Starting phenix.real_space_refine on Fri Nov 17 15:59:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aa5_11690/11_2023/7aa5_11690_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aa5_11690/11_2023/7aa5_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_11690/11_2023/7aa5_11690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aa5_11690/11_2023/7aa5_11690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aa5_11690/11_2023/7aa5_11690_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aa5_11690/11_2023/7aa5_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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 9.99, per 1000 atoms: 0.51 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: 8.32 Conformation dependent library (CDL) restraints added in 3.5 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: 1.75 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: 5.40 Time building geometry restraints manager: 8.95 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: 10612 17.58 - 35.16: 1116 35.16 - 52.73: 209 52.73 - 70.31: 46 70.31 - 87.89: 9 Dihedral angle restraints: 11992 sinusoidal: 4812 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 11989 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: 7.890 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: 0.450 Extract box with map and model: 28.410 Check model and map are aligned: 0.390 Set scattering table: 0.170 Process input model: 51.320 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.100 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.310 ------------------------------------------------------------------------------- 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 *********************** 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 : 2.460 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 outliers start: 44 outliers final: 19 residues processed: 280 average time/residue: 0.3033 time to fit residues: 132.4285 Evaluate side-chains 203 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 184 time to evaluate : 2.342 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1677 time to fit residues: 9.1970 ------------------------------------------------------------------------------- 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: 6.9990 chunk 63 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 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: 3.1990 ------------------------------------------------------------------------------- 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 ** 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 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: 0.8101 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20136 Z= 0.282 Angle : 0.652 7.133 27288 Z= 0.343 Chirality : 0.038 0.151 3136 Planarity : 0.004 0.047 3408 Dihedral : 5.920 40.467 2692 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 56.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.77 % Favored : 85.07 % Rotamer: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % 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: -3.11 (0.15), residues: 2424 helix: -0.75 (0.13), residues: 1368 sheet: -1.68 (0.53), residues: 76 loop : -4.13 (0.16), residues: 980 *********************** 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 226 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 2.486 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: symmetry clash outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.3161 time to fit residues: 111.2116 Evaluate side-chains 182 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 2.368 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2464 ------------------------------------------------------------------------------- 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: 5.9990 chunk 68 optimal weight: 0.9980 chunk 184 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 221 optimal weight: 20.0000 chunk 239 optimal weight: 0.4980 chunk 197 optimal weight: 1.9990 chunk 220 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 178 optimal weight: 5.9990 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 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 ASN ** 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: 0.7985 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20136 Z= 0.152 Angle : 0.509 6.382 27288 Z= 0.271 Chirality : 0.035 0.135 3136 Planarity : 0.003 0.061 3408 Dihedral : 5.298 35.330 2692 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 55.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.38 % Favored : 87.46 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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: -2.11 (0.17), residues: 2424 helix: 0.15 (0.13), residues: 1396 sheet: -1.15 (0.57), residues: 76 loop : -3.96 (0.17), residues: 952 *********************** 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 258 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 2.337 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 outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.2981 time to fit residues: 121.2795 Evaluate side-chains 189 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 2.397 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1584 ------------------------------------------------------------------------------- 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: 0.6980 chunk 115 optimal weight: 5.9990 chunk 24 optimal weight: 0.2980 chunk 105 optimal weight: 0.1980 chunk 149 optimal weight: 0.0770 chunk 222 optimal weight: 6.9990 chunk 235 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- 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 492 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20136 Z= 0.132 Angle : 0.490 11.020 27288 Z= 0.258 Chirality : 0.035 0.134 3136 Planarity : 0.003 0.050 3408 Dihedral : 4.956 31.283 2692 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 58.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.58 % Favored : 87.25 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % 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: -1.42 (0.17), residues: 2424 helix: 0.79 (0.14), residues: 1372 sheet: -0.98 (0.58), residues: 76 loop : -3.69 (0.18), residues: 976 *********************** 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 241 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 2.222 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 outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.3083 time to fit residues: 117.4125 Evaluate side-chains 197 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 2.740 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2901 ------------------------------------------------------------------------------- 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: 6.9990 chunk 133 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 120 optimal weight: 0.3980 chunk 211 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- 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 492 GLN ** 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 274 GLN ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 731 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20136 Z= 0.254 Angle : 0.580 6.361 27288 Z= 0.304 Chirality : 0.036 0.172 3136 Planarity : 0.004 0.044 3408 Dihedral : 5.130 30.401 2692 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 69.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.81 % Favored : 85.02 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: -1.53 (0.17), residues: 2424 helix: 0.65 (0.14), residues: 1400 sheet: -1.03 (0.57), residues: 76 loop : -3.78 (0.18), residues: 948 *********************** 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 225 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 2.322 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 outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2993 time to fit residues: 108.0154 Evaluate side-chains 191 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 2.582 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.5049 > 50: distance: 71 - 74: 5.082 distance: 74 - 75: 14.173 distance: 75 - 76: 9.001 distance: 75 - 78: 10.930 distance: 76 - 77: 30.826 distance: 76 - 83: 27.151 distance: 78 - 79: 23.146 distance: 79 - 80: 15.330 distance: 80 - 81: 11.046 distance: 80 - 82: 16.741 distance: 83 - 84: 10.378 distance: 84 - 85: 12.382 distance: 85 - 86: 40.895 distance: 85 - 88: 12.337 distance: 88 - 89: 9.573 distance: 89 - 90: 22.903 distance: 89 - 92: 18.040 distance: 90 - 91: 15.435 distance: 90 - 99: 29.074 distance: 92 - 93: 25.139 distance: 93 - 94: 30.727 distance: 95 - 96: 21.263 distance: 96 - 97: 20.763 distance: 96 - 98: 20.989 distance: 99 - 100: 11.517 distance: 100 - 101: 35.175 distance: 101 - 102: 21.738 distance: 101 - 103: 30.340 distance: 102 - 125: 23.951 distance: 103 - 104: 19.878 distance: 104 - 105: 11.389 distance: 105 - 106: 8.961 distance: 105 - 114: 4.942 distance: 106 - 136: 10.759 distance: 107 - 108: 11.303 distance: 108 - 109: 4.084 distance: 109 - 110: 3.281 distance: 110 - 111: 5.987 distance: 111 - 112: 5.852 distance: 111 - 113: 5.977 distance: 114 - 115: 6.748 distance: 115 - 116: 5.185 distance: 115 - 118: 11.920 distance: 116 - 117: 7.092 distance: 116 - 125: 4.517 distance: 118 - 119: 5.255 distance: 119 - 120: 5.836 distance: 121 - 123: 3.130 distance: 122 - 124: 3.510 distance: 123 - 124: 4.333 distance: 125 - 126: 10.080 distance: 126 - 127: 17.752 distance: 126 - 129: 14.683 distance: 127 - 128: 7.491 distance: 127 - 136: 15.907 distance: 129 - 130: 5.890 distance: 130 - 131: 7.988 distance: 130 - 132: 6.646 distance: 131 - 133: 9.347 distance: 132 - 134: 4.674 distance: 133 - 135: 8.611 distance: 134 - 135: 10.470 distance: 136 - 137: 8.275 distance: 137 - 138: 9.670 distance: 137 - 140: 8.614 distance: 138 - 139: 6.950 distance: 138 - 145: 14.606 distance: 140 - 141: 11.772 distance: 142 - 143: 9.196 distance: 145 - 146: 14.944 distance: 145 - 151: 21.546 distance: 146 - 147: 36.610 distance: 146 - 149: 11.573 distance: 147 - 148: 41.147 distance: 147 - 152: 15.241 distance: 149 - 150: 26.159 distance: 150 - 151: 7.296 distance: 152 - 153: 37.399 distance: 153 - 154: 15.068 distance: 153 - 156: 21.250 distance: 154 - 155: 5.863 distance: 154 - 161: 23.573 distance: 156 - 157: 7.002 distance: 157 - 158: 15.525 distance: 158 - 159: 16.505 distance: 159 - 160: 26.828