Starting phenix.real_space_refine on Sat Feb 17 10:06:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksl_23019/02_2024/7ksl_23019_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksl_23019/02_2024/7ksl_23019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksl_23019/02_2024/7ksl_23019.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksl_23019/02_2024/7ksl_23019.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksl_23019/02_2024/7ksl_23019_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksl_23019/02_2024/7ksl_23019_updated.pdb" } resolution = 3.5 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= 0.045 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 87 5.16 5 C 11611 2.51 5 N 3162 2.21 5 O 3436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 488": "OE1" <-> "OE2" Residue "C GLU 489": "OE1" <-> "OE2" Residue "C GLU 495": "OE1" <-> "OE2" Residue "C ARG 511": "NH1" <-> "NH2" Residue "C PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 534": "NH1" <-> "NH2" Residue "C ARG 538": "NH1" <-> "NH2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C ARG 672": "NH1" <-> "NH2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C PHE 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 785": "NH1" <-> "NH2" Residue "C ARG 786": "NH1" <-> "NH2" Residue "C GLU 801": "OE1" <-> "OE2" Residue "C GLU 812": "OE1" <-> "OE2" Residue "C ARG 871": "NH1" <-> "NH2" Residue "C ARG 874": "NH1" <-> "NH2" Residue "C GLU 897": "OE1" <-> "OE2" Residue "B PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 459": "NH1" <-> "NH2" Residue "B ARG 482": "NH1" <-> "NH2" Residue "B ARG 511": "NH1" <-> "NH2" Residue "B ARG 534": "NH1" <-> "NH2" Residue "B PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 652": "NH1" <-> "NH2" Residue "B ARG 672": "NH1" <-> "NH2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B ASP 744": "OD1" <-> "OD2" Residue "B ARG 785": "NH1" <-> "NH2" Residue "B ARG 871": "NH1" <-> "NH2" Residue "B ARG 874": "NH1" <-> "NH2" Residue "B GLU 882": "OE1" <-> "OE2" Residue "B ASP 919": "OD1" <-> "OD2" Residue "A ASP 449": "OD1" <-> "OD2" Residue "A GLU 454": "OE1" <-> "OE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A ARG 511": "NH1" <-> "NH2" Residue "A ARG 534": "NH1" <-> "NH2" Residue "A ARG 538": "NH1" <-> "NH2" Residue "A TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A ARG 650": "NH1" <-> "NH2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A GLU 736": "OE1" <-> "OE2" Residue "A ARG 785": "NH1" <-> "NH2" Residue "A ARG 786": "NH1" <-> "NH2" Residue "A ARG 822": "NH1" <-> "NH2" Residue "A ARG 871": "NH1" <-> "NH2" Residue "A GLU 941": "OE1" <-> "OE2" Residue "F ARG 459": "NH1" <-> "NH2" Residue "F ARG 482": "NH1" <-> "NH2" Residue "F ARG 511": "NH1" <-> "NH2" Residue "F ASP 590": "OD1" <-> "OD2" Residue "F GLU 591": "OE1" <-> "OE2" Residue "F GLU 647": "OE1" <-> "OE2" Residue "F GLU 671": "OE1" <-> "OE2" Residue "F ARG 672": "NH1" <-> "NH2" Residue "F ARG 679": "NH1" <-> "NH2" Residue "F GLU 706": "OE1" <-> "OE2" Residue "F GLU 736": "OE1" <-> "OE2" Residue "F PHE 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 755": "NH1" <-> "NH2" Residue "F ARG 785": "NH1" <-> "NH2" Residue "F ARG 786": "NH1" <-> "NH2" Residue "F GLU 801": "OE1" <-> "OE2" Residue "F GLU 941": "OE1" <-> "OE2" Residue "E ASP 439": "OD1" <-> "OD2" Residue "E TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 538": "NH1" <-> "NH2" Residue "E PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 654": "OE1" <-> "OE2" Residue "E ARG 679": "NH1" <-> "NH2" Residue "E ASP 685": "OD1" <-> "OD2" Residue "E GLU 717": "OE1" <-> "OE2" Residue "E PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 755": "NH1" <-> "NH2" Residue "E ARG 785": "NH1" <-> "NH2" Residue "E ARG 786": "NH1" <-> "NH2" Residue "E ASP 789": "OD1" <-> "OD2" Residue "E PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18306 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3291 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 22, 'TRANS': 466} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 545 Unresolved non-hydrogen angles: 684 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 4, 'GLU:plan': 22, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 335 Chain: "B" Number of atoms: 3770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3770 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 24, 'TRANS': 495} Chain breaks: 1 Unresolved non-hydrogen bonds: 289 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 177 Chain: "A" Number of atoms: 3826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3826 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 24, 'TRANS': 495} Chain breaks: 1 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 10, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 141 Chain: "F" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3881 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 24, 'TRANS': 495} Chain breaks: 1 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 116 Chain: "E" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3403 Classifications: {'peptide': 502} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 142} Link IDs: {'PTRANS': 23, 'TRANS': 478} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 538 Unresolved non-hydrogen angles: 671 Unresolved non-hydrogen dihedrals: 436 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 316 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.08, per 1000 atoms: 0.55 Number of scatterers: 18306 At special positions: 0 Unit cell: (117.3, 132.25, 132.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 87 16.00 P 10 15.00 O 3436 8.00 N 3162 7.00 C 11611 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.93 Conformation dependent library (CDL) restraints added in 3.6 seconds 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4754 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 103 helices and 24 sheets defined 41.8% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.76 Creating SS restraints... Processing helix chain 'C' and resid 422 through 427 Processing helix chain 'C' and resid 432 through 446 Processing helix chain 'C' and resid 453 through 467 Processing helix chain 'C' and resid 480 through 490 removed outlier: 3.611A pdb=" N ASP C 490 " --> pdb=" O VAL C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 510 Processing helix chain 'C' and resid 529 through 540 Processing helix chain 'C' and resid 558 through 580 removed outlier: 4.326A pdb=" N ILE C 573 " --> pdb=" O ILE C 558 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN C 575 " --> pdb=" O LYS C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 610 Processing helix chain 'C' and resid 613 through 616 No H-bonds generated for 'chain 'C' and resid 613 through 616' Processing helix chain 'C' and resid 647 through 650 No H-bonds generated for 'chain 'C' and resid 647 through 650' Processing helix chain 'C' and resid 663 through 672 Processing helix chain 'C' and resid 674 through 682 Processing helix chain 'C' and resid 693 through 702 Processing helix chain 'C' and resid 710 through 728 Processing helix chain 'C' and resid 741 through 745 Processing helix chain 'C' and resid 808 through 828 Processing helix chain 'C' and resid 850 through 869 Proline residue: C 854 - end of helix removed outlier: 5.281A pdb=" N GLY C 857 " --> pdb=" O GLY C 853 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N CYS C 858 " --> pdb=" O PRO C 854 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N THR C 859 " --> pdb=" O SER C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 904 Processing helix chain 'C' and resid 914 through 920 removed outlier: 4.886A pdb=" N LYS C 918 " --> pdb=" O GLU C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 945 Processing helix chain 'B' and resid 422 through 427 Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.879A pdb=" N VAL B 437 " --> pdb=" O HIS B 433 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LYS B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 467 removed outlier: 4.086A pdb=" N ASN B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU B 465 " --> pdb=" O TYR B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 removed outlier: 3.541A pdb=" N GLU B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 510 Processing helix chain 'B' and resid 529 through 540 Processing helix chain 'B' and resid 573 through 580 Processing helix chain 'B' and resid 592 through 594 No H-bonds generated for 'chain 'B' and resid 592 through 594' Processing helix chain 'B' and resid 604 through 610 Processing helix chain 'B' and resid 642 through 644 No H-bonds generated for 'chain 'B' and resid 642 through 644' Processing helix chain 'B' and resid 647 through 650 No H-bonds generated for 'chain 'B' and resid 647 through 650' Processing helix chain 'B' and resid 663 through 672 Processing helix chain 'B' and resid 674 through 682 Processing helix chain 'B' and resid 693 through 702 Processing helix chain 'B' and resid 710 through 729 Processing helix chain 'B' and resid 743 through 746 No H-bonds generated for 'chain 'B' and resid 743 through 746' Processing helix chain 'B' and resid 808 through 828 removed outlier: 3.545A pdb=" N GLN B 827 " --> pdb=" O ALA B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 855 No H-bonds generated for 'chain 'B' and resid 853 through 855' Processing helix chain 'B' and resid 857 through 869 Processing helix chain 'B' and resid 895 through 905 removed outlier: 3.651A pdb=" N ALA B 905 " --> pdb=" O ALA B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 920 removed outlier: 5.005A pdb=" N LYS B 918 " --> pdb=" O GLU B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 946 Processing helix chain 'A' and resid 423 through 427 Processing helix chain 'A' and resid 432 through 447 Processing helix chain 'A' and resid 453 through 467 Processing helix chain 'A' and resid 480 through 490 removed outlier: 3.834A pdb=" N ASP A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 510 Processing helix chain 'A' and resid 529 through 540 Processing helix chain 'A' and resid 555 through 559 removed outlier: 3.511A pdb=" N LYS A 559 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 580 Processing helix chain 'A' and resid 592 through 594 No H-bonds generated for 'chain 'A' and resid 592 through 594' Processing helix chain 'A' and resid 604 through 610 Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 647 through 652 removed outlier: 4.310A pdb=" N ARG A 652 " --> pdb=" O PRO A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 681 removed outlier: 4.890A pdb=" N VAL A 675 " --> pdb=" O GLU A 671 " (cutoff:3.500A) Proline residue: A 676 - end of helix Processing helix chain 'A' and resid 693 through 702 Processing helix chain 'A' and resid 710 through 728 Processing helix chain 'A' and resid 808 through 828 removed outlier: 3.755A pdb=" N GLN A 827 " --> pdb=" O ALA A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 855 Proline residue: A 854 - end of helix No H-bonds generated for 'chain 'A' and resid 850 through 855' Processing helix chain 'A' and resid 857 through 869 Processing helix chain 'A' and resid 895 through 904 Processing helix chain 'A' and resid 939 through 945 Processing helix chain 'F' and resid 422 through 427 Processing helix chain 'F' and resid 432 through 446 removed outlier: 3.686A pdb=" N ASP F 436 " --> pdb=" O LYS F 432 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL F 437 " --> pdb=" O HIS F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 466 Processing helix chain 'F' and resid 480 through 490 removed outlier: 3.907A pdb=" N ASP F 490 " --> pdb=" O VAL F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 510 Processing helix chain 'F' and resid 531 through 540 Processing helix chain 'F' and resid 555 through 559 Processing helix chain 'F' and resid 572 through 580 Processing helix chain 'F' and resid 604 through 610 Processing helix chain 'F' and resid 613 through 616 No H-bonds generated for 'chain 'F' and resid 613 through 616' Processing helix chain 'F' and resid 647 through 652 removed outlier: 4.051A pdb=" N ARG F 652 " --> pdb=" O PRO F 648 " (cutoff:3.500A) Processing helix chain 'F' and resid 663 through 672 Processing helix chain 'F' and resid 674 through 682 Processing helix chain 'F' and resid 693 through 703 Processing helix chain 'F' and resid 710 through 728 removed outlier: 3.666A pdb=" N LYS F 714 " --> pdb=" O ARG F 710 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL F 719 " --> pdb=" O GLN F 715 " (cutoff:3.500A) Processing helix chain 'F' and resid 742 through 745 No H-bonds generated for 'chain 'F' and resid 742 through 745' Processing helix chain 'F' and resid 808 through 828 Processing helix chain 'F' and resid 853 through 855 No H-bonds generated for 'chain 'F' and resid 853 through 855' Processing helix chain 'F' and resid 857 through 869 Processing helix chain 'F' and resid 895 through 904 Processing helix chain 'F' and resid 917 through 920 No H-bonds generated for 'chain 'F' and resid 917 through 920' Processing helix chain 'F' and resid 939 through 946 Processing helix chain 'E' and resid 422 through 425 No H-bonds generated for 'chain 'E' and resid 422 through 425' Processing helix chain 'E' and resid 432 through 446 Processing helix chain 'E' and resid 453 through 467 Processing helix chain 'E' and resid 480 through 489 removed outlier: 4.227A pdb=" N GLU E 488 " --> pdb=" O GLN E 484 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU E 489 " --> pdb=" O ALA E 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 509 Processing helix chain 'E' and resid 529 through 539 removed outlier: 3.559A pdb=" N ALA E 533 " --> pdb=" O LYS E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 580 Processing helix chain 'E' and resid 603 through 610 Processing helix chain 'E' and resid 647 through 650 No H-bonds generated for 'chain 'E' and resid 647 through 650' Processing helix chain 'E' and resid 663 through 672 Processing helix chain 'E' and resid 674 through 682 Processing helix chain 'E' and resid 693 through 702 Processing helix chain 'E' and resid 710 through 728 Processing helix chain 'E' and resid 808 through 826 Processing helix chain 'E' and resid 850 through 869 Proline residue: E 854 - end of helix removed outlier: 5.791A pdb=" N GLY E 857 " --> pdb=" O GLY E 853 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N CYS E 858 " --> pdb=" O PRO E 854 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N THR E 859 " --> pdb=" O SER E 855 " (cutoff:3.500A) Processing helix chain 'E' and resid 896 through 905 Processing helix chain 'E' and resid 914 through 921 removed outlier: 3.865A pdb=" N LYS E 917 " --> pdb=" O ALA E 914 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS E 918 " --> pdb=" O GLU E 915 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP E 919 " --> pdb=" O ASN E 916 " (cutoff:3.500A) Processing helix chain 'E' and resid 926 through 928 No H-bonds generated for 'chain 'E' and resid 926 through 928' Processing helix chain 'E' and resid 939 through 946 Processing sheet with id= A, first strand: chain 'C' and resid 636 through 638 removed outlier: 6.196A pdb=" N LEU C 519 " --> pdb=" O CYS C 637 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLU C 654 " --> pdb=" O CYS C 520 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N TYR C 522 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE C 656 " --> pdb=" O TYR C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 764 through 771 Processing sheet with id= C, first strand: chain 'C' and resid 877 through 879 removed outlier: 6.760A pdb=" N CYS C 909 " --> pdb=" O ALA C 878 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLU C 932 " --> pdb=" O ILE C 910 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LEU C 912 " --> pdb=" O GLU C 932 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N HIS C 934 " --> pdb=" O LEU C 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 654 through 657 removed outlier: 6.244A pdb=" N PHE B 635 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N PHE B 521 " --> pdb=" O PHE B 635 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N CYS B 637 " --> pdb=" O PHE B 521 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N PHE B 545 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ASP B 590 " --> pdb=" O PHE B 545 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE B 547 " --> pdb=" O ASP B 590 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 764 through 771 removed outlier: 6.360A pdb=" N SER B 799 " --> pdb=" O ILE B 840 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU B 842 " --> pdb=" O SER B 799 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLU B 801 " --> pdb=" O LEU B 842 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 909 through 913 removed outlier: 6.032A pdb=" N GLU B 932 " --> pdb=" O ILE B 910 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU B 912 " --> pdb=" O GLU B 932 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N HIS B 934 " --> pdb=" O LEU B 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 636 through 639 removed outlier: 6.804A pdb=" N LEU A 519 " --> pdb=" O CYS A 637 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ALA A 639 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N PHE A 521 " --> pdb=" O ALA A 639 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU A 654 " --> pdb=" O CYS A 520 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TYR A 522 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE A 656 " --> pdb=" O TYR A 522 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 545 through 548 Processing sheet with id= I, first strand: chain 'A' and resid 689 through 691 removed outlier: 7.116A pdb=" N VAL A 735 " --> pdb=" O LYS A 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 764 through 767 removed outlier: 6.398A pdb=" N SER A 799 " --> pdb=" O ILE A 840 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU A 842 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU A 801 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 877 through 879 removed outlier: 6.667A pdb=" N CYS A 909 " --> pdb=" O ALA A 878 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU A 932 " --> pdb=" O ILE A 910 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU A 912 " --> pdb=" O GLU A 932 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N HIS A 934 " --> pdb=" O LEU A 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 636 through 639 removed outlier: 6.786A pdb=" N LEU F 519 " --> pdb=" O CYS F 637 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ALA F 639 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE F 521 " --> pdb=" O ALA F 639 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 545 through 548 Processing sheet with id= N, first strand: chain 'F' and resid 689 through 691 removed outlier: 7.340A pdb=" N VAL F 735 " --> pdb=" O LYS F 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'F' and resid 764 through 766 Processing sheet with id= P, first strand: chain 'F' and resid 769 through 771 Processing sheet with id= Q, first strand: chain 'F' and resid 799 through 803 removed outlier: 3.525A pdb=" N ILE F 840 " --> pdb=" O SER F 799 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 877 through 879 removed outlier: 6.420A pdb=" N CYS F 909 " --> pdb=" O ALA F 878 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLU F 932 " --> pdb=" O ILE F 910 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU F 912 " --> pdb=" O GLU F 932 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N HIS F 934 " --> pdb=" O LEU F 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'E' and resid 520 through 523 Processing sheet with id= T, first strand: chain 'E' and resid 546 through 548 removed outlier: 6.012A pdb=" N LEU E 588 " --> pdb=" O PHE E 547 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 689 through 691 removed outlier: 7.275A pdb=" N VAL E 735 " --> pdb=" O LYS E 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'E' and resid 765 through 771 Processing sheet with id= W, first strand: chain 'E' and resid 781 through 784 removed outlier: 6.114A pdb=" N SER E 799 " --> pdb=" O ILE E 840 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU E 842 " --> pdb=" O SER E 799 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLU E 801 " --> pdb=" O LEU E 842 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 877 through 880 removed outlier: 6.502A pdb=" N CYS E 909 " --> pdb=" O ALA E 878 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N THR E 880 " --> pdb=" O CYS E 909 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL E 911 " --> pdb=" O THR E 880 " (cutoff:3.500A) No H-bonds generated for sheet with id= X 698 hydrogen bonds defined for protein. 2007 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: 5.15 Time building geometry restraints manager: 7.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6077 1.34 - 1.46: 3026 1.46 - 1.57: 9370 1.57 - 1.69: 15 1.69 - 1.81: 139 Bond restraints: 18627 Sorted by residual: bond pdb=" C VAL E 911 " pdb=" N LEU E 912 " ideal model delta sigma weight residual 1.331 1.252 0.079 1.59e-02 3.96e+03 2.46e+01 bond pdb=" C ILE B 889 " pdb=" N LEU B 890 " ideal model delta sigma weight residual 1.331 1.229 0.102 2.07e-02 2.33e+03 2.44e+01 bond pdb=" CA ASP A 643 " pdb=" C ASP A 643 " ideal model delta sigma weight residual 1.523 1.492 0.032 1.34e-02 5.57e+03 5.59e+00 bond pdb=" CA LYS C 918 " pdb=" C LYS C 918 " ideal model delta sigma weight residual 1.522 1.491 0.031 1.72e-02 3.38e+03 3.22e+00 bond pdb=" C4 ADP B1000 " pdb=" C5 ADP B1000 " ideal model delta sigma weight residual 1.490 1.456 0.034 2.00e-02 2.50e+03 2.88e+00 ... (remaining 18622 not shown) Histogram of bond angle deviations from ideal: 98.67 - 106.16: 517 106.16 - 113.64: 10842 113.64 - 121.12: 9103 121.12 - 128.61: 4862 128.61 - 136.09: 96 Bond angle restraints: 25420 Sorted by residual: angle pdb=" N VAL B 555 " pdb=" CA VAL B 555 " pdb=" C VAL B 555 " ideal model delta sigma weight residual 112.80 106.85 5.95 1.15e+00 7.56e-01 2.68e+01 angle pdb=" N GLN B 875 " pdb=" CA GLN B 875 " pdb=" C GLN B 875 " ideal model delta sigma weight residual 110.97 115.36 -4.39 1.09e+00 8.42e-01 1.62e+01 angle pdb=" N GLY A 571 " pdb=" CA GLY A 571 " pdb=" C GLY A 571 " ideal model delta sigma weight residual 113.18 121.46 -8.28 2.37e+00 1.78e-01 1.22e+01 angle pdb=" N VAL A 555 " pdb=" CA VAL A 555 " pdb=" C VAL A 555 " ideal model delta sigma weight residual 112.04 107.25 4.79 1.40e+00 5.10e-01 1.17e+01 angle pdb=" C GLU A 557 " pdb=" N ILE A 558 " pdb=" CA ILE A 558 " ideal model delta sigma weight residual 123.08 119.82 3.26 1.01e+00 9.80e-01 1.04e+01 ... (remaining 25415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.36: 10646 24.36 - 48.72: 460 48.72 - 73.08: 33 73.08 - 97.44: 21 97.44 - 121.80: 2 Dihedral angle restraints: 11162 sinusoidal: 3808 harmonic: 7354 Sorted by residual: dihedral pdb=" O1B ADP E1000 " pdb=" O3A ADP E1000 " pdb=" PB ADP E1000 " pdb=" PA ADP E1000 " ideal model delta sinusoidal sigma weight residual 300.00 178.20 121.80 1 2.00e+01 2.50e-03 3.66e+01 dihedral pdb=" C5' ADP A1000 " pdb=" O5' ADP A1000 " pdb=" PA ADP A1000 " pdb=" O2A ADP A1000 " ideal model delta sinusoidal sigma weight residual -60.00 -165.05 105.05 1 2.00e+01 2.50e-03 3.02e+01 dihedral pdb=" CA ARG C 874 " pdb=" C ARG C 874 " pdb=" N GLN C 875 " pdb=" CA GLN C 875 " ideal model delta harmonic sigma weight residual -180.00 -155.42 -24.58 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 11159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1674 0.033 - 0.066: 937 0.066 - 0.100: 332 0.100 - 0.133: 117 0.133 - 0.166: 15 Chirality restraints: 3075 Sorted by residual: chirality pdb=" CA PRO A 762 " pdb=" N PRO A 762 " pdb=" C PRO A 762 " pdb=" CB PRO A 762 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" C4' ADP B1000 " pdb=" C3' ADP B1000 " pdb=" C5' ADP B1000 " pdb=" O4' ADP B1000 " both_signs ideal model delta sigma weight residual False -2.50 -2.66 0.16 2.00e-01 2.50e+01 6.77e-01 chirality pdb=" CB ILE E 636 " pdb=" CA ILE E 636 " pdb=" CG1 ILE E 636 " pdb=" CG2 ILE E 636 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.64e-01 ... (remaining 3072 not shown) Planarity restraints: 3261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN F 584 " 0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO F 585 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO F 585 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 585 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 572 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.56e+00 pdb=" C LYS A 572 " -0.037 2.00e-02 2.50e+03 pdb=" O LYS A 572 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE A 573 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 849 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO F 850 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO F 850 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 850 " -0.030 5.00e-02 4.00e+02 ... (remaining 3258 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 418 2.69 - 3.24: 18931 3.24 - 3.79: 28590 3.79 - 4.35: 36813 4.35 - 4.90: 60270 Nonbonded interactions: 145022 Sorted by model distance: nonbonded pdb=" OG1 THR B 886 " pdb=" OH TYR A 757 " model vdw 2.133 2.440 nonbonded pdb=" O VAL E 527 " pdb=" OH TYR E 661 " model vdw 2.142 2.440 nonbonded pdb=" OE2 GLU A 671 " pdb=" OG SER A 693 " model vdw 2.149 2.440 nonbonded pdb=" OG1 THR E 771 " pdb=" O GLY E 774 " model vdw 2.183 2.440 nonbonded pdb=" O VAL C 527 " pdb=" OH TYR C 661 " model vdw 2.195 2.440 ... (remaining 145017 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 421 through 430 and (name N or name CA or name C or name \ O or name CB )) or resid 431 through 432 or (resid 433 through 445 and (name N o \ r name CA or name C or name O or name CB )) or resid 446 or (resid 447 through 4 \ 68 and (name N or name CA or name C or name O or name CB )) or resid 469 or (res \ id 470 and (name N or name CA or name C or name O or name CB )) or (resid 471 th \ rough 473 and (name N or name CA or name C or name O or name CB )) or resid 474 \ or (resid 475 through 483 and (name N or name CA or name C or name O or name CB \ )) or resid 484 through 488 or (resid 489 through 490 and (name N or name CA or \ name C or name O or name CB )) or resid 491 through 493 or (resid 494 through 49 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 497 through \ 498 or (resid 499 and (name N or name CA or name C or name O or name CB )) or re \ sid 500 or (resid 501 and (name N or name CA or name C or name O or name CB )) o \ r resid 502 through 503 or (resid 504 through 506 and (name N or name CA or name \ C or name O or name CB )) or resid 507 through 508 or (resid 509 through 511 an \ d (name N or name CA or name C or name O or name CB )) or resid 512 or resid 520 \ through 521 or (resid 522 and (name N or name CA or name C or name O or name CB \ )) or resid 523 through 533 or (resid 534 and (name N or name CA or name C or n \ ame O or name CB )) or resid 535 or (resid 536 through 537 and (name N or name C \ A or name C or name O or name CB )) or resid 538 through 539 or (resid 540 throu \ gh 544 and (name N or name CA or name C or name O or name CB )) or resid 545 or \ (resid 546 and (name N or name CA or name C or name O or name CB )) or resid 547 \ through 548 or (resid 549 and (name N or name CA or name C or name O or name CB \ )) or (resid 554 through 558 and (name N or name CA or name C or name O or name \ CB )) or (resid 571 through 575 and (name N or name CA or name C or name O or n \ ame CB )) or resid 576 or (resid 577 through 583 and (name N or name CA or name \ C or name O or name CB )) or resid 584 through 585 or (resid 586 through 588 and \ (name N or name CA or name C or name O or name CB )) or resid 589 through 590 o \ r (resid 591 through 612 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 618 through 626 and (name N or name CA or name C or name O or name C \ B )) or resid 627 or (resid 628 through 629 and (name N or name CA or name C or \ name O or name CB )) or resid 630 through 631 or (resid 632 and (name N or name \ CA or name C or name O or name CB )) or resid 633 or (resid 634 and (name N or n \ ame CA or name C or name O or name CB )) or resid 635 through 639 or (resid 640 \ and (name N or name CA or name C or name O or name CB )) or resid 641 through 64 \ 3 or (resid 644 and (name N or name CA or name C or name O or name CB )) or resi \ d 645 through 646 or (resid 647 and (name N or name CA or name C or name O or na \ me CB )) or resid 648 through 649 or (resid 650 through 652 and (name N or name \ CA or name C or name O or name CB )) or resid 653 or (resid 654 through 655 and \ (name N or name CA or name C or name O or name CB )) or resid 656 through 664 or \ (resid 665 through 666 and (name N or name CA or name C or name O or name CB )) \ or resid 667 through 668 or (resid 669 through 673 and (name N or name CA or na \ me C or name O or name CB )) or resid 674 through 676 or (resid 677 through 678 \ and (name N or name CA or name C or name O or name CB )) or resid 679 through 68 \ 3 or (resid 684 through 686 and (name N or name CA or name C or name O or name C \ B )) or resid 687 or resid 692 through 694 or (resid 695 and (name N or name CA \ or name C or name O or name CB )) or resid 696 through 702 or (resid 703 and (na \ me N or name CA or name C or name O or name CB )) or resid 704 or (resid 705 thr \ ough 706 and (name N or name CA or name C or name O or name CB )) or resid 707 t \ hrough 709 or (resid 710 and (name N or name CA or name C or name O or name CB ) \ ) or resid 711 through 721 or (resid 722 and (name N or name CA or name C or nam \ e O or name CB )) or resid 723 through 725 or (resid 726 and (name N or name CA \ or name C or name O or name CB )) or resid 727 through 731 or (resid 741 and (na \ me N or name CA or name C or name O or name CB )) or resid 742 or (resid 743 thr \ ough 744 and (name N or name CA or name C or name O or name CB )) or resid 745 t \ hrough 747 or (resid 748 and (name N or name CA or name C or name O or name CB ) \ ) or resid 749 through 751 or (resid 752 through 755 and (name N or name CA or n \ ame C or name O or name CB )) or resid 756 through 772 or (resid 773 and (name N \ or name CA or name C or name O or name CB )) or resid 774 through 786 or (resid \ 787 through 791 and (name N or name CA or name C or name O or name CB )) or res \ id 798 through 800 or (resid 801 and (name N or name CA or name C or name O or n \ ame CB )) or resid 802 through 804 or (resid 805 and (name N or name CA or name \ C or name O or name CB )) or resid 806 through 821 or (resid 822 through 823 and \ (name N or name CA or name C or name O or name CB )) or resid 824 through 825 o \ r (resid 826 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 27 through 832 or (resid 833 and (name N or name CA or name C or name O or name \ CB )) or resid 834 through 836 or (resid 837 and (name N or name CA or name C or \ name O or name CB )) or resid 838 through 850 or (resid 851 and (name N or name \ CA or name C or name O or name CB )) or resid 852 through 870 or (resid 871 and \ (name N or name CA or name C or name O or name CB )) or resid 872 through 874 o \ r (resid 875 through 876 and (name N or name CA or name C or name O or name CB ) \ ) or resid 877 through 884 or (resid 885 through 886 and (name N or name CA or n \ ame C or name O or name CB )) or resid 887 or (resid 888 and (name N or name CA \ or name C or name O or name CB )) or resid 889 through 895 or (resid 896 and (na \ me N or name CA or name C or name O or name CB )) or resid 897 or (resid 898 and \ (name N or name CA or name C or name O or name CB )) or resid 899 through 916 o \ r (resid 917 through 918 and (name N or name CA or name C or name O or name CB ) \ ) or resid 919 through 921 or (resid 922 and (name N or name CA or name C or nam \ e O or name CB )) or resid 923 through 928 or (resid 929 and (name N or name CA \ or name C or name O or name CB )) or resid 930 through 936 or (resid 937 through \ 938 and (name N or name CA or name C or name O or name CB )) or resid 939 throu \ gh 947 or resid 1000)) selection = (chain 'B' and (resid 421 through 432 or (resid 433 through 445 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 446 through 468 and (name N o \ r name CA or name C or name O or name CB )) or resid 469 or (resid 470 and (name \ N or name CA or name C or name O or name CB )) or resid 471 or (resid 472 throu \ gh 473 and (name N or name CA or name C or name O or name CB )) or resid 474 or \ (resid 475 through 483 and (name N or name CA or name C or name O or name CB )) \ or resid 484 through 488 or (resid 489 through 490 and (name N or name CA or nam \ e C or name O or name CB )) or resid 491 through 493 or (resid 494 through 496 a \ nd (name N or name CA or name C or name O or name CB )) or resid 497 through 498 \ or (resid 499 and (name N or name CA or name C or name O or name CB )) or resid \ 500 or (resid 501 and (name N or name CA or name C or name O or name CB )) or r \ esid 502 through 503 or (resid 504 through 506 and (name N or name CA or name C \ or name O or name CB )) or resid 507 through 508 or (resid 509 through 511 and ( \ name N or name CA or name C or name O or name CB )) or resid 512 or resid 520 th \ rough 521 or (resid 522 and (name N or name CA or name C or name O or name CB )) \ or resid 523 through 533 or (resid 534 and (name N or name CA or name C or name \ O or name CB )) or resid 535 or (resid 536 through 537 and (name N or name CA o \ r name C or name O or name CB )) or resid 538 through 539 or (resid 540 through \ 544 and (name N or name CA or name C or name O or name CB )) or resid 545 throug \ h 548 or (resid 549 and (name N or name CA or name C or name O or name CB )) or \ (resid 554 through 558 and (name N or name CA or name C or name O or name CB )) \ or resid 571 or (resid 572 through 575 and (name N or name CA or name C or name \ O or name CB )) or resid 576 or (resid 577 through 583 and (name N or name CA or \ name C or name O or name CB )) or resid 584 through 585 or (resid 586 through 5 \ 88 and (name N or name CA or name C or name O or name CB )) or resid 589 through \ 591 or (resid 592 through 612 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 618 through 626 and (name N or name CA or name C or name O or \ name CB )) or resid 627 or (resid 628 through 629 and (name N or name CA or name \ C or name O or name CB )) or resid 630 through 631 or (resid 632 and (name N or \ name CA or name C or name O or name CB )) or resid 633 or (resid 634 and (name \ N or name CA or name C or name O or name CB )) or resid 635 through 639 or (resi \ d 640 and (name N or name CA or name C or name O or name CB )) or resid 641 thro \ ugh 646 or (resid 647 and (name N or name CA or name C or name O or name CB )) o \ r resid 648 through 650 or (resid 651 through 652 and (name N or name CA or name \ C or name O or name CB )) or resid 653 or (resid 654 through 655 and (name N or \ name CA or name C or name O or name CB )) or resid 656 through 665 or (resid 66 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 667 through \ 668 or (resid 669 through 673 and (name N or name CA or name C or name O or name \ CB )) or resid 674 through 676 or (resid 677 through 678 and (name N or name CA \ or name C or name O or name CB )) or resid 679 through 683 or (resid 684 throug \ h 686 and (name N or name CA or name C or name O or name CB )) or resid 687 or r \ esid 692 through 694 or (resid 695 and (name N or name CA or name C or name O or \ name CB )) or resid 696 through 702 or (resid 703 and (name N or name CA or nam \ e C or name O or name CB )) or resid 704 or (resid 705 through 706 and (name N o \ r name CA or name C or name O or name CB )) or resid 707 through 709 or (resid 7 \ 10 and (name N or name CA or name C or name O or name CB )) or resid 711 through \ 716 or (resid 717 and (name N or name CA or name C or name O or name CB )) or r \ esid 718 through 721 or (resid 722 and (name N or name CA or name C or name O or \ name CB )) or resid 723 through 730 or (resid 731 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 741 and (name N or name CA or name C or na \ me O or name CB )) or resid 742 or (resid 743 through 744 and (name N or name CA \ or name C or name O or name CB )) or resid 745 through 747 or (resid 748 and (n \ ame N or name CA or name C or name O or name CB )) or resid 749 through 751 or ( \ resid 752 through 755 and (name N or name CA or name C or name O or name CB )) o \ r resid 756 through 772 or (resid 773 and (name N or name CA or name C or name O \ or name CB )) or resid 774 through 786 or (resid 787 through 791 and (name N or \ name CA or name C or name O or name CB )) or resid 798 through 804 or (resid 80 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 806 through \ 825 or (resid 826 and (name N or name CA or name C or name O or name CB )) or re \ sid 827 through 832 or (resid 833 and (name N or name CA or name C or name O or \ name CB )) or resid 834 through 836 or (resid 837 and (name N or name CA or name \ C or name O or name CB )) or resid 838 through 850 or (resid 851 and (name N or \ name CA or name C or name O or name CB )) or resid 852 through 870 or (resid 87 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 872 through \ 874 or (resid 875 through 876 and (name N or name CA or name C or name O or name \ CB )) or resid 877 through 884 or (resid 885 through 886 and (name N or name CA \ or name C or name O or name CB )) or resid 887 or (resid 888 and (name N or nam \ e CA or name C or name O or name CB )) or resid 889 through 895 or (resid 896 an \ d (name N or name CA or name C or name O or name CB )) or resid 897 or (resid 89 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 899 through \ 921 or (resid 922 and (name N or name CA or name C or name O or name CB )) or re \ sid 923 through 937 or (resid 938 and (name N or name CA or name C or name O or \ name CB )) or resid 939 through 947 or resid 1000)) selection = (chain 'C' and ((resid 421 through 430 and (name N or name CA or name C or name \ O or name CB )) or resid 431 through 462 or (resid 463 through 468 and (name N o \ r name CA or name C or name O or name CB )) or resid 469 through 474 or (resid 4 \ 75 through 483 and (name N or name CA or name C or name O or name CB )) or resid \ 484 through 488 or (resid 489 through 490 and (name N or name CA or name C or n \ ame O or name CB )) or resid 491 through 493 or (resid 494 through 496 and (name \ N or name CA or name C or name O or name CB )) or resid 497 through 498 or (res \ id 499 and (name N or name CA or name C or name O or name CB )) or resid 500 or \ (resid 501 and (name N or name CA or name C or name O or name CB )) or resid 502 \ through 504 or (resid 505 through 506 and (name N or name CA or name C or name \ O or name CB )) or resid 507 through 508 or (resid 509 through 511 and (name N o \ r name CA or name C or name O or name CB )) or resid 512 or resid 520 through 53 \ 3 or (resid 534 and (name N or name CA or name C or name O or name CB )) or resi \ d 535 through 540 or (resid 541 through 544 and (name N or name CA or name C or \ name O or name CB )) or resid 545 through 548 or (resid 549 and (name N or name \ CA or name C or name O or name CB )) or (resid 554 through 558 and (name N or na \ me CA or name C or name O or name CB )) or (resid 571 through 575 and (name N or \ name CA or name C or name O or name CB )) or resid 576 or (resid 577 through 58 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 584 through \ 585 or (resid 586 through 588 and (name N or name CA or name C or name O or name \ CB )) or resid 589 through 591 or (resid 592 through 612 and (name N or name CA \ or name C or name O or name CB )) or (resid 618 through 626 and (name N or name \ CA or name C or name O or name CB )) or resid 627 through 643 or (resid 644 and \ (name N or name CA or name C or name O or name CB )) or resid 645 through 671 o \ r (resid 672 through 673 and (name N or name CA or name C or name O or name CB ) \ ) or resid 674 through 694 or (resid 695 and (name N or name CA or name C or nam \ e O or name CB )) or resid 696 through 800 or (resid 801 and (name N or name CA \ or name C or name O or name CB )) or resid 802 through 821 or (resid 822 through \ 823 and (name N or name CA or name C or name O or name CB )) or resid 824 throu \ gh 825 or (resid 826 and (name N or name CA or name C or name O or name CB )) or \ resid 827 through 832 or (resid 833 and (name N or name CA or name C or name O \ or name CB )) or resid 834 through 870 or (resid 871 and (name N or name CA or n \ ame C or name O or name CB )) or resid 872 through 874 or (resid 875 through 876 \ and (name N or name CA or name C or name O or name CB )) or resid 877 through 8 \ 84 or (resid 885 through 886 and (name N or name CA or name C or name O or name \ CB )) or resid 887 through 897 or (resid 898 and (name N or name CA or name C or \ name O or name CB )) or resid 899 through 928 or (resid 929 and (name N or name \ CA or name C or name O or name CB )) or resid 930 through 937 or (resid 938 and \ (name N or name CA or name C or name O or name CB )) or resid 939 or (resid 940 \ and (name N or name CA or name C or name O or name CB )) or resid 941 through 9 \ 47 or resid 1000)) selection = (chain 'E' and (resid 421 through 433 or (resid 434 through 445 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 446 through 468 and (name N o \ r name CA or name C or name O or name CB )) or resid 469 through 472 or (resid 4 \ 73 and (name N or name CA or name C or name O or name CB )) or resid 474 through \ 494 or (resid 495 through 496 and (name N or name CA or name C or name O or nam \ e CB )) or resid 497 through 502 or (resid 503 through 506 and (name N or name C \ A or name C or name O or name CB )) or resid 507 through 521 or (resid 522 and ( \ name N or name CA or name C or name O or name CB )) or resid 523 through 535 or \ (resid 536 through 537 and (name N or name CA or name C or name O or name CB )) \ or resid 538 through 558 or resid 571 through 581 or (resid 582 through 583 and \ (name N or name CA or name C or name O or name CB )) or resid 584 through 589 or \ (resid 590 through 595 and (name N or name CA or name C or name O or name CB )) \ or (resid 603 through 626 and (name N or name CA or name C or name O or name CB \ )) or resid 627 or (resid 628 through 629 and (name N or name CA or name C or n \ ame O or name CB )) or resid 630 through 631 or (resid 632 and (name N or name C \ A or name C or name O or name CB )) or resid 633 or (resid 634 and (name N or na \ me CA or name C or name O or name CB )) or resid 635 through 639 or (resid 640 a \ nd (name N or name CA or name C or name O or name CB )) or resid 641 through 642 \ or (resid 643 through 644 and (name N or name CA or name C or name O or name CB \ )) or resid 645 through 653 or (resid 654 through 655 and (name N or name CA or \ name C or name O or name CB )) or resid 656 through 664 or (resid 665 through 6 \ 66 and (name N or name CA or name C or name O or name CB )) or resid 667 through \ 668 or (resid 669 through 673 and (name N or name CA or name C or name O or nam \ e CB )) or resid 674 through 676 or (resid 677 through 678 and (name N or name C \ A or name C or name O or name CB )) or resid 679 through 683 or (resid 684 throu \ gh 686 and (name N or name CA or name C or name O or name CB )) or resid 687 or \ resid 692 through 702 or (resid 703 and (name N or name CA or name C or name O o \ r name CB )) or resid 704 or (resid 705 through 706 and (name N or name CA or na \ me C or name O or name CB )) or resid 707 through 709 or (resid 710 and (name N \ or name CA or name C or name O or name CB )) or resid 711 through 716 or (resid \ 717 and (name N or name CA or name C or name O or name CB )) or resid 718 throug \ h 721 or (resid 722 and (name N or name CA or name C or name O or name CB )) or \ resid 723 through 725 or (resid 726 and (name N or name CA or name C or name O o \ r name CB )) or resid 727 through 730 or (resid 731 and (name N or name CA or na \ me C or name O or name CB )) or (resid 741 and (name N or name CA or name C or n \ ame O or name CB )) or resid 742 through 743 or (resid 744 and (name N or name C \ A or name C or name O or name CB )) or resid 745 through 747 or (resid 748 and ( \ name N or name CA or name C or name O or name CB )) or resid 749 through 751 or \ (resid 752 through 755 and (name N or name CA or name C or name O or name CB )) \ or resid 756 through 772 or (resid 773 and (name N or name CA or name C or name \ O or name CB )) or resid 774 through 786 or (resid 787 through 795 and (name N o \ r name CA or name C or name O or name CB )) or resid 798 through 800 or (resid 8 \ 01 and (name N or name CA or name C or name O or name CB )) or resid 802 through \ 804 or (resid 805 and (name N or name CA or name C or name O or name CB )) or r \ esid 806 through 845 or (resid 846 and (name N or name CA or name C or name O or \ name CB )) or resid 847 through 850 or (resid 851 and (name N or name CA or nam \ e C or name O or name CB )) or resid 852 through 874 or (resid 875 through 876 a \ nd (name N or name CA or name C or name O or name CB )) or resid 877 through 885 \ or (resid 886 and (name N or name CA or name C or name O or name CB )) or resid \ 887 through 895 or (resid 896 and (name N or name CA or name C or name O or nam \ e CB )) or resid 897 through 921 or (resid 922 and (name N or name CA or name C \ or name O or name CB )) or resid 923 through 947 or resid 1000)) selection = (chain 'F' and ((resid 421 through 430 and (name N or name CA or name C or name \ O or name CB )) or resid 431 or (resid 432 through 445 and (name N or name CA or \ name C or name O or name CB )) or resid 446 or (resid 447 through 468 and (name \ N or name CA or name C or name O or name CB )) or resid 469 or (resid 470 and ( \ name N or name CA or name C or name O or name CB )) or resid 471 or (resid 472 t \ hrough 473 and (name N or name CA or name C or name O or name CB )) or resid 474 \ or (resid 475 through 483 and (name N or name CA or name C or name O or name CB \ )) or resid 484 through 488 or (resid 489 through 490 and (name N or name CA or \ name C or name O or name CB )) or resid 491 through 493 or (resid 494 through 4 \ 96 and (name N or name CA or name C or name O or name CB )) or resid 497 through \ 498 or (resid 499 and (name N or name CA or name C or name O or name CB )) or r \ esid 500 or (resid 501 and (name N or name CA or name C or name O or name CB )) \ or resid 502 through 503 or (resid 504 through 506 and (name N or name CA or nam \ e C or name O or name CB )) or resid 507 through 508 or (resid 509 through 511 a \ nd (name N or name CA or name C or name O or name CB )) or resid 512 or resid 52 \ 0 through 521 or (resid 522 and (name N or name CA or name C or name O or name C \ B )) or resid 523 through 535 or (resid 536 through 537 and (name N or name CA o \ r name C or name O or name CB )) or resid 538 through 539 or (resid 540 through \ 544 and (name N or name CA or name C or name O or name CB )) or resid 545 or (re \ sid 546 and (name N or name CA or name C or name O or name CB )) or resid 547 th \ rough 548 or (resid 549 and (name N or name CA or name C or name O or name CB )) \ or (resid 554 through 558 and (name N or name CA or name C or name O or name CB \ )) or resid 571 or (resid 572 through 575 and (name N or name CA or name C or n \ ame O or name CB )) or resid 576 or (resid 577 through 583 and (name N or name C \ A or name C or name O or name CB )) or resid 584 through 585 or (resid 586 throu \ gh 588 and (name N or name CA or name C or name O or name CB )) or resid 589 or \ (resid 590 through 612 and (name N or name CA or name C or name O or name CB )) \ or (resid 618 through 626 and (name N or name CA or name C or name O or name CB \ )) or resid 627 or (resid 628 through 629 and (name N or name CA or name C or na \ me O or name CB )) or resid 630 through 633 or (resid 634 and (name N or name CA \ or name C or name O or name CB )) or resid 635 through 639 or (resid 640 and (n \ ame N or name CA or name C or name O or name CB )) or resid 641 through 642 or ( \ resid 643 through 644 and (name N or name CA or name C or name O or name CB )) o \ r resid 645 through 646 or (resid 647 and (name N or name CA or name C or name O \ or name CB )) or resid 648 through 650 or (resid 651 through 652 and (name N or \ name CA or name C or name O or name CB )) or resid 653 or (resid 654 through 65 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 656 through \ 664 or (resid 665 through 666 and (name N or name CA or name C or name O or name \ CB )) or resid 667 through 668 or (resid 669 through 673 and (name N or name CA \ or name C or name O or name CB )) or resid 674 through 676 or (resid 677 throug \ h 678 and (name N or name CA or name C or name O or name CB )) or resid 679 thro \ ugh 683 or (resid 684 through 686 and (name N or name CA or name C or name O or \ name CB )) or resid 687 or resid 692 through 694 or (resid 695 and (name N or na \ me CA or name C or name O or name CB )) or resid 696 through 702 or (resid 703 a \ nd (name N or name CA or name C or name O or name CB )) or resid 704 or (resid 7 \ 05 through 706 and (name N or name CA or name C or name O or name CB )) or resid \ 707 through 709 or (resid 710 and (name N or name CA or name C or name O or nam \ e CB )) or resid 711 through 716 or (resid 717 and (name N or name CA or name C \ or name O or name CB )) or resid 718 through 721 or (resid 722 and (name N or na \ me CA or name C or name O or name CB )) or resid 723 through 725 or (resid 726 a \ nd (name N or name CA or name C or name O or name CB )) or resid 727 through 730 \ or (resid 731 and (name N or name CA or name C or name O or name CB )) or (resi \ d 741 and (name N or name CA or name C or name O or name CB )) or resid 742 or ( \ resid 743 through 744 and (name N or name CA or name C or name O or name CB )) o \ r resid 745 through 747 or (resid 748 and (name N or name CA or name C or name O \ or name CB )) or resid 749 through 751 or (resid 752 through 755 and (name N or \ name CA or name C or name O or name CB )) or resid 756 through 772 or (resid 77 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 774 through \ 786 or (resid 787 through 791 and (name N or name CA or name C or name O or name \ CB )) or resid 798 through 800 or (resid 801 and (name N or name CA or name C o \ r name O or name CB )) or resid 802 through 804 or (resid 805 and (name N or nam \ e CA or name C or name O or name CB )) or resid 806 through 825 or (resid 826 an \ d (name N or name CA or name C or name O or name CB )) or resid 827 through 836 \ or (resid 837 and (name N or name CA or name C or name O or name CB )) or resid \ 838 through 850 or (resid 851 and (name N or name CA or name C or name O or name \ CB )) or resid 852 through 870 or (resid 871 and (name N or name CA or name C o \ r name O or name CB )) or resid 872 through 875 or (resid 876 and (name N or nam \ e CA or name C or name O or name CB )) or resid 877 through 884 or (resid 885 th \ rough 886 and (name N or name CA or name C or name O or name CB )) or resid 887 \ or (resid 888 and (name N or name CA or name C or name O or name CB )) or resid \ 889 through 895 or (resid 896 and (name N or name CA or name C or name O or name \ CB )) or resid 897 or (resid 898 and (name N or name CA or name C or name O or \ name CB )) or resid 899 through 914 or (resid 915 and (name N or name CA or name \ C or name O or name CB )) or resid 916 or (resid 917 through 918 and (name N or \ name CA or name C or name O or name CB )) or resid 919 through 921 or (resid 92 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 923 through \ 936 or (resid 937 through 938 and (name N or name CA or name C or name O or name \ CB )) or resid 939 through 947 or resid 1000)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.990 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 48.340 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 : 0.007 0.102 18627 Z= 0.479 Angle : 0.776 9.130 25420 Z= 0.417 Chirality : 0.047 0.166 3075 Planarity : 0.005 0.057 3261 Dihedral : 14.074 121.800 6408 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 0.12 % Allowed : 9.62 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.14), residues: 2515 helix: -1.77 (0.13), residues: 1125 sheet: -2.30 (0.25), residues: 322 loop : -2.89 (0.16), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 470 HIS 0.008 0.002 HIS F 841 PHE 0.020 0.002 PHE A 820 TYR 0.022 0.003 TYR A 939 ARG 0.007 0.001 ARG B 786 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 248 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 517 LYS cc_start: 0.7459 (mmtp) cc_final: 0.7153 (mtmt) REVERT: C 715 GLN cc_start: 0.7033 (mm-40) cc_final: 0.6695 (mm-40) REVERT: C 720 LEU cc_start: 0.7647 (tt) cc_final: 0.7337 (tt) REVERT: B 647 GLU cc_start: 0.7835 (tp30) cc_final: 0.7568 (tp30) REVERT: A 879 MET cc_start: 0.8947 (ptp) cc_final: 0.8747 (ptp) REVERT: F 435 MET cc_start: 0.7690 (mmm) cc_final: 0.7482 (tpp) REVERT: F 461 TYR cc_start: 0.5914 (t80) cc_final: 0.4941 (m-10) REVERT: F 543 GLU cc_start: 0.8135 (mp0) cc_final: 0.7613 (mp0) REVERT: F 612 ASP cc_start: 0.6467 (m-30) cc_final: 0.6023 (m-30) REVERT: E 810 MET cc_start: 0.8147 (tpt) cc_final: 0.7850 (tpp) REVERT: E 934 HIS cc_start: 0.7876 (m170) cc_final: 0.7508 (m170) outliers start: 2 outliers final: 1 residues processed: 250 average time/residue: 0.3158 time to fit residues: 119.6891 Evaluate side-chains 189 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 802 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 214 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 129 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 148 optimal weight: 30.0000 chunk 230 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS C 843 HIS B 715 GLN B 743 GLN ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS A 841 HIS A 876 ASN ** F 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 702 GLN E 677 GLN E 916 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18627 Z= 0.263 Angle : 0.615 8.110 25420 Z= 0.300 Chirality : 0.043 0.188 3075 Planarity : 0.005 0.055 3261 Dihedral : 7.454 108.877 2753 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.10 % Allowed : 14.23 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.16), residues: 2515 helix: -0.15 (0.15), residues: 1123 sheet: -1.82 (0.26), residues: 324 loop : -2.17 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 470 HIS 0.004 0.001 HIS A 491 PHE 0.014 0.001 PHE A 820 TYR 0.017 0.002 TYR A 939 ARG 0.004 0.000 ARG E 815 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 210 time to evaluate : 2.324 Fit side-chains revert: symmetry clash REVERT: C 517 LYS cc_start: 0.7363 (mmtp) cc_final: 0.7153 (mtmt) REVERT: C 552 MET cc_start: 0.6246 (ptm) cc_final: 0.5681 (ttp) REVERT: C 720 LEU cc_start: 0.7709 (tt) cc_final: 0.7454 (tt) REVERT: F 435 MET cc_start: 0.7702 (mmm) cc_final: 0.7421 (tpp) REVERT: F 461 TYR cc_start: 0.5871 (t80) cc_final: 0.4953 (m-10) REVERT: F 543 GLU cc_start: 0.7927 (mp0) cc_final: 0.7541 (mp0) REVERT: F 612 ASP cc_start: 0.6403 (m-30) cc_final: 0.6011 (m-30) REVERT: E 655 MET cc_start: 0.5847 (mmp) cc_final: 0.5282 (mmp) REVERT: E 810 MET cc_start: 0.8220 (tpt) cc_final: 0.7734 (tpp) REVERT: E 869 MET cc_start: 0.7019 (mtp) cc_final: 0.6816 (mtp) REVERT: E 882 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7191 (tp30) REVERT: E 934 HIS cc_start: 0.7762 (m170) cc_final: 0.7396 (m170) outliers start: 36 outliers final: 24 residues processed: 236 average time/residue: 0.2817 time to fit residues: 105.0071 Evaluate side-chains 211 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 186 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 637 CYS Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain F residue 576 CYS Chi-restraints excluded: chain F residue 592 VAL Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 502 LEU Chi-restraints excluded: chain E residue 658 VAL Chi-restraints excluded: chain E residue 760 THR Chi-restraints excluded: chain E residue 802 VAL Chi-restraints excluded: chain E residue 844 VAL Chi-restraints excluded: chain E residue 882 GLU Chi-restraints excluded: chain E residue 933 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 0.3980 chunk 191 optimal weight: 0.9980 chunk 157 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 249 optimal weight: 9.9990 chunk 205 optimal weight: 3.9990 chunk 229 optimal weight: 6.9990 chunk 78 optimal weight: 0.2980 chunk 185 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 618 ASN ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 477 ASN F 575 GLN ** E 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18627 Z= 0.153 Angle : 0.547 9.025 25420 Z= 0.260 Chirality : 0.040 0.143 3075 Planarity : 0.004 0.047 3261 Dihedral : 6.853 101.492 2753 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.69 % Allowed : 16.27 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.17), residues: 2515 helix: 0.79 (0.16), residues: 1118 sheet: -1.33 (0.27), residues: 336 loop : -1.68 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 470 HIS 0.003 0.001 HIS F 839 PHE 0.015 0.001 PHE F 545 TYR 0.012 0.001 TYR C 544 ARG 0.004 0.000 ARG F 482 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 227 time to evaluate : 1.905 Fit side-chains revert: symmetry clash REVERT: C 517 LYS cc_start: 0.7411 (mmtp) cc_final: 0.7198 (mtmt) REVERT: C 552 MET cc_start: 0.5688 (ptm) cc_final: 0.5091 (ttp) REVERT: A 618 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.7623 (p0) REVERT: F 435 MET cc_start: 0.7518 (mmm) cc_final: 0.7031 (tpp) REVERT: F 461 TYR cc_start: 0.5656 (t80) cc_final: 0.4760 (m-10) REVERT: F 541 ASN cc_start: 0.8490 (t0) cc_final: 0.8276 (t0) REVERT: F 543 GLU cc_start: 0.7937 (mp0) cc_final: 0.7518 (mp0) REVERT: F 569 MET cc_start: 0.7389 (ptm) cc_final: 0.7175 (ptp) REVERT: F 612 ASP cc_start: 0.6436 (m-30) cc_final: 0.5950 (m-30) REVERT: F 619 PHE cc_start: 0.6456 (t80) cc_final: 0.6111 (t80) REVERT: F 766 MET cc_start: 0.7735 (mtp) cc_final: 0.7518 (ttm) REVERT: E 643 ASP cc_start: 0.6085 (m-30) cc_final: 0.5408 (m-30) REVERT: E 655 MET cc_start: 0.5750 (mmp) cc_final: 0.5100 (mmp) REVERT: E 810 MET cc_start: 0.8110 (tpt) cc_final: 0.7725 (tpp) REVERT: E 934 HIS cc_start: 0.7743 (m170) cc_final: 0.7377 (m170) outliers start: 29 outliers final: 21 residues processed: 247 average time/residue: 0.2610 time to fit residues: 102.3123 Evaluate side-chains 217 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 195 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 941 GLU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain F residue 576 CYS Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 592 VAL Chi-restraints excluded: chain E residue 502 LEU Chi-restraints excluded: chain E residue 658 VAL Chi-restraints excluded: chain E residue 802 VAL Chi-restraints excluded: chain E residue 844 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 228 optimal weight: 20.0000 chunk 173 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 25 optimal weight: 30.0000 chunk 110 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 chunk 231 optimal weight: 5.9990 chunk 245 optimal weight: 20.0000 chunk 121 optimal weight: 5.9990 chunk 219 optimal weight: 50.0000 chunk 66 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 618 ASN ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 484 GLN ** E 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18627 Z= 0.306 Angle : 0.603 7.582 25420 Z= 0.292 Chirality : 0.043 0.152 3075 Planarity : 0.005 0.055 3261 Dihedral : 6.968 93.687 2753 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.14 % Allowed : 16.97 % Favored : 78.89 % 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: -0.67 (0.17), residues: 2515 helix: 0.84 (0.16), residues: 1113 sheet: -1.07 (0.28), residues: 322 loop : -1.61 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 470 HIS 0.006 0.001 HIS B 491 PHE 0.018 0.002 PHE A 820 TYR 0.018 0.002 TYR A 939 ARG 0.003 0.000 ARG A 755 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 193 time to evaluate : 1.865 Fit side-chains revert: symmetry clash REVERT: C 552 MET cc_start: 0.6043 (ptm) cc_final: 0.5540 (ttp) REVERT: C 757 TYR cc_start: 0.6698 (m-10) cc_final: 0.6181 (m-10) REVERT: A 618 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.7670 (p0) REVERT: A 665 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7820 (mt-10) REVERT: F 435 MET cc_start: 0.7593 (mmm) cc_final: 0.7136 (tpp) REVERT: F 461 TYR cc_start: 0.5845 (t80) cc_final: 0.4921 (m-10) REVERT: F 541 ASN cc_start: 0.8426 (t0) cc_final: 0.8218 (t0) REVERT: F 543 GLU cc_start: 0.8024 (mp0) cc_final: 0.7715 (mp0) REVERT: F 561 HIS cc_start: 0.6200 (m170) cc_final: 0.5962 (m-70) REVERT: F 612 ASP cc_start: 0.6377 (m-30) cc_final: 0.5968 (m-30) REVERT: F 619 PHE cc_start: 0.6551 (t80) cc_final: 0.6185 (t80) REVERT: F 840 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.9193 (mm) REVERT: E 655 MET cc_start: 0.5839 (mmp) cc_final: 0.5160 (mmp) REVERT: E 810 MET cc_start: 0.8155 (tpt) cc_final: 0.7738 (tpp) REVERT: E 934 HIS cc_start: 0.7745 (m170) cc_final: 0.7353 (m170) outliers start: 71 outliers final: 52 residues processed: 252 average time/residue: 0.2644 time to fit residues: 107.1172 Evaluate side-chains 237 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 183 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 637 CYS Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 941 GLU Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain F residue 505 ILE Chi-restraints excluded: chain F residue 576 CYS Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 592 VAL Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 735 VAL Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 836 VAL Chi-restraints excluded: chain F residue 840 ILE Chi-restraints excluded: chain F residue 933 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 502 LEU Chi-restraints excluded: chain E residue 584 ASN Chi-restraints excluded: chain E residue 658 VAL Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 760 THR Chi-restraints excluded: chain E residue 802 VAL Chi-restraints excluded: chain E residue 844 VAL Chi-restraints excluded: chain E residue 933 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 204 optimal weight: 50.0000 chunk 139 optimal weight: 1.9990 chunk 3 optimal weight: 40.0000 chunk 182 optimal weight: 8.9990 chunk 101 optimal weight: 30.0000 chunk 209 optimal weight: 0.0470 chunk 169 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 chunk 125 optimal weight: 6.9990 chunk 220 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 overall best weight: 5.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 618 ASN ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18627 Z= 0.281 Angle : 0.599 9.674 25420 Z= 0.288 Chirality : 0.042 0.148 3075 Planarity : 0.004 0.056 3261 Dihedral : 6.916 86.195 2753 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.14 % Allowed : 17.61 % Favored : 78.25 % 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: -0.56 (0.17), residues: 2515 helix: 0.92 (0.16), residues: 1111 sheet: -0.99 (0.28), residues: 322 loop : -1.54 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 470 HIS 0.005 0.001 HIS B 491 PHE 0.017 0.001 PHE C 820 TYR 0.018 0.002 TYR A 939 ARG 0.002 0.000 ARG F 652 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 199 time to evaluate : 2.225 Fit side-chains revert: symmetry clash REVERT: C 552 MET cc_start: 0.6107 (ptm) cc_final: 0.5668 (ttp) REVERT: A 618 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.7673 (p0) REVERT: F 435 MET cc_start: 0.7503 (mmm) cc_final: 0.7027 (tpp) REVERT: F 461 TYR cc_start: 0.5855 (t80) cc_final: 0.4983 (m-10) REVERT: F 541 ASN cc_start: 0.8356 (t0) cc_final: 0.8141 (t0) REVERT: F 543 GLU cc_start: 0.8051 (mp0) cc_final: 0.7681 (mp0) REVERT: F 552 MET cc_start: 0.3070 (ppp) cc_final: 0.2671 (ppp) REVERT: F 561 HIS cc_start: 0.6220 (m170) cc_final: 0.6001 (m-70) REVERT: F 612 ASP cc_start: 0.6376 (m-30) cc_final: 0.5954 (m-30) REVERT: F 619 PHE cc_start: 0.6559 (t80) cc_final: 0.6200 (t80) REVERT: E 655 MET cc_start: 0.5814 (mmp) cc_final: 0.5188 (mmp) REVERT: E 934 HIS cc_start: 0.7746 (m170) cc_final: 0.7357 (m170) outliers start: 71 outliers final: 64 residues processed: 256 average time/residue: 0.2517 time to fit residues: 103.2640 Evaluate side-chains 253 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 188 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 637 CYS Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain C residue 941 GLU Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain F residue 505 ILE Chi-restraints excluded: chain F residue 576 CYS Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 592 VAL Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 735 VAL Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 836 VAL Chi-restraints excluded: chain F residue 933 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 502 LEU Chi-restraints excluded: chain E residue 584 ASN Chi-restraints excluded: chain E residue 658 VAL Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 760 THR Chi-restraints excluded: chain E residue 802 VAL Chi-restraints excluded: chain E residue 844 VAL Chi-restraints excluded: chain E residue 877 LEU Chi-restraints excluded: chain E residue 883 VAL Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 933 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 82 optimal weight: 7.9990 chunk 221 optimal weight: 7.9990 chunk 48 optimal weight: 30.0000 chunk 144 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 245 optimal weight: 1.9990 chunk 204 optimal weight: 50.0000 chunk 113 optimal weight: 2.9990 chunk 20 optimal weight: 30.0000 chunk 81 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 618 ASN ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18627 Z= 0.230 Angle : 0.572 7.477 25420 Z= 0.274 Chirality : 0.041 0.145 3075 Planarity : 0.004 0.055 3261 Dihedral : 6.707 86.436 2753 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.20 % Allowed : 18.60 % Favored : 77.20 % 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: -0.40 (0.17), residues: 2515 helix: 1.06 (0.16), residues: 1114 sheet: -1.01 (0.28), residues: 342 loop : -1.42 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 470 HIS 0.004 0.001 HIS B 491 PHE 0.019 0.001 PHE F 545 TYR 0.016 0.002 TYR B 757 ARG 0.003 0.000 ARG F 652 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 204 time to evaluate : 1.961 Fit side-chains revert: symmetry clash REVERT: C 552 MET cc_start: 0.5961 (ptm) cc_final: 0.5544 (ttp) REVERT: C 757 TYR cc_start: 0.6939 (m-10) cc_final: 0.6502 (m-10) REVERT: A 618 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.7603 (p0) REVERT: F 435 MET cc_start: 0.7575 (mmm) cc_final: 0.7092 (tpp) REVERT: F 461 TYR cc_start: 0.5756 (t80) cc_final: 0.4896 (m-10) REVERT: F 543 GLU cc_start: 0.8026 (mp0) cc_final: 0.7659 (mp0) REVERT: F 552 MET cc_start: 0.3012 (ppp) cc_final: 0.2638 (ppp) REVERT: F 561 HIS cc_start: 0.6123 (m170) cc_final: 0.5898 (m-70) REVERT: F 612 ASP cc_start: 0.6328 (m-30) cc_final: 0.5925 (m-30) REVERT: F 619 PHE cc_start: 0.6551 (t80) cc_final: 0.6207 (t80) REVERT: F 840 ILE cc_start: 0.9429 (OUTLIER) cc_final: 0.9210 (mm) REVERT: E 643 ASP cc_start: 0.6729 (m-30) cc_final: 0.6038 (m-30) REVERT: E 655 MET cc_start: 0.5819 (mmp) cc_final: 0.5475 (mmp) REVERT: E 810 MET cc_start: 0.8207 (tpt) cc_final: 0.7933 (tpp) REVERT: E 934 HIS cc_start: 0.7747 (m170) cc_final: 0.7351 (m170) outliers start: 72 outliers final: 64 residues processed: 263 average time/residue: 0.2555 time to fit residues: 107.7211 Evaluate side-chains 253 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 187 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 637 CYS Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain C residue 941 GLU Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain F residue 505 ILE Chi-restraints excluded: chain F residue 509 GLN Chi-restraints excluded: chain F residue 576 CYS Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 592 VAL Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 641 VAL Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 735 VAL Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 827 GLN Chi-restraints excluded: chain F residue 836 VAL Chi-restraints excluded: chain F residue 840 ILE Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 502 LEU Chi-restraints excluded: chain E residue 584 ASN Chi-restraints excluded: chain E residue 658 VAL Chi-restraints excluded: chain E residue 709 VAL Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 760 THR Chi-restraints excluded: chain E residue 802 VAL Chi-restraints excluded: chain E residue 840 ILE Chi-restraints excluded: chain E residue 844 VAL Chi-restraints excluded: chain E residue 877 LEU Chi-restraints excluded: chain E residue 883 VAL Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 933 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 236 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 140 optimal weight: 0.3980 chunk 179 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 206 optimal weight: 50.0000 chunk 137 optimal weight: 0.0980 chunk 244 optimal weight: 10.0000 chunk 153 optimal weight: 20.0000 chunk 149 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 618 ASN ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18627 Z= 0.208 Angle : 0.562 7.535 25420 Z= 0.268 Chirality : 0.041 0.145 3075 Planarity : 0.004 0.054 3261 Dihedral : 6.525 86.713 2753 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.61 % Allowed : 18.95 % Favored : 76.44 % 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: -0.25 (0.17), residues: 2515 helix: 1.15 (0.16), residues: 1111 sheet: -0.87 (0.28), residues: 349 loop : -1.33 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 470 HIS 0.004 0.001 HIS B 491 PHE 0.017 0.001 PHE F 545 TYR 0.015 0.001 TYR A 939 ARG 0.003 0.000 ARG F 652 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 205 time to evaluate : 2.101 Fit side-chains revert: symmetry clash REVERT: C 552 MET cc_start: 0.5820 (ptm) cc_final: 0.5414 (ttp) REVERT: A 557 GLU cc_start: 0.6908 (tt0) cc_final: 0.6621 (mm-30) REVERT: A 607 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8436 (mp) REVERT: A 618 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.7546 (p0) REVERT: F 461 TYR cc_start: 0.5797 (t80) cc_final: 0.4967 (m-10) REVERT: F 543 GLU cc_start: 0.8001 (mp0) cc_final: 0.7652 (mp0) REVERT: F 552 MET cc_start: 0.2961 (ppp) cc_final: 0.2661 (ppp) REVERT: F 561 HIS cc_start: 0.6147 (m170) cc_final: 0.5916 (m-70) REVERT: F 612 ASP cc_start: 0.6309 (m-30) cc_final: 0.5890 (m-30) REVERT: F 619 PHE cc_start: 0.6527 (t80) cc_final: 0.6180 (t80) REVERT: E 643 ASP cc_start: 0.6636 (m-30) cc_final: 0.5931 (m-30) REVERT: E 655 MET cc_start: 0.5821 (mmp) cc_final: 0.5469 (mmp) REVERT: E 810 MET cc_start: 0.8199 (tpt) cc_final: 0.7894 (tpp) REVERT: E 934 HIS cc_start: 0.7737 (m170) cc_final: 0.7334 (m170) outliers start: 79 outliers final: 70 residues processed: 269 average time/residue: 0.2591 time to fit residues: 112.2553 Evaluate side-chains 264 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 192 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 637 CYS Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain C residue 941 GLU Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain F residue 509 GLN Chi-restraints excluded: chain F residue 576 CYS Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 592 VAL Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 766 MET Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 827 GLN Chi-restraints excluded: chain F residue 836 VAL Chi-restraints excluded: chain F residue 933 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 502 LEU Chi-restraints excluded: chain E residue 584 ASN Chi-restraints excluded: chain E residue 658 VAL Chi-restraints excluded: chain E residue 709 VAL Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 760 THR Chi-restraints excluded: chain E residue 802 VAL Chi-restraints excluded: chain E residue 840 ILE Chi-restraints excluded: chain E residue 844 VAL Chi-restraints excluded: chain E residue 877 LEU Chi-restraints excluded: chain E residue 883 VAL Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 933 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 151 optimal weight: 8.9990 chunk 97 optimal weight: 0.7980 chunk 146 optimal weight: 0.3980 chunk 73 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 chunk 166 optimal weight: 30.0000 chunk 121 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 618 ASN ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18627 Z= 0.199 Angle : 0.559 8.007 25420 Z= 0.266 Chirality : 0.041 0.144 3075 Planarity : 0.004 0.053 3261 Dihedral : 6.442 86.792 2753 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.49 % Allowed : 19.48 % Favored : 76.03 % 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: -0.13 (0.17), residues: 2515 helix: 1.23 (0.16), residues: 1109 sheet: -0.78 (0.28), residues: 349 loop : -1.25 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 470 HIS 0.004 0.001 HIS B 491 PHE 0.015 0.001 PHE F 545 TYR 0.015 0.001 TYR A 939 ARG 0.003 0.000 ARG F 482 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 201 time to evaluate : 1.907 Fit side-chains revert: symmetry clash REVERT: C 552 MET cc_start: 0.5766 (ptm) cc_final: 0.5354 (ttp) REVERT: C 577 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6310 (tp) REVERT: C 757 TYR cc_start: 0.6970 (m-10) cc_final: 0.6394 (m-10) REVERT: A 618 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.7580 (p0) REVERT: F 461 TYR cc_start: 0.5795 (t80) cc_final: 0.4957 (m-10) REVERT: F 543 GLU cc_start: 0.7987 (mp0) cc_final: 0.7645 (mp0) REVERT: F 552 MET cc_start: 0.2912 (ppp) cc_final: 0.2630 (ppp) REVERT: F 561 HIS cc_start: 0.6202 (m170) cc_final: 0.5976 (m-70) REVERT: F 612 ASP cc_start: 0.6295 (m-30) cc_final: 0.5869 (m-30) REVERT: F 619 PHE cc_start: 0.6514 (t80) cc_final: 0.6169 (t80) REVERT: E 469 PRO cc_start: 0.6305 (Cg_exo) cc_final: 0.6085 (Cg_endo) REVERT: E 643 ASP cc_start: 0.6625 (m-30) cc_final: 0.5920 (m-30) REVERT: E 655 MET cc_start: 0.5785 (mmp) cc_final: 0.5408 (mmp) REVERT: E 810 MET cc_start: 0.8177 (tpt) cc_final: 0.7947 (tpt) REVERT: E 934 HIS cc_start: 0.7726 (m170) cc_final: 0.7324 (m170) outliers start: 77 outliers final: 70 residues processed: 262 average time/residue: 0.2565 time to fit residues: 108.9828 Evaluate side-chains 267 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 195 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 637 CYS Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain C residue 941 GLU Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain F residue 505 ILE Chi-restraints excluded: chain F residue 509 GLN Chi-restraints excluded: chain F residue 576 CYS Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 592 VAL Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 702 GLN Chi-restraints excluded: chain F residue 735 VAL Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 766 MET Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 827 GLN Chi-restraints excluded: chain F residue 836 VAL Chi-restraints excluded: chain F residue 933 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 502 LEU Chi-restraints excluded: chain E residue 658 VAL Chi-restraints excluded: chain E residue 709 VAL Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 760 THR Chi-restraints excluded: chain E residue 802 VAL Chi-restraints excluded: chain E residue 840 ILE Chi-restraints excluded: chain E residue 844 VAL Chi-restraints excluded: chain E residue 877 LEU Chi-restraints excluded: chain E residue 910 ILE Chi-restraints excluded: chain E residue 933 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 222 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 chunk 213 optimal weight: 20.0000 chunk 228 optimal weight: 0.0770 chunk 137 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 179 optimal weight: 0.6980 chunk 70 optimal weight: 0.0470 chunk 206 optimal weight: 50.0000 chunk 215 optimal weight: 0.6980 chunk 227 optimal weight: 9.9990 overall best weight: 1.1038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 618 ASN ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN E 484 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18627 Z= 0.138 Angle : 0.531 8.808 25420 Z= 0.248 Chirality : 0.040 0.143 3075 Planarity : 0.004 0.050 3261 Dihedral : 6.093 87.770 2753 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.68 % Allowed : 21.63 % Favored : 75.69 % 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: 0.18 (0.17), residues: 2515 helix: 1.52 (0.17), residues: 1100 sheet: -0.59 (0.29), residues: 342 loop : -1.11 (0.18), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 470 HIS 0.004 0.001 HIS A 561 PHE 0.015 0.001 PHE F 545 TYR 0.010 0.001 TYR A 939 ARG 0.004 0.000 ARG F 482 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 212 time to evaluate : 2.126 Fit side-chains revert: symmetry clash REVERT: C 517 LYS cc_start: 0.3991 (ptpt) cc_final: 0.3731 (mtmt) REVERT: C 552 MET cc_start: 0.5496 (ptm) cc_final: 0.4933 (ttp) REVERT: C 577 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6285 (tp) REVERT: C 757 TYR cc_start: 0.6849 (m-10) cc_final: 0.6299 (m-10) REVERT: A 607 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8425 (mp) REVERT: F 461 TYR cc_start: 0.5589 (t80) cc_final: 0.4820 (m-10) REVERT: F 543 GLU cc_start: 0.7762 (mp0) cc_final: 0.7518 (mp0) REVERT: F 612 ASP cc_start: 0.6230 (m-30) cc_final: 0.5779 (m-30) REVERT: F 619 PHE cc_start: 0.6470 (t80) cc_final: 0.6138 (t80) REVERT: E 469 PRO cc_start: 0.6243 (Cg_exo) cc_final: 0.6033 (Cg_endo) REVERT: E 643 ASP cc_start: 0.6368 (m-30) cc_final: 0.5617 (m-30) REVERT: E 655 MET cc_start: 0.5570 (mmp) cc_final: 0.5321 (mmp) REVERT: E 810 MET cc_start: 0.8190 (tpt) cc_final: 0.7853 (tpp) REVERT: E 879 MET cc_start: 0.8023 (ptp) cc_final: 0.7560 (ptp) outliers start: 46 outliers final: 37 residues processed: 247 average time/residue: 0.2579 time to fit residues: 101.8487 Evaluate side-chains 243 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 204 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 635 PHE Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain C residue 941 GLU Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain F residue 509 GLN Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 592 VAL Chi-restraints excluded: chain F residue 735 VAL Chi-restraints excluded: chain F residue 766 MET Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain E residue 502 LEU Chi-restraints excluded: chain E residue 709 VAL Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 802 VAL Chi-restraints excluded: chain E residue 844 VAL Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 933 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 149 optimal weight: 0.0370 chunk 241 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 chunk 114 optimal weight: 40.0000 chunk 167 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 chunk 232 optimal weight: 4.9990 chunk 201 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 chunk 123 optimal weight: 0.9980 overall best weight: 3.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 618 ASN ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 18627 Z= 0.222 Angle : 0.714 59.199 25420 Z= 0.390 Chirality : 0.041 0.217 3075 Planarity : 0.004 0.062 3261 Dihedral : 6.096 87.787 2753 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.45 % Allowed : 22.10 % Favored : 75.45 % 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: 0.19 (0.17), residues: 2515 helix: 1.50 (0.17), residues: 1101 sheet: -0.59 (0.29), residues: 344 loop : -1.08 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 470 HIS 0.003 0.001 HIS A 561 PHE 0.013 0.001 PHE F 545 TYR 0.011 0.001 TYR A 939 ARG 0.003 0.000 ARG F 652 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 204 time to evaluate : 2.009 Fit side-chains revert: symmetry clash REVERT: C 552 MET cc_start: 0.5519 (ptm) cc_final: 0.4936 (ttp) REVERT: C 577 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6284 (tp) REVERT: C 757 TYR cc_start: 0.6857 (m-10) cc_final: 0.6301 (m-10) REVERT: F 461 TYR cc_start: 0.5592 (t80) cc_final: 0.4822 (m-10) REVERT: F 543 GLU cc_start: 0.7769 (mp0) cc_final: 0.7520 (mp0) REVERT: F 612 ASP cc_start: 0.6131 (m-30) cc_final: 0.5789 (m-30) REVERT: F 619 PHE cc_start: 0.6477 (t80) cc_final: 0.6139 (t80) REVERT: E 469 PRO cc_start: 0.6246 (Cg_exo) cc_final: 0.6033 (Cg_endo) REVERT: E 643 ASP cc_start: 0.6369 (m-30) cc_final: 0.5613 (m-30) REVERT: E 655 MET cc_start: 0.5566 (mmp) cc_final: 0.5316 (mmp) REVERT: E 810 MET cc_start: 0.8135 (tpt) cc_final: 0.7869 (tpp) REVERT: E 879 MET cc_start: 0.8031 (ptp) cc_final: 0.7563 (ptp) outliers start: 42 outliers final: 39 residues processed: 237 average time/residue: 0.2658 time to fit residues: 99.8934 Evaluate side-chains 242 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 202 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 635 PHE Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain C residue 941 GLU Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain F residue 509 GLN Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 592 VAL Chi-restraints excluded: chain F residue 735 VAL Chi-restraints excluded: chain F residue 766 MET Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain E residue 502 LEU Chi-restraints excluded: chain E residue 709 VAL Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 802 VAL Chi-restraints excluded: chain E residue 844 VAL Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 933 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 160 optimal weight: 4.9990 chunk 214 optimal weight: 20.0000 chunk 61 optimal weight: 0.0970 chunk 185 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 201 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 207 optimal weight: 50.0000 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 618 ASN ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.126797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.099680 restraints weight = 35014.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.096062 restraints weight = 32370.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.097319 restraints weight = 34941.837| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 18627 Z= 0.222 Angle : 0.714 59.200 25420 Z= 0.390 Chirality : 0.041 0.217 3075 Planarity : 0.004 0.062 3261 Dihedral : 6.096 87.787 2753 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.33 % Allowed : 22.10 % Favored : 75.57 % 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: 0.19 (0.17), residues: 2515 helix: 1.50 (0.17), residues: 1101 sheet: -0.59 (0.29), residues: 344 loop : -1.08 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 470 HIS 0.003 0.001 HIS A 561 PHE 0.013 0.001 PHE F 545 TYR 0.011 0.001 TYR A 939 ARG 0.003 0.000 ARG F 652 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3062.22 seconds wall clock time: 57 minutes 23.25 seconds (3443.25 seconds total)