: 0.9223 (tp) cc_final: 0.8964 (tp) REVERT: A 761 MET cc_start: 0.8207 (mmp) cc_final: 0.7956 (mmp) REVERT: B 587 MET cc_start: 0.8699 (mtm) cc_final: 0.8485 (mtp) REVERT: B 622 LEU cc_start: 0.9207 (tp) cc_final: 0.8991 (tp) REVERT: B 710 LEU cc_start: 0.9816 (mm) cc_final: 0.9611 (mp) REVERT: B 761 MET cc_start: 0.8132 (mmp) cc_final: 0.7922 (mmp) REVERT: B 778 PHE cc_start: 0.7947 (t80) cc_final: 0.7088 (t80) REVERT: C 176 HIS cc_start: 0.9067 (t-90) cc_final: 0.8814 (t-90) REVERT: C 482 MET cc_start: 0.8212 (mmm) cc_final: 0.7699 (mmt) REVERT: C 622 LEU cc_start: 0.9091 (tp) cc_final: 0.8793 (tp) REVERT: C 713 MET cc_start: 0.9262 (tmm) cc_final: 0.9047 (tmm) REVERT: D 482 MET cc_start: 0.8179 (mmm) cc_final: 0.7394 (mmt) REVERT: D 556 TYR cc_start: 0.9212 (t80) cc_final: 0.8873 (t80) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.2843 time to fit residues: 109.1388 Evaluate side-chains 202 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 8.9990 chunk 26 optimal weight: 0.0870 chunk 134 optimal weight: 0.0770 chunk 172 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 198 optimal weight: 0.4980 chunk 131 optimal weight: 4.9990 chunk 235 optimal weight: 9.9990 chunk 147 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 108 optimal weight: 9.9990 overall best weight: 1.3320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20136 Z= 0.145 Angle : 0.478 5.996 27288 Z= 0.252 Chirality : 0.034 0.127 3136 Planarity : 0.003 0.032 3408 Dihedral : 4.619 27.114 2692 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 64.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.57 % Favored : 86.26 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % 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: -0.76 (0.18), residues: 2424 helix: 1.42 (0.14), residues: 1376 sheet: -0.89 (0.57), residues: 76 loop : -3.57 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 586 HIS 0.003 0.001 HIS D 731 PHE 0.027 0.001 PHE B 624 TYR 0.012 0.001 TYR D 628 ARG 0.002 0.000 ARG C 594 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 232 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 HIS cc_start: 0.9070 (t-90) cc_final: 0.8819 (t-90) REVERT: A 482 MET cc_start: 0.8178 (mmm) cc_final: 0.7588 (mmt) REVERT: A 605 MET cc_start: 0.9323 (ptm) cc_final: 0.9054 (ptm) REVERT: A 622 LEU cc_start: 0.9197 (tp) cc_final: 0.8966 (tp) REVERT: A 761 MET cc_start: 0.8156 (mmp) cc_final: 0.7888 (mmp) REVERT: B 397 GLU cc_start: 0.8830 (pm20) cc_final: 0.8517 (tm-30) REVERT: B 587 MET cc_start: 0.8767 (mtm) cc_final: 0.8512 (mtp) REVERT: B 622 LEU cc_start: 0.9236 (tp) cc_final: 0.8986 (tp) REVERT: B 642 MET cc_start: 0.8648 (tpt) cc_final: 0.8443 (tpp) REVERT: B 761 MET cc_start: 0.8192 (mmp) cc_final: 0.7975 (mmp) REVERT: B 778 PHE cc_start: 0.7873 (t80) cc_final: 0.7013 (t80) REVERT: C 176 HIS cc_start: 0.9080 (t-90) cc_final: 0.8824 (t-90) REVERT: C 482 MET cc_start: 0.8209 (mmm) cc_final: 0.7695 (mmt) REVERT: C 622 LEU cc_start: 0.9083 (tp) cc_final: 0.8763 (tp) REVERT: C 713 MET cc_start: 0.9285 (tmm) cc_final: 0.9083 (tmm) REVERT: D 482 MET cc_start: 0.8178 (mmm) cc_final: 0.7397 (mmt) REVERT: D 556 TYR cc_start: 0.9225 (t80) cc_final: 0.8883 (t80) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.2685 time to fit residues: 100.3339 Evaluate side-chains 197 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.9980 chunk 93 optimal weight: 0.3980 chunk 140 optimal weight: 0.0980 chunk 70 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 160 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 21 optimal weight: 0.0980 chunk 184 optimal weight: 5.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20136 Z= 0.153 Angle : 0.480 5.226 27288 Z= 0.252 Chirality : 0.035 0.141 3136 Planarity : 0.003 0.047 3408 Dihedral : 4.563 26.235 2692 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 66.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.78 % Favored : 86.06 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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 (0.18), residues: 2424 helix: 1.49 (0.14), residues: 1376 sheet: -0.90 (0.57), residues: 76 loop : -3.54 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 586 HIS 0.003 0.001 HIS C 326 PHE 0.022 0.001 PHE D 624 TYR 0.012 0.001 TYR D 628 ARG 0.004 0.000 ARG D 510 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 230 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 2.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 HIS cc_start: 0.9071 (t-90) cc_final: 0.8816 (t-90) REVERT: A 482 MET cc_start: 0.8187 (mmm) cc_final: 0.7600 (mmt) REVERT: A 605 MET cc_start: 0.9342 (ptm) cc_final: 0.9082 (ptm) REVERT: A 622 LEU cc_start: 0.9188 (tp) cc_final: 0.8930 (tp) REVERT: A 761 MET cc_start: 0.8150 (mmp) cc_final: 0.7861 (mmp) REVERT: B 397 GLU cc_start: 0.8829 (pm20) cc_final: 0.8526 (tm-30) REVERT: B 587 MET cc_start: 0.8723 (mtm) cc_final: 0.8507 (mtp) REVERT: B 622 LEU cc_start: 0.9208 (tp) cc_final: 0.8995 (tp) REVERT: B 624 PHE cc_start: 0.8998 (m-80) cc_final: 0.8781 (m-80) REVERT: B 642 MET cc_start: 0.8647 (tpt) cc_final: 0.8435 (tpp) REVERT: B 761 MET cc_start: 0.8206 (mmp) cc_final: 0.7985 (mmp) REVERT: B 778 PHE cc_start: 0.7848 (t80) cc_final: 0.7030 (t80) REVERT: C 176 HIS cc_start: 0.9077 (t-90) cc_final: 0.8816 (t-90) REVERT: C 482 MET cc_start: 0.8235 (mmm) cc_final: 0.7691 (mmt) REVERT: C 622 LEU cc_start: 0.9091 (tp) cc_final: 0.8789 (tp) REVERT: C 713 MET cc_start: 0.9288 (tmm) cc_final: 0.9077 (tmm) REVERT: D 482 MET cc_start: 0.8171 (mmm) cc_final: 0.7375 (mmt) REVERT: D 556 TYR cc_start: 0.9217 (t80) cc_final: 0.8861 (t80) REVERT: D 587 MET cc_start: 0.8849 (mtm) cc_final: 0.8643 (mtp) REVERT: D 625 MET cc_start: 0.8882 (ptp) cc_final: 0.8477 (ptp) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2834 time to fit residues: 103.6326 Evaluate side-chains 198 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.7980 chunk 225 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 219 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 172 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 198 optimal weight: 0.9980 chunk 207 optimal weight: 0.6980 chunk 218 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 ASN ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 ASN ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 588 ASN ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 588 ASN ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20136 Z= 0.115 Angle : 0.451 5.327 27288 Z= 0.237 Chirality : 0.034 0.114 3136 Planarity : 0.003 0.036 3408 Dihedral : 4.346 25.335 2692 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 63.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.29 % Favored : 87.54 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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 (0.18), residues: 2424 helix: 1.72 (0.14), residues: 1384 sheet: -0.75 (0.58), residues: 76 loop : -3.37 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 586 HIS 0.003 0.001 HIS C 447 PHE 0.016 0.001 PHE D 624 TYR 0.011 0.001 TYR D 628 ARG 0.005 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 237 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 HIS cc_start: 0.9073 (t-90) cc_final: 0.8826 (t-90) REVERT: A 482 MET cc_start: 0.8145 (mmm) cc_final: 0.7644 (mmt) REVERT: A 605 MET cc_start: 0.9349 (ptm) cc_final: 0.9141 (ptm) REVERT: A 622 LEU cc_start: 0.9172 (tp) cc_final: 0.8899 (tp) REVERT: A 704 ILE cc_start: 0.9727 (mm) cc_final: 0.9522 (tp) REVERT: A 761 MET cc_start: 0.8102 (mmp) cc_final: 0.7857 (mmp) REVERT: A 778 PHE cc_start: 0.7475 (t80) cc_final: 0.6937 (t80) REVERT: B 397 GLU cc_start: 0.8777 (pm20) cc_final: 0.8524 (tm-30) REVERT: B 449 MET cc_start: 0.8972 (mtt) cc_final: 0.8739 (mtt) REVERT: B 621 TYR cc_start: 0.9048 (t80) cc_final: 0.8700 (t80) REVERT: B 622 LEU cc_start: 0.9200 (tp) cc_final: 0.8965 (tp) REVERT: B 642 MET cc_start: 0.8601 (tpt) cc_final: 0.8389 (tpp) REVERT: B 778 PHE cc_start: 0.7841 (t80) cc_final: 0.7137 (t80) REVERT: C 176 HIS cc_start: 0.9076 (t-90) cc_final: 0.8819 (t-90) REVERT: C 449 MET cc_start: 0.9026 (mtt) cc_final: 0.8816 (mtt) REVERT: C 482 MET cc_start: 0.8171 (mmm) cc_final: 0.7696 (mmt) REVERT: C 622 LEU cc_start: 0.9084 (tp) cc_final: 0.8732 (tp) REVERT: D 397 GLU cc_start: 0.8753 (pm20) cc_final: 0.8504 (tm-30) REVERT: D 449 MET cc_start: 0.9015 (mtt) cc_final: 0.8777 (mtt) REVERT: D 482 MET cc_start: 0.8179 (mmm) cc_final: 0.7379 (mmt) REVERT: D 556 TYR cc_start: 0.9210 (t80) cc_final: 0.8894 (t80) REVERT: D 625 MET cc_start: 0.8878 (ptp) cc_final: 0.8479 (ptp) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.2668 time to fit residues: 102.6244 Evaluate side-chains 201 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.5980 chunk 231 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 243 optimal weight: 8.9990 chunk 223 optimal weight: 30.0000 chunk 193 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 118 optimal weight: 8.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20136 Z= 0.127 Angle : 0.458 7.464 27288 Z= 0.240 Chirality : 0.034 0.118 3136 Planarity : 0.003 0.033 3408 Dihedral : 4.310 24.099 2692 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 64.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.58 % Favored : 87.25 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % 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: -0.27 (0.18), residues: 2424 helix: 1.79 (0.14), residues: 1376 sheet: -0.88 (0.58), residues: 76 loop : -3.29 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 586 HIS 0.002 0.001 HIS D 388 PHE 0.028 0.001 PHE A 624 TYR 0.012 0.001 TYR B 235 ARG 0.004 0.000 ARG B 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.277 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: A 176 HIS cc_start: 0.9079 (t-90) cc_final: 0.8827 (t-90) REVERT: A 482 MET cc_start: 0.8157 (mmm) cc_final: 0.7646 (mmt) REVERT: A 605 MET cc_start: 0.9352 (ptm) cc_final: 0.9129 (ptm) REVERT: A 622 LEU cc_start: 0.9188 (tp) cc_final: 0.8907 (tp) REVERT: A 761 MET cc_start: 0.8101 (mmp) cc_final: 0.7851 (mmp) REVERT: B 397 GLU cc_start: 0.8778 (pm20) cc_final: 0.8528 (tm-30) REVERT: B 449 MET cc_start: 0.8970 (mtt) cc_final: 0.8736 (mtt) REVERT: B 622 LEU cc_start: 0.9196 (tp) cc_final: 0.8946 (tp) REVERT: B 642 MET cc_start: 0.8610 (tpt) cc_final: 0.8387 (tpp) REVERT: B 778 PHE cc_start: 0.7801 (t80) cc_final: 0.7102 (t80) REVERT: C 176 HIS cc_start: 0.9085 (t-90) cc_final: 0.8822 (t-90) REVERT: C 449 MET cc_start: 0.9035 (mtt) cc_final: 0.8823 (mtt) REVERT: C 482 MET cc_start: 0.8200 (mmm) cc_final: 0.7715 (mmt) REVERT: C 605 MET cc_start: 0.9301 (ptm) cc_final: 0.9034 (ptm) REVERT: C 622 LEU cc_start: 0.9122 (tp) cc_final: 0.8752 (tp) REVERT: C 713 MET cc_start: 0.9266 (tmm) cc_final: 0.9028 (tmm) REVERT: D 397 GLU cc_start: 0.8740 (pm20) cc_final: 0.8496 (tm-30) REVERT: D 482 MET cc_start: 0.8159 (mmm) cc_final: 0.7391 (mmt) REVERT: D 556 TYR cc_start: 0.9200 (t80) cc_final: 0.8860 (t80) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.2760 time to fit residues: 102.1130 Evaluate side-chains 196 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 0.6980 chunk 206 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 193 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 199 optimal weight: 0.4980 chunk 24 optimal weight: 0.0030 chunk 35 optimal weight: 0.3980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 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 = 0.3750 r_free = 0.3750 target = 0.091680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.070064 restraints weight = 96707.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.072240 restraints weight = 56571.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.073663 restraints weight = 39246.504| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20136 Z= 0.104 Angle : 0.440 5.595 27288 Z= 0.230 Chirality : 0.034 0.107 3136 Planarity : 0.003 0.031 3408 Dihedral : 4.122 22.984 2692 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 61.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.43 % Favored : 88.41 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % 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: 0.04 (0.18), residues: 2424 helix: 1.93 (0.14), residues: 1392 sheet: -0.61 (0.59), residues: 76 loop : -3.05 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 586 HIS 0.003 0.001 HIS C 447 PHE 0.019 0.001 PHE A 778 TYR 0.014 0.001 TYR B 478 ARG 0.004 0.000 ARG B 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3835.22 seconds wall clock time: 72 minutes 1.22 seconds (4321.22 seconds total)