Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 16:29:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e92_27953/04_2023/8e92_27953.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e92_27953/04_2023/8e92_27953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e92_27953/04_2023/8e92_27953.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e92_27953/04_2023/8e92_27953.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e92_27953/04_2023/8e92_27953.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e92_27953/04_2023/8e92_27953.pdb" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.008 sd= 0.472 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 11549 2.51 5 N 3025 2.21 5 O 3365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C GLU 739": "OE1" <-> "OE2" Residue "D GLU 376": "OE1" <-> "OE2" Residue "D TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 18011 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 4526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 654, 4526 Classifications: {'peptide': 654} Incomplete info: {'truncation_to_alanine': 166} Link IDs: {'PTRANS': 29, 'TRANS': 624} Chain breaks: 1 Unresolved non-hydrogen bonds: 678 Unresolved non-hydrogen angles: 818 Unresolved non-hydrogen dihedrals: 566 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 16, 'TYR:plan': 3, 'ASN:plan1': 14, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 37, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 451 Chain: "B" Number of atoms: 4229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4229 Classifications: {'peptide': 633} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PTRANS': 38, 'TRANS': 594} Chain breaks: 3 Unresolved non-hydrogen bonds: 706 Unresolved non-hydrogen angles: 866 Unresolved non-hydrogen dihedrals: 592 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 8, 'TYR:plan': 6, 'ASN:plan1': 8, 'ASP:plan': 17, 'PHE:plan': 6, 'GLU:plan': 24, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 513 Chain: "C" Number of atoms: 4468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 4468 Classifications: {'peptide': 655} Incomplete info: {'truncation_to_alanine': 184} Link IDs: {'PTRANS': 29, 'TRANS': 625} Chain breaks: 1 Unresolved non-hydrogen bonds: 740 Unresolved non-hydrogen angles: 886 Unresolved non-hydrogen dihedrals: 619 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 18, 'TYR:plan': 3, 'ASN:plan1': 16, 'HIS:plan': 5, 'PHE:plan': 3, 'GLU:plan': 38, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 489 Chain: "D" Number of atoms: 4366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 4366 Classifications: {'peptide': 638} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 39, 'TRANS': 598} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 593 Unresolved non-hydrogen angles: 723 Unresolved non-hydrogen dihedrals: 492 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 16, 'PHE:plan': 4, 'GLU:plan': 23, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 411 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.36, per 1000 atoms: 0.52 Number of scatterers: 18011 At special positions: 0 Unit cell: (134.392, 145.52, 134.392, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3365 8.00 N 3025 7.00 C 11549 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.08 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.02 Simple disulfide: pdb=" SG CYS B 82 " - pdb=" SG CYS B 317 " distance=2.04 Simple disulfide: pdb=" SG CYS B 426 " - pdb=" SG CYS B 453 " distance=2.04 Simple disulfide: pdb=" SG CYS B 433 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 798 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.04 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.04 Simple disulfide: pdb=" SG CYS D 82 " - pdb=" SG CYS D 317 " distance=2.04 Simple disulfide: pdb=" SG CYS D 426 " - pdb=" SG CYS D 453 " distance=2.04 Simple disulfide: pdb=" SG CYS D 433 " - pdb=" SG CYS D 454 " distance=2.04 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 798 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A 901 " - " ASN A 61 " " NAG A 903 " - " ASN A 203 " " NAG C 901 " - " ASN C 203 " " NAG C 902 " - " ASN C 368 " " NAG D 901 " - " ASN D 685 " " NAG E 1 " - " ASN A 276 " " NAG F 1 " - " ASN A 771 " " NAG G 1 " - " ASN A 368 " " NAG H 1 " - " ASN B 337 " " NAG I 1 " - " ASN B 685 " " NAG J 1 " - " ASN C 61 " " NAG K 1 " - " ASN C 276 " " NAG L 1 " - " ASN C 771 " " NAG M 1 " - " ASN C 350 " " NAG N 1 " - " ASN D 337 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.60 Conformation dependent library (CDL) restraints added in 3.0 seconds 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4780 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 28 sheets defined 37.3% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 36 through 50 removed outlier: 3.884A pdb=" N GLN A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 53 No H-bonds generated for 'chain 'A' and resid 51 through 53' Processing helix chain 'A' and resid 70 through 85 Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.898A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 143 through 158 removed outlier: 4.361A pdb=" N GLN A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 188 removed outlier: 4.068A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.531A pdb=" N LEU A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.837A pdb=" N ILE A 254 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 277 through 296 removed outlier: 4.066A pdb=" N GLY A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.589A pdb=" N GLY A 503 " --> pdb=" O ASN A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 4.166A pdb=" N GLN A 525 " --> pdb=" O ASN A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 694 removed outlier: 3.604A pdb=" N ILE A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 707 removed outlier: 3.783A pdb=" N TYR A 703 " --> pdb=" O LEU A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 716 No H-bonds generated for 'chain 'A' and resid 714 through 716' Processing helix chain 'A' and resid 717 through 723 removed outlier: 4.114A pdb=" N VAL A 721 " --> pdb=" O ALA A 717 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A 722 " --> pdb=" O ILE A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 768 through 782 Processing helix chain 'A' and resid 783 through 794 Processing helix chain 'B' and resid 42 through 50 removed outlier: 3.702A pdb=" N PHE B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 89 Processing helix chain 'B' and resid 103 through 116 removed outlier: 3.713A pdb=" N ILE B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 161 Processing helix chain 'B' and resid 174 through 187 removed outlier: 4.073A pdb=" N PHE B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 219 removed outlier: 3.933A pdb=" N ARG B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 244 Processing helix chain 'B' and resid 284 through 303 removed outlier: 3.707A pdb=" N VAL B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR B 303 " --> pdb=" O GLY B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 334 removed outlier: 3.511A pdb=" N TYR B 332 " --> pdb=" O ARG B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 470 Processing helix chain 'B' and resid 486 through 490 Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'B' and resid 513 through 518 removed outlier: 3.611A pdb=" N GLU B 518 " --> pdb=" O GLU B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 688 through 693 Processing helix chain 'B' and resid 698 through 703 removed outlier: 3.808A pdb=" N HIS B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 721 Processing helix chain 'B' and resid 730 through 739 removed outlier: 3.629A pdb=" N LYS B 739 " --> pdb=" O TYR B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 753 Processing helix chain 'B' and resid 768 through 783 removed outlier: 3.936A pdb=" N ALA B 772 " --> pdb=" O HIS B 768 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 792 Processing helix chain 'C' and resid 35 through 53 Processing helix chain 'C' and resid 70 through 85 Processing helix chain 'C' and resid 103 through 113 removed outlier: 4.287A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.841A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 148 through 159 removed outlier: 3.826A pdb=" N PHE C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 removed outlier: 3.731A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 212 Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'C' and resid 251 through 254 removed outlier: 3.612A pdb=" N ILE C 254 " --> pdb=" O GLU C 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 251 through 254' Processing helix chain 'C' and resid 278 through 296 Processing helix chain 'C' and resid 317 through 327 removed outlier: 3.594A pdb=" N PHE C 321 " --> pdb=" O THR C 317 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 468 Processing helix chain 'C' and resid 501 through 508 Processing helix chain 'C' and resid 520 through 527 removed outlier: 3.637A pdb=" N ALA C 524 " --> pdb=" O ASN C 520 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN C 525 " --> pdb=" O ASN C 521 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TYR C 526 " --> pdb=" O GLU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 removed outlier: 3.685A pdb=" N ARG C 673 " --> pdb=" O ASP C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 694 removed outlier: 3.565A pdb=" N ILE C 691 " --> pdb=" O SER C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 708 Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 743 removed outlier: 4.072A pdb=" N SER C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 782 removed outlier: 4.132A pdb=" N GLN C 770 " --> pdb=" O SER C 766 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 777 " --> pdb=" O SER C 773 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN C 782 " --> pdb=" O LYS C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 794 Processing helix chain 'D' and resid 42 through 51 Processing helix chain 'D' and resid 52 through 54 No H-bonds generated for 'chain 'D' and resid 52 through 54' Processing helix chain 'D' and resid 73 through 89 Processing helix chain 'D' and resid 103 through 116 removed outlier: 4.035A pdb=" N ILE D 107 " --> pdb=" O ALA D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 158 removed outlier: 3.515A pdb=" N GLN D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 187 Processing helix chain 'D' and resid 208 through 218 removed outlier: 3.678A pdb=" N THR D 212 " --> pdb=" O PRO D 208 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN D 218 " --> pdb=" O ARG D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 243 removed outlier: 4.050A pdb=" N VAL D 235 " --> pdb=" O GLU D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 308 Processing helix chain 'D' and resid 327 through 336 Processing helix chain 'D' and resid 457 through 470 removed outlier: 3.649A pdb=" N VAL D 468 " --> pdb=" O LYS D 464 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 469 " --> pdb=" O LEU D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 500 Processing helix chain 'D' and resid 513 through 518 removed outlier: 3.800A pdb=" N GLU D 518 " --> pdb=" O GLU D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 688 through 696 Processing helix chain 'D' and resid 698 through 703 Processing helix chain 'D' and resid 710 through 721 Processing helix chain 'D' and resid 730 through 739 removed outlier: 3.662A pdb=" N TYR D 735 " --> pdb=" O ALA D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 767 through 784 removed outlier: 3.952A pdb=" N ARG D 771 " --> pdb=" O SER D 767 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY D 784 " --> pdb=" O PHE D 780 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 794 removed outlier: 4.192A pdb=" N LYS D 788 " --> pdb=" O GLY D 784 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU D 789 " --> pdb=" O GLU D 785 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA2, first strand: chain 'A' and resid 195 through 196 removed outlier: 6.755A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 222 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 270 removed outlier: 6.630A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 366 " --> pdb=" O ILE A 373 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 476 through 478 removed outlier: 6.178A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA6, first strand: chain 'A' and resid 681 through 682 removed outlier: 3.561A pdb=" N ALA A 682 " --> pdb=" O ALA A 728 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE A 730 " --> pdb=" O ALA A 682 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 64 through 66 removed outlier: 6.131A pdb=" N ILE B 93 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 198 through 201 removed outlier: 3.880A pdb=" N TYR B 227 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B 170 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL B 276 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET B 358 " --> pdb=" O TRP B 375 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ALA B 362 " --> pdb=" O MET B 371 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N MET B 371 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 339 through 340 removed outlier: 3.919A pdb=" N TRP B 340 " --> pdb=" O ARG B 343 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 414 through 417 removed outlier: 4.460A pdb=" N LEU B 475 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 477 " --> pdb=" O ARG B 434 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU B 403 " --> pdb=" O ASP B 474 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N TYR B 476 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL B 405 " --> pdb=" O TYR B 476 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 527 through 528 removed outlier: 4.158A pdb=" N VAL B 527 " --> pdb=" O TYR B 759 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 531 through 534 Processing sheet with id=AB4, first strand: chain 'C' and resid 59 through 65 removed outlier: 11.720A pdb=" N ILE C 26 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 10.389A pdb=" N ALA C 89 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ASN C 28 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N LEU C 91 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLY C 30 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 138 " --> pdb=" O VAL C 118 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 195 through 197 removed outlier: 8.051A pdb=" N LEU C 195 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 267 through 271 removed outlier: 7.024A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 473 through 478 removed outlier: 3.553A pdb=" N THR C 402 " --> pdb=" O HIS C 477 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 409 through 412 Processing sheet with id=AB9, first strand: chain 'C' and resid 485 through 488 removed outlier: 3.638A pdb=" N THR C 486 " --> pdb=" O ASN C 499 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN C 499 " --> pdb=" O THR C 486 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 528 through 529 removed outlier: 3.792A pdb=" N GLU C 528 " --> pdb=" O MET C 762 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET C 762 " --> pdb=" O GLU C 528 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 681 through 682 removed outlier: 6.590A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 749 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL C 542 " --> pdb=" O VAL C 747 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL C 747 " --> pdb=" O VAL C 542 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 681 through 682 removed outlier: 6.590A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 65 through 66 removed outlier: 6.300A pdb=" N ALA D 33 " --> pdb=" O VAL D 94 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 198 through 201 removed outlier: 3.678A pdb=" N TYR D 227 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER D 170 " --> pdb=" O TYR D 227 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N PHE D 224 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 275 through 277 removed outlier: 3.617A pdb=" N SER D 275 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA D 362 " --> pdb=" O MET D 371 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N MET D 371 " --> pdb=" O ALA D 362 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU D 376 " --> pdb=" O VAL D 379 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 472 through 477 removed outlier: 7.314A pdb=" N LEU D 403 " --> pdb=" O ASP D 474 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N TYR D 476 " --> pdb=" O LEU D 403 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL D 405 " --> pdb=" O TYR D 476 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET D 505 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA D 762 " --> pdb=" O ALA D 506 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP D 521 " --> pdb=" O MET D 763 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 416 through 417 Processing sheet with id=AC9, first strand: chain 'D' and resid 726 through 729 Processing sheet with id=AD1, first strand: chain 'D' and resid 726 through 729 removed outlier: 4.734A pdb=" N ILE D 531 " --> pdb=" O ALA D 755 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ALA D 755 " --> pdb=" O ILE D 531 " (cutoff:3.500A) 718 hydrogen bonds defined for protein. 2043 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: 5.99 Time building geometry restraints manager: 7.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.31: 2870 1.31 - 1.62: 15445 1.62 - 1.93: 108 1.93 - 2.24: 1 2.24 - 2.55: 1 Bond restraints: 18425 Sorted by residual: bond pdb=" CB PRO D 677 " pdb=" CG PRO D 677 " ideal model delta sigma weight residual 1.492 2.552 -1.060 5.00e-02 4.00e+02 4.50e+02 bond pdb=" CG PRO D 677 " pdb=" CD PRO D 677 " ideal model delta sigma weight residual 1.503 1.005 0.498 3.40e-02 8.65e+02 2.15e+02 bond pdb=" CG PRO B 388 " pdb=" CD PRO B 388 " ideal model delta sigma weight residual 1.503 1.024 0.479 3.40e-02 8.65e+02 1.99e+02 bond pdb=" CA CYS A 454 " pdb=" CB CYS A 454 " ideal model delta sigma weight residual 1.530 1.671 -0.141 1.48e-02 4.57e+03 9.10e+01 bond pdb=" CG1 ILE C 519 " pdb=" CD1 ILE C 519 " ideal model delta sigma weight residual 1.513 1.155 0.358 3.90e-02 6.57e+02 8.43e+01 ... (remaining 18420 not shown) Histogram of bond angle deviations from ideal: 0.03 - 28.03: 1 28.03 - 56.02: 0 56.02 - 84.02: 4 84.02 - 112.02: 10203 112.02 - 140.02: 15191 Bond angle restraints: 25399 Sorted by residual: angle pdb=" CB PRO D 677 " pdb=" CG PRO D 677 " pdb=" CD PRO D 677 " ideal model delta sigma weight residual 106.10 0.03 106.07 3.20e+00 9.77e-02 1.10e+03 angle pdb=" N PRO B 388 " pdb=" CD PRO B 388 " pdb=" CG PRO B 388 " ideal model delta sigma weight residual 103.20 70.88 32.32 1.50e+00 4.44e-01 4.64e+02 angle pdb=" CA PRO D 677 " pdb=" N PRO D 677 " pdb=" CD PRO D 677 " ideal model delta sigma weight residual 112.00 83.47 28.53 1.40e+00 5.10e-01 4.15e+02 angle pdb=" CA PRO B 388 " pdb=" CB PRO B 388 " pdb=" CG PRO B 388 " ideal model delta sigma weight residual 104.50 73.72 30.78 1.90e+00 2.77e-01 2.62e+02 angle pdb=" N PRO D 677 " pdb=" CA PRO D 677 " pdb=" CB PRO D 677 " ideal model delta sigma weight residual 103.25 86.80 16.45 1.05e+00 9.07e-01 2.46e+02 ... (remaining 25394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.06: 9726 23.06 - 46.11: 626 46.11 - 69.17: 59 69.17 - 92.23: 8 92.23 - 115.28: 1 Dihedral angle restraints: 10420 sinusoidal: 3003 harmonic: 7417 Sorted by residual: dihedral pdb=" CA GLY B 204 " pdb=" C GLY B 204 " pdb=" N PRO B 205 " pdb=" CA PRO B 205 " ideal model delta harmonic sigma weight residual -180.00 -137.31 -42.69 0 5.00e+00 4.00e-02 7.29e+01 dihedral pdb=" C TYR D 473 " pdb=" N TYR D 473 " pdb=" CA TYR D 473 " pdb=" CB TYR D 473 " ideal model delta harmonic sigma weight residual -122.60 -102.10 -20.50 0 2.50e+00 1.60e-01 6.72e+01 dihedral pdb=" CB CYS D 82 " pdb=" SG CYS D 82 " pdb=" SG CYS D 317 " pdb=" CB CYS D 317 " ideal model delta sinusoidal sigma weight residual 93.00 29.08 63.92 1 1.00e+01 1.00e-02 5.38e+01 ... (remaining 10417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 3125 0.116 - 0.233: 89 0.233 - 0.349: 14 0.349 - 0.465: 4 0.465 - 0.582: 1 Chirality restraints: 3233 Sorted by residual: chirality pdb=" CA VAL D 468 " pdb=" N VAL D 468 " pdb=" C VAL D 468 " pdb=" CB VAL D 468 " both_signs ideal model delta sigma weight residual False 2.44 1.86 0.58 2.00e-01 2.50e+01 8.46e+00 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 7.02e+00 chirality pdb=" CA ARG D 401 " pdb=" N ARG D 401 " pdb=" C ARG D 401 " pdb=" CB ARG D 401 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.33e+00 ... (remaining 3230 not shown) Planarity restraints: 3217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 438 " 0.113 5.00e-02 4.00e+02 1.58e-01 3.99e+01 pdb=" N PRO A 439 " -0.272 5.00e-02 4.00e+02 pdb=" CA PRO A 439 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO A 439 " 0.085 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 676 " -0.110 5.00e-02 4.00e+02 1.51e-01 3.67e+01 pdb=" N PRO D 677 " 0.261 5.00e-02 4.00e+02 pdb=" CA PRO D 677 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO D 677 " -0.086 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 463 " 0.023 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C LYS D 463 " -0.085 2.00e-02 2.50e+03 pdb=" O LYS D 463 " 0.033 2.00e-02 2.50e+03 pdb=" N LYS D 464 " 0.028 2.00e-02 2.50e+03 ... (remaining 3214 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 567 2.68 - 3.24: 18036 3.24 - 3.79: 26024 3.79 - 4.35: 30346 4.35 - 4.90: 50504 Nonbonded interactions: 125477 Sorted by model distance: nonbonded pdb=" O GLN D 779 " pdb=" OD1 ASP D 783 " model vdw 2.130 3.040 nonbonded pdb=" OG1 THR A 312 " pdb=" O THR B 72 " model vdw 2.170 2.440 nonbonded pdb=" O SER D 400 " pdb=" OG SER D 400 " model vdw 2.184 2.440 nonbonded pdb=" O6 NAG M 1 " pdb=" O7 NAG M 2 " model vdw 2.201 2.440 nonbonded pdb=" O4 NAG L 1 " pdb=" O7 NAG L 1 " model vdw 2.202 2.440 ... (remaining 125472 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 25 through 35 or (resid 36 through 42 and (name N or name \ CA or name C or name O or name CB )) or resid 43 through 46 or (resid 47 through \ 52 and (name N or name CA or name C or name O or name CB )) or resid 53 through \ 79 or (resid 80 and (name N or name CA or name C or name O or name CB )) or res \ id 81 through 100 or (resid 101 through 102 and (name N or name CA or name C or \ name O or name CB )) or resid 103 through 146 or (resid 147 and (name N or name \ CA or name C or name O or name CB )) or resid 148 through 155 or (resid 156 and \ (name N or name CA or name C or name O or name CB )) or resid 157 through 212 or \ (resid 213 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 4 through 225 or (resid 226 through 229 and (name N or name CA or name C or name \ O or name CB )) or resid 230 through 239 or (resid 240 and (name N or name CA o \ r name C or name O or name CB )) or resid 241 through 251 or (resid 252 through \ 253 and (name N or name CA or name C or name O or name CB )) or resid 254 throug \ h 263 or (resid 264 and (name N or name CA or name C or name O or name CB )) or \ resid 265 through 266 or (resid 267 and (name N or name CA or name C or name O o \ r name CB )) or resid 268 through 272 or (resid 273 and (name N or name CA or na \ me C or name O or name CB )) or resid 274 through 300 or (resid 301 and (name N \ or name CA or name C or name O or name CB )) or resid 302 or (resid 303 and (nam \ e N or name CA or name C or name O or name CB )) or resid 304 through 310 or (re \ sid 311 and (name N or name CA or name C or name O or name CB )) or resid 312 th \ rough 347 or (resid 348 through 349 and (name N or name CA or name C or name O o \ r name CB )) or resid 350 through 356 or (resid 357 and (name N or name CA or na \ me C or name O or name CB )) or resid 358 through 359 or (resid 360 and (name N \ or name CA or name C or name O or name CB )) or resid 361 through 376 or (resid \ 377 through 379 and (name N or name CA or name C or name O or name CB )) or resi \ d 380 through 391 or (resid 392 through 394 and (name N or name CA or name C or \ name O or name CB )) or resid 395 through 418 or (resid 419 and (name N or name \ CA or name C or name O or name CB )) or resid 420 through 424 or (resid 425 thro \ ugh 427 and (name N or name CA or name C or name O or name CB )) or resid 428 th \ rough 442 or (resid 443 and (name N or name CA or name C or name O or name CB )) \ or resid 444 through 445 or (resid 446 and (name N or name CA or name C or name \ O or name CB )) or resid 447 through 448 or (resid 449 and (name N or name CA o \ r name C or name O or name CB )) or resid 450 through 464 or (resid 465 and (nam \ e N or name CA or name C or name O or name CB )) or resid 466 through 467 or (re \ sid 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 47 \ 1 through 498 or (resid 499 and (name N or name CA or name C or name O or name C \ B )) or resid 500 through 527 or (resid 528 and (name N or name CA or name C or \ name O or name CB )) or resid 529 through 530 or (resid 531 and (name N or name \ CA or name C or name O or name CB )) or resid 532 through 533 or (resid 534 and \ (name N or name CA or name C or name O or name CB )) or resid 535 through 544 or \ resid 664 through 684 or (resid 685 and (name N or name CA or name C or name O \ or name CB )) or resid 686 through 701 or (resid 702 through 704 and (name N or \ name CA or name C or name O or name CB )) or resid 705 through 708 or (resid 709 \ through 711 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 12 through 754 or (resid 755 and (name N or name CA or name C or name O or name \ CB )) or resid 756 through 764 or (resid 765 and (name N or name CA or name C or \ name O or name CB )) or resid 766 through 788 or (resid 789 through 790 and (na \ me N or name CA or name C or name O or name CB )) or resid 791 through 796 or re \ sid 903 through 904)) selection = (chain 'C' and (resid 25 through 55 or (resid 56 through 57 and (name N or name \ CA or name C or name O or name CB )) or resid 58 through 101 or (resid 102 and ( \ name N or name CA or name C or name O or name CB )) or resid 103 through 173 or \ (resid 174 through 176 and (name N or name CA or name C or name O or name CB )) \ or resid 177 through 214 or (resid 215 through 217 and (name N or name CA or nam \ e C or name O or name CB )) or resid 218 through 271 or (resid 272 through 273 a \ nd (name N or name CA or name C or name O or name CB )) or resid 274 through 340 \ or (resid 341 through 342 and (name N or name CA or name C or name O or name CB \ )) or resid 343 through 366 or (resid 367 and (name N or name CA or name C or n \ ame O or name CB )) or resid 368 through 378 or (resid 379 and (name N or name C \ A or name C or name O or name CB )) or resid 380 through 398 or (resid 399 and ( \ name N or name CA or name C or name O or name CB )) or resid 400 through 423 or \ (resid 424 through 427 and (name N or name CA or name C or name O or name CB )) \ or resid 428 through 474 or (resid 475 and (name N or name CA or name C or name \ O or name CB )) or resid 476 through 480 or (resid 481 and (name N or name CA or \ name C or name O or name CB )) or resid 482 through 510 or (resid 511 and (name \ N or name CA or name C or name O or name CB )) or resid 512 through 519 or (res \ id 520 and (name N or name CA or name C or name O or name CB )) or resid 521 thr \ ough 540 or (resid 541 and (name N or name CA or name C or name O or name CB )) \ or resid 542 through 544 or (resid 664 through 665 and (name N or name CA or nam \ e C or name O or name CB )) or resid 666 through 667 or (resid 668 through 669 a \ nd (name N or name CA or name C or name O or name CB )) or resid 670 through 693 \ or (resid 694 through 699 and (name N or name CA or name C or name O or name CB \ )) or resid 700 through 706 or (resid 707 through 711 and (name N or name CA or \ name C or name O or name CB )) or resid 712 through 721 or (resid 722 through 7 \ 26 and (name N or name CA or name C or name O or name CB )) or resid 727 through \ 796 or resid 901 through 902)) } ncs_group { reference = (chain 'B' and (resid 31 through 53 or (resid 54 through 58 and (name N or name \ CA or name C or name O or name CB )) or resid 59 through 88 or (resid 89 through \ 91 and (name N or name CA or name C or name O or name CB )) or resid 92 through \ 96 or (resid 97 through 103 and (name N or name CA or name C or name O or name \ CB )) or resid 104 through 105 or (resid 106 and (name N or name CA or name C or \ name O or name CB )) or resid 107 through 133 or (resid 134 and (name N or name \ CA or name C or name O or name CB )) or resid 135 through 179 or (resid 180 and \ (name N or name CA or name C or name O or name CB )) or resid 181 through 182 o \ r (resid 183 through 184 and (name N or name CA or name C or name O or name CB ) \ ) or resid 185 through 186 or (resid 187 through 188 and (name N or name CA or n \ ame C or name O or name CB )) or resid 189 through 216 or (resid 217 and (name N \ or name CA or name C or name O or name CB )) or resid 218 through 231 or (resid \ 232 through 234 and (name N or name CA or name C or name O or name CB )) or res \ id 235 through 258 or (resid 259 and (name N or name CA or name C or name O or n \ ame CB )) or resid 260 through 284 or (resid 285 through 288 and (name N or name \ CA or name C or name O or name CB )) or resid 289 through 302 or (resid 303 and \ (name N or name CA or name C or name O or name CB )) or resid 304 through 335 o \ r (resid 336 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 37 through 343 or (resid 344 and (name N or name CA or name C or name O or name \ CB )) or resid 345 through 363 or (resid 364 through 365 and (name N or name CA \ or name C or name O or name CB )) or resid 366 through 434 or (resid 435 through \ 436 and (name N or name CA or name C or name O or name CB )) or resid 437 or (r \ esid 448 through 449 and (name N or name CA or name C or name O or name CB )) or \ resid 450 through 459 or (resid 460 and (name N or name CA or name C or name O \ or name CB )) or resid 461 through 500 or (resid 501 and (name N or name CA or n \ ame C or name O or name CB )) or resid 502 through 701 or (resid 702 through 703 \ and (name N or name CA or name C or name O or name CB )) or resid 704 through 7 \ 05 or (resid 706 through 709 and (name N or name CA or name C or name O or name \ CB )) or resid 710 through 767 or (resid 768 and (name N or name CA or name C or \ name O or name CB )) or resid 769 through 786 or (resid 787 through 788 and (na \ me N or name CA or name C or name O or name CB )) or resid 789 through 798)) selection = (chain 'D' and (resid 31 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 77 or (resid 78 and (name N or nam \ e CA or name C or name O or name CB )) or resid 79 through 89 or (resid 90 throu \ gh 91 and (name N or name CA or name C or name O or name CB )) or resid 92 throu \ gh 113 or (resid 114 and (name N or name CA or name C or name O or name CB )) or \ resid 115 through 147 or (resid 148 and (name N or name CA or name C or name O \ or name CB )) or resid 149 through 158 or (resid 159 through 161 and (name N or \ name CA or name C or name O or name CB )) or resid 162 through 171 or (resid 172 \ and (name N or name CA or name C or name O or name CB )) or resid 173 through 1 \ 93 or (resid 194 and (name N or name CA or name C or name O or name CB )) or res \ id 195 through 208 or (resid 209 through 211 and (name N or name CA or name C or \ name O or name CB )) or resid 212 or (resid 213 through 214 and (name N or name \ CA or name C or name O or name CB )) or resid 215 through 238 or (resid 239 thr \ ough 243 and (name N or name CA or name C or name O or name CB )) or resid 244 o \ r (resid 245 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 46 through 270 or (resid 271 and (name N or name CA or name C or name O or name \ CB )) or resid 272 through 278 or (resid 279 and (name N or name CA or name C or \ name O or name CB )) or resid 280 through 285 or (resid 286 through 288 and (na \ me N or name CA or name C or name O or name CB )) or resid 289 or (resid 290 thr \ ough 291 and (name N or name CA or name C or name O or name CB )) or resid 292 t \ hrough 306 or (resid 307 and (name N or name CA or name C or name O or name CB ) \ ) or resid 308 through 333 or (resid 334 and (name N or name CA or name C or nam \ e O or name CB )) or resid 335 through 347 or (resid 348 and (name N or name CA \ or name C or name O or name CB )) or resid 349 through 382 or (resid 383 through \ 384 and (name N or name CA or name C or name O or name CB )) or resid 385 throu \ gh 389 or (resid 390 and (name N or name CA or name C or name O or name CB )) or \ resid 391 or resid 398 or (resid 399 and (name N or name CA or name C or name O \ or name CB )) or resid 400 through 401 or (resid 402 and (name N or name CA or \ name C or name O or name CB )) or resid 403 through 437 or (resid 448 through 44 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 450 through \ 470 or (resid 471 and (name N or name CA or name C or name O or name CB )) or re \ sid 472 through 479 or (resid 480 and (name N or name CA or name C or name O or \ name CB )) or resid 481 through 484 or (resid 485 through 486 and (name N or nam \ e CA or name C or name O or name CB )) or resid 487 through 514 or (resid 515 an \ d (name N or name CA or name C or name O or name CB )) or resid 516 through 527 \ or (resid 528 and (name N or name CA or name C or name O or name CB )) or resid \ 529 through 664 or (resid 665 through 670 and (name N or name CA or name C or na \ me O or name CB )) or resid 671 through 672 or (resid 673 through 675 and (name \ N or name CA or name C or name O or name CB )) or resid 676 through 679 or (resi \ d 680 and (name N or name CA or name C or name O or name CB )) or resid 681 thro \ ugh 692 or (resid 693 and (name N or name CA or name C or name O or name CB )) o \ r resid 694 or (resid 695 through 697 and (name N or name CA or name C or name O \ or name CB )) or resid 698 through 728 or (resid 729 through 731 and (name N or \ name CA or name C or name O or name CB )) or resid 732 through 733 or (resid 73 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 735 through \ 763 or (resid 764 through 766 and (name N or name CA or name C or name O or name \ CB )) or resid 767 through 770 or (resid 771 through 772 and (name N or name CA \ or name C or name O or name CB )) or resid 773 through 782 or (resid 783 and (n \ ame N or name CA or name C or name O or name CB )) or resid 784 through 798)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 15.590 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 46.370 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.140 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 : 0.012 1.060 18425 Z= 0.670 Angle : 1.201 106.070 25399 Z= 0.619 Chirality : 0.055 0.582 3233 Planarity : 0.007 0.158 3202 Dihedral : 14.651 115.282 5598 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.81 % Favored : 90.07 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.99 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.16), residues: 2558 helix: -0.14 (0.18), residues: 814 sheet: -1.95 (0.26), residues: 370 loop : -2.91 (0.16), residues: 1374 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 219 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 232 average time/residue: 0.2351 time to fit residues: 91.4565 Evaluate side-chains 220 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 210 time to evaluate : 2.232 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2241 time to fit residues: 6.5367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 232 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 HIS A 477 HIS B 175 HIS B 218 GLN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS D 334 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 1.036 18425 Z= 0.514 Angle : 0.991 101.983 25399 Z= 0.445 Chirality : 0.048 0.289 3233 Planarity : 0.005 0.078 3202 Dihedral : 5.747 42.006 2689 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.85 % Favored : 88.08 % Rotamer Outliers : 5.78 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.16), residues: 2558 helix: 0.07 (0.18), residues: 853 sheet: -1.89 (0.26), residues: 377 loop : -2.91 (0.16), residues: 1328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 205 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 56 residues processed: 271 average time/residue: 0.2404 time to fit residues: 110.6017 Evaluate side-chains 261 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 205 time to evaluate : 2.108 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.1704 time to fit residues: 20.7245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 193 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 232 optimal weight: 0.0970 chunk 251 optimal weight: 0.4980 chunk 207 optimal weight: 1.9990 chunk 230 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 186 optimal weight: 20.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS B 218 GLN D 148 GLN D 175 HIS D 334 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 1.030 18425 Z= 0.449 Angle : 0.958 104.749 25399 Z= 0.417 Chirality : 0.047 0.270 3233 Planarity : 0.005 0.098 3202 Dihedral : 5.604 41.914 2689 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.79 % Favored : 89.17 % Rotamer Outliers : 2.89 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.17), residues: 2558 helix: 0.30 (0.18), residues: 858 sheet: -1.88 (0.26), residues: 377 loop : -2.83 (0.16), residues: 1323 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 220 time to evaluate : 2.022 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 19 residues processed: 260 average time/residue: 0.2214 time to fit residues: 98.2536 Evaluate side-chains 223 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 204 time to evaluate : 2.162 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1549 time to fit residues: 8.3275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 9.9990 chunk 175 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 25 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 156 optimal weight: 0.6980 chunk 233 optimal weight: 4.9990 chunk 247 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 221 optimal weight: 3.9990 chunk 66 optimal weight: 30.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 GLN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN D 334 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 1.017 18425 Z= 0.488 Angle : 0.994 106.099 25399 Z= 0.439 Chirality : 0.047 0.263 3233 Planarity : 0.005 0.108 3202 Dihedral : 5.615 42.025 2689 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.06 % Favored : 88.90 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.16), residues: 2558 helix: 0.32 (0.18), residues: 857 sheet: -1.90 (0.26), residues: 386 loop : -2.85 (0.16), residues: 1315 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 201 time to evaluate : 2.179 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 16 residues processed: 225 average time/residue: 0.2308 time to fit residues: 88.5464 Evaluate side-chains 213 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 197 time to evaluate : 2.070 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1701 time to fit residues: 7.8489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 chunk 3 optimal weight: 0.0970 chunk 184 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 211 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 222 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 1.017 18425 Z= 0.488 Angle : 0.994 106.100 25399 Z= 0.439 Chirality : 0.047 0.263 3233 Planarity : 0.005 0.108 3202 Dihedral : 5.615 42.026 2689 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.06 % Favored : 88.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.16), residues: 2558 helix: 0.32 (0.18), residues: 857 sheet: -1.90 (0.26), residues: 386 loop : -2.85 (0.16), residues: 1315 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 2.070 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.2506 time to fit residues: 84.1167 Evaluate side-chains 198 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.230 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 9.9990 chunk 222 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 247 optimal weight: 8.9990 chunk 205 optimal weight: 1.9990 chunk 114 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 1.017 18425 Z= 0.488 Angle : 0.994 106.100 25399 Z= 0.439 Chirality : 0.047 0.263 3233 Planarity : 0.005 0.108 3202 Dihedral : 5.615 42.026 2689 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.06 % Favored : 88.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.16), residues: 2558 helix: 0.32 (0.18), residues: 857 sheet: -1.90 (0.26), residues: 386 loop : -2.85 (0.16), residues: 1315 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.196 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2494 time to fit residues: 83.9838 Evaluate side-chains 198 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.046 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 3.9990 chunk 27 optimal weight: 0.0060 chunk 141 optimal weight: 0.0970 chunk 180 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 246 optimal weight: 7.9990 chunk 154 optimal weight: 0.6980 chunk 150 optimal weight: 0.5980 chunk 113 optimal weight: 10.0000 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 1.017 18425 Z= 0.488 Angle : 0.994 106.100 25399 Z= 0.439 Chirality : 0.047 0.263 3233 Planarity : 0.005 0.108 3202 Dihedral : 5.615 42.026 2689 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.06 % Favored : 88.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.16), residues: 2558 helix: 0.32 (0.18), residues: 857 sheet: -1.90 (0.26), residues: 386 loop : -2.85 (0.16), residues: 1315 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.063 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2563 time to fit residues: 86.1167 Evaluate side-chains 198 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.079 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 3.9990 chunk 98 optimal weight: 0.0970 chunk 147 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 193 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 1.017 18425 Z= 0.488 Angle : 0.994 106.100 25399 Z= 0.439 Chirality : 0.047 0.263 3233 Planarity : 0.005 0.108 3202 Dihedral : 5.615 42.026 2689 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.06 % Favored : 88.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.16), residues: 2558 helix: 0.32 (0.18), residues: 857 sheet: -1.90 (0.26), residues: 386 loop : -2.85 (0.16), residues: 1315 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.964 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2354 time to fit residues: 79.0209 Evaluate side-chains 198 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.082 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 229 optimal weight: 0.8980 chunk 138 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 180 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 217 optimal weight: 20.0000 chunk 150 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 1.017 18425 Z= 0.488 Angle : 0.994 106.100 25399 Z= 0.439 Chirality : 0.047 0.263 3233 Planarity : 0.005 0.108 3202 Dihedral : 5.615 42.026 2689 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.06 % Favored : 88.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.16), residues: 2558 helix: 0.32 (0.18), residues: 857 sheet: -1.90 (0.26), residues: 386 loop : -2.85 (0.16), residues: 1315 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.053 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2387 time to fit residues: 80.3869 Evaluate side-chains 198 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.004 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 115 optimal weight: 0.0770 chunk 169 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 chunk 234 optimal weight: 7.9990 chunk 203 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 overall best weight: 3.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 1.017 18425 Z= 0.488 Angle : 0.994 106.100 25399 Z= 0.439 Chirality : 0.047 0.263 3233 Planarity : 0.005 0.108 3202 Dihedral : 5.615 42.026 2689 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.06 % Favored : 88.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.16), residues: 2558 helix: 0.32 (0.18), residues: 857 sheet: -1.90 (0.26), residues: 386 loop : -2.85 (0.16), residues: 1315 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.083 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2414 time to fit residues: 81.1874 Evaluate side-chains 198 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.132 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 3.9990 chunk 62 optimal weight: 0.0770 chunk 187 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 203 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 178 optimal weight: 0.4980 overall best weight: 1.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.109446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.092224 restraints weight = 64824.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.094292 restraints weight = 37911.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.095714 restraints weight = 26270.579| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 1.017 18425 Z= 0.488 Angle : 0.994 106.100 25399 Z= 0.439 Chirality : 0.047 0.263 3233 Planarity : 0.005 0.108 3202 Dihedral : 5.615 42.026 2689 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.06 % Favored : 88.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.16), residues: 2558 helix: 0.32 (0.18), residues: 857 sheet: -1.90 (0.26), residues: 386 loop : -2.85 (0.16), residues: 1315 =============================================================================== Job complete usr+sys time: 3038.01 seconds wall clock time: 56 minutes 22.87 seconds (3382.87 seconds total)