Starting phenix.real_space_refine on Fri Nov 17 15:57:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oab_20000/11_2023/6oab_20000_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oab_20000/11_2023/6oab_20000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oab_20000/11_2023/6oab_20000.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oab_20000/11_2023/6oab_20000.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oab_20000/11_2023/6oab_20000_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oab_20000/11_2023/6oab_20000_neut_updated.pdb" } resolution = 3.6 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= 0.014 sd= 0.087 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: 7 Type Number sf(0) Gaussians P 20 5.49 5 S 87 5.16 5 Be 8 3.05 5 C 12272 2.51 5 N 3446 2.21 5 O 3833 1.98 5 F 24 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 220": "NH1" <-> "NH2" Residue "D ARG 227": "NH1" <-> "NH2" Residue "D TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 291": "OE1" <-> "OE2" Residue "D GLU 293": "OE1" <-> "OE2" Residue "D ARG 297": "NH1" <-> "NH2" Residue "D PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 301": "OE1" <-> "OE2" Residue "D GLU 315": "OE1" <-> "OE2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ASP 343": "OD1" <-> "OD2" Residue "D ARG 348": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D ARG 372": "NH1" <-> "NH2" Residue "D ASP 383": "OD1" <-> "OD2" Residue "D GLU 389": "OE1" <-> "OE2" Residue "D ARG 392": "NH1" <-> "NH2" Residue "D GLU 407": "OE1" <-> "OE2" Residue "D TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 434": "NH1" <-> "NH2" Residue "D PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 476": "OE1" <-> "OE2" Residue "D ASP 493": "OD1" <-> "OD2" Residue "D GLU 501": "OE1" <-> "OE2" Residue "D PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 544": "OE1" <-> "OE2" Residue "D PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 566": "OE1" <-> "OE2" Residue "D ASP 571": "OD1" <-> "OD2" Residue "D PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 590": "OD1" <-> "OD2" Residue "D ARG 596": "NH1" <-> "NH2" Residue "D GLU 617": "OE1" <-> "OE2" Residue "D ASP 659": "OD1" <-> "OD2" Residue "D ARG 703": "NH1" <-> "NH2" Residue "D TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 717": "NH1" <-> "NH2" Residue "D TYR 752": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 771": "OD1" <-> "OD2" Residue "D ARG 776": "NH1" <-> "NH2" Residue "D ARG 788": "NH1" <-> "NH2" Residue "E ARG 220": "NH1" <-> "NH2" Residue "E GLU 231": "OE1" <-> "OE2" Residue "E TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 283": "OE1" <-> "OE2" Residue "E ARG 297": "NH1" <-> "NH2" Residue "E PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 302": "OE1" <-> "OE2" Residue "E GLU 315": "OE1" <-> "OE2" Residue "E ASP 317": "OD1" <-> "OD2" Residue "E ARG 323": "NH1" <-> "NH2" Residue "E ARG 332": "NH1" <-> "NH2" Residue "E ARG 348": "NH1" <-> "NH2" Residue "E ARG 369": "NH1" <-> "NH2" Residue "E ARG 372": "NH1" <-> "NH2" Residue "E ASP 374": "OD1" <-> "OD2" Residue "E GLU 376": "OE1" <-> "OE2" Residue "E ASP 378": "OD1" <-> "OD2" Residue "E ASP 383": "OD1" <-> "OD2" Residue "E ARG 392": "NH1" <-> "NH2" Residue "E ASP 402": "OD1" <-> "OD2" Residue "E ASP 403": "OD1" <-> "OD2" Residue "E ASP 405": "OD1" <-> "OD2" Residue "E GLU 407": "OE1" <-> "OE2" Residue "E TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 434": "NH1" <-> "NH2" Residue "E ASP 493": "OD1" <-> "OD2" Residue "E GLU 494": "OE1" <-> "OE2" Residue "E GLU 497": "OE1" <-> "OE2" Residue "E TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 564": "OE1" <-> "OE2" Residue "E ASP 571": "OD1" <-> "OD2" Residue "E PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 577": "NH1" <-> "NH2" Residue "E ARG 596": "NH1" <-> "NH2" Residue "E ASP 608": "OD1" <-> "OD2" Residue "E ARG 645": "NH1" <-> "NH2" Residue "E ASP 650": "OD1" <-> "OD2" Residue "E GLU 660": "OE1" <-> "OE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 227": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "B PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 301": "OE1" <-> "OE2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B ASP 317": "OD1" <-> "OD2" Residue "B ARG 323": "NH1" <-> "NH2" Residue "B ASP 324": "OD1" <-> "OD2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 348": "NH1" <-> "NH2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B ARG 368": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 372": "NH1" <-> "NH2" Residue "B ASP 374": "OD1" <-> "OD2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B ASP 403": "OD1" <-> "OD2" Residue "B GLU 407": "OE1" <-> "OE2" Residue "B TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B ASP 445": "OD1" <-> "OD2" Residue "B GLU 446": "OE1" <-> "OE2" Residue "B GLU 450": "OE1" <-> "OE2" Residue "B PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 476": "OE1" <-> "OE2" Residue "B GLU 494": "OE1" <-> "OE2" Residue "B PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 587": "OD1" <-> "OD2" Residue "B ARG 596": "NH1" <-> "NH2" Residue "B ASP 602": "OD1" <-> "OD2" Residue "B ARG 645": "NH1" <-> "NH2" Residue "B ARG 648": "NH1" <-> "NH2" Residue "B ASP 650": "OD1" <-> "OD2" Residue "B GLU 681": "OE1" <-> "OE2" Residue "B ARG 703": "NH1" <-> "NH2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 717": "NH1" <-> "NH2" Residue "C ARG 220": "NH1" <-> "NH2" Residue "C ARG 227": "NH1" <-> "NH2" Residue "C GLU 228": "OE1" <-> "OE2" Residue "C ARG 266": "NH1" <-> "NH2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "C PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 317": "OD1" <-> "OD2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C ASP 324": "OD1" <-> "OD2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ASP 343": "OD1" <-> "OD2" Residue "C GLU 376": "OE1" <-> "OE2" Residue "C ARG 392": "NH1" <-> "NH2" Residue "C ASP 402": "OD1" <-> "OD2" Residue "C ASP 405": "OD1" <-> "OD2" Residue "C GLU 407": "OE1" <-> "OE2" Residue "C TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 434": "NH1" <-> "NH2" Residue "C ASP 438": "OD1" <-> "OD2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 494": "OE1" <-> "OE2" Residue "C PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 571": "OD1" <-> "OD2" Residue "C PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 577": "NH1" <-> "NH2" Residue "C ASP 619": "OD1" <-> "OD2" Residue "C ARG 635": "NH1" <-> "NH2" Residue "C ARG 648": "NH1" <-> "NH2" Residue "C ARG 663": "NH1" <-> "NH2" Residue "C ASP 696": "OD1" <-> "OD2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 711": "OD1" <-> "OD2" Residue "C ARG 717": "NH1" <-> "NH2" Residue "C PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 771": "OD1" <-> "OD2" Residue "C ARG 776": "NH1" <-> "NH2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A ARG 323": "NH1" <-> "NH2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A ASP 402": "OD1" <-> "OD2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A ARG 434": "NH1" <-> "NH2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A ASP 460": "OD1" <-> "OD2" Residue "A ASP 493": "OD1" <-> "OD2" Residue "A GLU 497": "OE1" <-> "OE2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "A TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 566": "OE1" <-> "OE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 617": "OE1" <-> "OE2" Residue "A PHE 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 637": "OD1" <-> "OD2" Residue "A ASP 640": "OD1" <-> "OD2" Residue "A ASP 650": "OD1" <-> "OD2" Residue "A ASP 659": "OD1" <-> "OD2" Residue "A GLU 660": "OE1" <-> "OE2" Residue "A ARG 663": "NH1" <-> "NH2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A ASP 696": "OD1" <-> "OD2" Residue "A GLU 714": "OE1" <-> "OE2" Residue "A ARG 717": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 19690 Number of models: 1 Model: "" Number of chains: 11 Chain: "D" Number of atoms: 4130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4130 Classifications: {'peptide': 537} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 507} Chain breaks: 2 Chain: "E" Number of atoms: 3383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3383 Classifications: {'peptide': 442} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 23, 'TRANS': 415} Chain breaks: 1 Chain: "B" Number of atoms: 3897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3897 Classifications: {'peptide': 509} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 481} Chain: "C" Number of atoms: 4088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4088 Classifications: {'peptide': 532} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 27, 'TRANS': 500} Chain breaks: 2 Chain: "A" Number of atoms: 3770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3770 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 465} Chain breaks: 1 Chain: "H" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {'ADP': 2, 'BEF': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 66 Unusual residues: {'ADP': 2, 'BEF': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {'ADP': 2, 'BEF': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {'ADP': 2, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 10.48, per 1000 atoms: 0.53 Number of scatterers: 19690 At special positions: 0 Unit cell: (146.05, 129.95, 104.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 87 16.00 P 20 15.00 F 24 9.00 O 3833 8.00 N 3446 7.00 C 12272 6.00 Be 8 4.00 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=25, symmetry=0 Number of additional bonds: simple=25, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.85 Conformation dependent library (CDL) restraints added in 3.4 seconds 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4680 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 113 helices and 14 sheets defined 33.7% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.96 Creating SS restraints... Processing helix chain 'D' and resid 223 through 235 removed outlier: 3.692A pdb=" N MET D 229 " --> pdb=" O GLN D 225 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL D 230 " --> pdb=" O ILE D 226 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 263 through 272 removed outlier: 3.920A pdb=" N ASN D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR D 272 " --> pdb=" O VAL D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 removed outlier: 3.562A pdb=" N PHE D 300 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU D 302 " --> pdb=" O LYS D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 340 removed outlier: 3.577A pdb=" N VAL D 335 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU D 339 " --> pdb=" O VAL D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 362 No H-bonds generated for 'chain 'D' and resid 360 through 362' Processing helix chain 'D' and resid 387 through 391 removed outlier: 3.559A pdb=" N LEU D 391 " --> pdb=" O ARG D 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 387 through 391' Processing helix chain 'D' and resid 419 through 435 Processing helix chain 'D' and resid 459 through 466 Processing helix chain 'D' and resid 472 through 474 No H-bonds generated for 'chain 'D' and resid 472 through 474' Processing helix chain 'D' and resid 493 through 503 removed outlier: 3.855A pdb=" N GLU D 498 " --> pdb=" O GLU D 494 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR D 502 " --> pdb=" O GLU D 498 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL D 503 " --> pdb=" O LEU D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 508 No H-bonds generated for 'chain 'D' and resid 505 through 508' Processing helix chain 'D' and resid 511 through 516 removed outlier: 3.591A pdb=" N PHE D 516 " --> pdb=" O GLN D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 540 Processing helix chain 'D' and resid 567 through 577 removed outlier: 3.579A pdb=" N ILE D 572 " --> pdb=" O ASN D 568 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE D 573 " --> pdb=" O ILE D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 591 No H-bonds generated for 'chain 'D' and resid 589 through 591' Processing helix chain 'D' and resid 609 through 618 removed outlier: 3.618A pdb=" N MET D 618 " --> pdb=" O LEU D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 669 Processing helix chain 'D' and resid 683 through 688 Processing helix chain 'D' and resid 694 through 697 No H-bonds generated for 'chain 'D' and resid 694 through 697' Processing helix chain 'D' and resid 702 through 707 Processing helix chain 'D' and resid 710 through 715 removed outlier: 3.875A pdb=" N GLU D 714 " --> pdb=" O LYS D 710 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA D 715 " --> pdb=" O ASP D 711 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 710 through 715' Processing helix chain 'D' and resid 771 through 774 No H-bonds generated for 'chain 'D' and resid 771 through 774' Processing helix chain 'E' and resid 221 through 227 removed outlier: 3.587A pdb=" N ILE E 226 " --> pdb=" O GLN E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 235 Processing helix chain 'E' and resid 237 through 240 No H-bonds generated for 'chain 'E' and resid 237 through 240' Processing helix chain 'E' and resid 262 through 272 removed outlier: 3.854A pdb=" N ALA E 267 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL E 268 " --> pdb=" O MET E 264 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR E 272 " --> pdb=" O VAL E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 284 No H-bonds generated for 'chain 'E' and resid 281 through 284' Processing helix chain 'E' and resid 291 through 293 No H-bonds generated for 'chain 'E' and resid 291 through 293' Processing helix chain 'E' and resid 297 through 305 removed outlier: 3.816A pdb=" N LYS E 305 " --> pdb=" O GLU E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 334 removed outlier: 3.691A pdb=" N VAL E 334 " --> pdb=" O VAL E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 341 removed outlier: 3.572A pdb=" N LEU E 341 " --> pdb=" O GLN E 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 337 through 341' Processing helix chain 'E' and resid 387 through 394 removed outlier: 3.662A pdb=" N ILE E 393 " --> pdb=" O GLU E 389 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS E 394 " --> pdb=" O VAL E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 412 Processing helix chain 'E' and resid 420 through 435 removed outlier: 3.882A pdb=" N SER E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN E 432 " --> pdb=" O ALA E 428 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE E 433 " --> pdb=" O ALA E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 467 removed outlier: 3.622A pdb=" N ALA E 465 " --> pdb=" O ASN E 461 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY E 467 " --> pdb=" O ARG E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 474 No H-bonds generated for 'chain 'E' and resid 472 through 474' Processing helix chain 'E' and resid 493 through 502 removed outlier: 3.782A pdb=" N GLU E 497 " --> pdb=" O ASP E 493 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLU E 498 " --> pdb=" O GLU E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 508 No H-bonds generated for 'chain 'E' and resid 505 through 508' Processing helix chain 'E' and resid 510 through 516 removed outlier: 3.678A pdb=" N THR E 514 " --> pdb=" O PRO E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 544 removed outlier: 4.245A pdb=" N ALA E 542 " --> pdb=" O ALA E 538 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU E 544 " --> pdb=" O ALA E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 578 removed outlier: 4.417A pdb=" N ILE E 572 " --> pdb=" O ASN E 568 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE E 573 " --> pdb=" O ILE E 569 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS E 575 " --> pdb=" O ASP E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 591 No H-bonds generated for 'chain 'E' and resid 589 through 591' Processing helix chain 'E' and resid 609 through 615 Processing helix chain 'E' and resid 641 through 644 No H-bonds generated for 'chain 'E' and resid 641 through 644' Processing helix chain 'E' and resid 660 through 663 No H-bonds generated for 'chain 'E' and resid 660 through 663' Processing helix chain 'B' and resid 220 through 227 removed outlier: 4.050A pdb=" N ALA B 224 " --> pdb=" O ARG B 220 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLN B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 226 " --> pdb=" O GLN B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 263 through 267 Processing helix chain 'B' and resid 292 through 305 removed outlier: 3.794A pdb=" N ARG B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 344 removed outlier: 3.532A pdb=" N LEU B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU B 339 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 365 through 367 No H-bonds generated for 'chain 'B' and resid 365 through 367' Processing helix chain 'B' and resid 388 through 394 removed outlier: 3.623A pdb=" N ILE B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 412 removed outlier: 4.087A pdb=" N ALA B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA B 411 " --> pdb=" O GLU B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 435 Processing helix chain 'B' and resid 459 through 465 Processing helix chain 'B' and resid 472 through 474 No H-bonds generated for 'chain 'B' and resid 472 through 474' Processing helix chain 'B' and resid 496 through 508 removed outlier: 3.521A pdb=" N THR B 502 " --> pdb=" O GLU B 498 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR B 505 " --> pdb=" O GLU B 501 " (cutoff:3.500A) Proline residue: B 506 - end of helix Processing helix chain 'B' and resid 512 through 516 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 564 through 578 removed outlier: 4.182A pdb=" N ILE B 569 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 570 " --> pdb=" O GLU B 566 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 572 " --> pdb=" O ASN B 568 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE B 573 " --> pdb=" O ILE B 569 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA B 576 " --> pdb=" O ILE B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 591 No H-bonds generated for 'chain 'B' and resid 589 through 591' Processing helix chain 'B' and resid 594 through 596 No H-bonds generated for 'chain 'B' and resid 594 through 596' Processing helix chain 'B' and resid 607 through 619 removed outlier: 3.713A pdb=" N VAL B 611 " --> pdb=" O SER B 607 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN B 612 " --> pdb=" O ASP B 608 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU B 617 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET B 618 " --> pdb=" O LEU B 614 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASP B 619 " --> pdb=" O LEU B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 670 removed outlier: 3.681A pdb=" N LEU B 664 " --> pdb=" O GLU B 660 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER B 665 " --> pdb=" O ASN B 661 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 666 " --> pdb=" O ALA B 662 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 667 " --> pdb=" O ARG B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 688 Processing helix chain 'B' and resid 694 through 715 removed outlier: 3.654A pdb=" N LEU B 698 " --> pdb=" O GLY B 694 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 709 " --> pdb=" O ALA B 705 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP B 711 " --> pdb=" O TYR B 707 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER B 712 " --> pdb=" O ALA B 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 230 removed outlier: 4.435A pdb=" N MET C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL C 230 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 235 No H-bonds generated for 'chain 'C' and resid 232 through 235' Processing helix chain 'C' and resid 264 through 269 removed outlier: 3.922A pdb=" N VAL C 268 " --> pdb=" O MET C 264 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA C 269 " --> pdb=" O ALA C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 269' Processing helix chain 'C' and resid 291 through 305 removed outlier: 4.120A pdb=" N ASN C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU C 296 " --> pdb=" O SER C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 331 through 337 Processing helix chain 'C' and resid 365 through 367 No H-bonds generated for 'chain 'C' and resid 365 through 367' Processing helix chain 'C' and resid 389 through 393 removed outlier: 3.640A pdb=" N ILE C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 389 through 393' Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 420 through 436 removed outlier: 3.712A pdb=" N CYS C 425 " --> pdb=" O ILE C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 465 No H-bonds generated for 'chain 'C' and resid 462 through 465' Processing helix chain 'C' and resid 475 through 477 No H-bonds generated for 'chain 'C' and resid 475 through 477' Processing helix chain 'C' and resid 493 through 508 removed outlier: 3.636A pdb=" N GLU C 497 " --> pdb=" O ASP C 493 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR C 502 " --> pdb=" O GLU C 498 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL C 503 " --> pdb=" O LEU C 499 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR C 505 " --> pdb=" O GLU C 501 " (cutoff:3.500A) Proline residue: C 506 - end of helix Processing helix chain 'C' and resid 511 through 516 removed outlier: 3.627A pdb=" N PHE C 516 " --> pdb=" O GLN C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 543 No H-bonds generated for 'chain 'C' and resid 540 through 543' Processing helix chain 'C' and resid 564 through 578 removed outlier: 4.842A pdb=" N ILE C 569 " --> pdb=" O SER C 565 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE C 572 " --> pdb=" O ASN C 568 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE C 573 " --> pdb=" O ILE C 569 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP C 574 " --> pdb=" O ARG C 570 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS C 575 " --> pdb=" O ASP C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 591 No H-bonds generated for 'chain 'C' and resid 589 through 591' Processing helix chain 'C' and resid 609 through 618 Processing helix chain 'C' and resid 668 through 671 No H-bonds generated for 'chain 'C' and resid 668 through 671' Processing helix chain 'C' and resid 683 through 687 Processing helix chain 'C' and resid 696 through 710 removed outlier: 3.570A pdb=" N VAL C 701 " --> pdb=" O LEU C 697 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA C 705 " --> pdb=" O VAL C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 759 Processing helix chain 'C' and resid 771 through 777 removed outlier: 3.802A pdb=" N ARG C 775 " --> pdb=" O ASP C 771 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG C 776 " --> pdb=" O ALA C 772 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR C 777 " --> pdb=" O GLU C 773 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 771 through 777' Processing helix chain 'A' and resid 220 through 223 No H-bonds generated for 'chain 'A' and resid 220 through 223' Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 263 through 271 removed outlier: 3.918A pdb=" N ALA A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 294 through 305 removed outlier: 3.776A pdb=" N PHE A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU A 304 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 337 through 344 removed outlier: 3.730A pdb=" N ASP A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 387 through 392 removed outlier: 3.992A pdb=" N LEU A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 412 Processing helix chain 'A' and resid 421 through 435 removed outlier: 3.860A pdb=" N CYS A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 429 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET A 430 " --> pdb=" O SER A 426 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU A 435 " --> pdb=" O GLN A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 466 removed outlier: 3.809A pdb=" N ALA A 465 " --> pdb=" O ASN A 461 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 508 removed outlier: 3.615A pdb=" N LEU A 499 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) Proline residue: A 506 - end of helix Processing helix chain 'A' and resid 511 through 516 Processing helix chain 'A' and resid 536 through 543 removed outlier: 3.526A pdb=" N ALA A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 542 " --> pdb=" O ALA A 538 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR A 543 " --> pdb=" O LYS A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 556 No H-bonds generated for 'chain 'A' and resid 554 through 556' Processing helix chain 'A' and resid 564 through 579 removed outlier: 4.005A pdb=" N ILE A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE A 573 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 576 " --> pdb=" O ILE A 572 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA A 578 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ALA A 579 " --> pdb=" O LYS A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 593 No H-bonds generated for 'chain 'A' and resid 590 through 593' Processing helix chain 'A' and resid 610 through 617 removed outlier: 3.637A pdb=" N LEU A 614 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 615 " --> pdb=" O VAL A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 663 through 670 removed outlier: 3.563A pdb=" N GLN A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 688 removed outlier: 3.548A pdb=" N ALA A 688 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 715 removed outlier: 3.528A pdb=" N ILE A 700 " --> pdb=" O ASP A 696 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 708 " --> pdb=" O ALA A 704 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP A 711 " --> pdb=" O TYR A 707 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER A 712 " --> pdb=" O ALA A 708 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 713 " --> pdb=" O ILE A 709 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'D' and resid 377 through 379 removed outlier: 3.656A pdb=" N VAL D 377 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N VAL D 251 " --> pdb=" O VAL D 351 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL D 353 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N MET D 253 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ALA D 355 " --> pdb=" O MET D 253 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N GLY D 255 " --> pdb=" O ALA D 355 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA D 309 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ILE D 354 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE D 311 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ALA D 356 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE D 313 " --> pdb=" O ALA D 356 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N PHE D 275 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE D 312 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE D 277 " --> pdb=" O PHE D 312 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ASP D 314 " --> pdb=" O PHE D 277 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE D 279 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 548 through 552 removed outlier: 4.120A pdb=" N ASP D 587 " --> pdb=" O VAL D 552 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 353 through 357 removed outlier: 3.967A pdb=" N GLY E 255 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR E 254 " --> pdb=" O VAL E 377 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 548 through 551 removed outlier: 7.514A pdb=" N LEU E 525 " --> pdb=" O ASP E 650 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU E 652 " --> pdb=" O LEU E 525 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TYR E 527 " --> pdb=" O LEU E 652 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TYR E 654 " --> pdb=" O TYR E 527 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 250 through 253 removed outlier: 6.723A pdb=" N VAL B 353 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N MET B 253 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA B 355 " --> pdb=" O MET B 253 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 275 through 279 Processing sheet with id= G, first strand: chain 'B' and resid 651 through 655 removed outlier: 3.854A pdb=" N LEU B 525 " --> pdb=" O GLN B 651 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B 653 " --> pdb=" O LEU B 525 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 527 " --> pdb=" O ILE B 653 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 655 " --> pdb=" O TYR B 527 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY B 528 " --> pdb=" O THR B 633 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE B 628 " --> pdb=" O THR B 582 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ASN B 548 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N PHE B 585 " --> pdb=" O ASN B 548 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE B 550 " --> pdb=" O PHE B 585 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ASP B 587 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL B 552 " --> pdb=" O ASP B 587 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 252 through 254 removed outlier: 3.727A pdb=" N VAL C 377 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 275 through 280 removed outlier: 6.887A pdb=" N VAL C 352 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ILE C 313 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE C 354 " --> pdb=" O ILE C 313 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 651 through 653 removed outlier: 8.299A pdb=" N VAL C 524 " --> pdb=" O VAL C 627 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL C 629 " --> pdb=" O VAL C 524 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N PHE C 526 " --> pdb=" O VAL C 629 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY C 631 " --> pdb=" O PHE C 526 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR C 582 " --> pdb=" O PHE C 628 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ILE C 630 " --> pdb=" O THR C 582 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL C 584 " --> pdb=" O ILE C 630 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ALA C 632 " --> pdb=" O VAL C 584 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU C 586 " --> pdb=" O ALA C 632 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASN C 548 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE C 585 " --> pdb=" O ASN C 548 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE C 550 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ASP C 587 " --> pdb=" O ILE C 550 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C 552 " --> pdb=" O ASP C 587 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 354 through 356 removed outlier: 7.102A pdb=" N VAL A 251 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG A 375 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N TYR A 254 " --> pdb=" O ARG A 375 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 377 " --> pdb=" O TYR A 254 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'A' and resid 309 through 311 removed outlier: 4.054A pdb=" N VAL A 352 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 311 " --> pdb=" O VAL A 352 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'A' and resid 630 through 632 removed outlier: 7.034A pdb=" N VAL A 524 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLN A 651 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N TYR A 527 " --> pdb=" O GLN A 651 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE A 653 " --> pdb=" O TYR A 527 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'A' and resid 548 through 551 319 hydrogen bonds defined for protein. 951 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: 5.18 Time building geometry restraints manager: 8.34 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: 6480 1.34 - 1.46: 3683 1.46 - 1.58: 9656 1.58 - 1.70: 31 1.70 - 1.83: 164 Bond restraints: 20014 Sorted by residual: bond pdb=" C4 ADP E 902 " pdb=" C5 ADP E 902 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C4 ADP E 901 " pdb=" C5 ADP E 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C4 ADP A 901 " pdb=" C5 ADP A 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C4 ADP C 902 " pdb=" C5 ADP C 902 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C4 ADP D 904 " pdb=" C5 ADP D 904 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 ... (remaining 20009 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.95: 614 105.95 - 113.37: 10879 113.37 - 120.79: 9120 120.79 - 128.21: 6380 128.21 - 135.63: 121 Bond angle restraints: 27114 Sorted by residual: angle pdb=" N GLY D 290 " pdb=" CA GLY D 290 " pdb=" C GLY D 290 " ideal model delta sigma weight residual 111.95 105.09 6.86 9.50e-01 1.11e+00 5.21e+01 angle pdb=" CA GLY D 290 " pdb=" C GLY D 290 " pdb=" O GLY D 290 " ideal model delta sigma weight residual 122.22 118.82 3.40 6.50e-01 2.37e+00 2.74e+01 angle pdb=" N VAL A 541 " pdb=" CA VAL A 541 " pdb=" C VAL A 541 " ideal model delta sigma weight residual 112.83 107.65 5.18 9.90e-01 1.02e+00 2.74e+01 angle pdb=" C ALA E 593 " pdb=" N LYS E 594 " pdb=" CA LYS E 594 " ideal model delta sigma weight residual 121.54 131.51 -9.97 1.91e+00 2.74e-01 2.73e+01 angle pdb=" N GLU B 283 " pdb=" CA GLU B 283 " pdb=" C GLU B 283 " ideal model delta sigma weight residual 114.75 108.37 6.38 1.26e+00 6.30e-01 2.57e+01 ... (remaining 27109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.21: 11978 35.21 - 70.42: 242 70.42 - 105.63: 28 105.63 - 140.84: 10 140.84 - 176.05: 7 Dihedral angle restraints: 12265 sinusoidal: 5006 harmonic: 7259 Sorted by residual: dihedral pdb=" CA ALA A 580 " pdb=" C ALA A 580 " pdb=" N PRO A 581 " pdb=" CA PRO A 581 " ideal model delta harmonic sigma weight residual 180.00 133.21 46.79 0 5.00e+00 4.00e-02 8.76e+01 dihedral pdb=" C2' ADP D 904 " pdb=" C1' ADP D 904 " pdb=" N9 ADP D 904 " pdb=" C4 ADP D 904 " ideal model delta sinusoidal sigma weight residual 91.55 -92.40 -176.05 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C2' ADP E 901 " pdb=" C1' ADP E 901 " pdb=" N9 ADP E 901 " pdb=" C4 ADP E 901 " ideal model delta sinusoidal sigma weight residual 91.55 -94.04 -174.41 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 12262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2426 0.060 - 0.120: 524 0.120 - 0.180: 94 0.180 - 0.240: 11 0.240 - 0.300: 6 Chirality restraints: 3061 Sorted by residual: chirality pdb=" CA ALA H 17 " pdb=" N ALA H 17 " pdb=" C ALA H 17 " pdb=" CB ALA H 17 " both_signs ideal model delta sigma weight residual False 2.48 2.19 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB THR A 477 " pdb=" CA THR A 477 " pdb=" OG1 THR A 477 " pdb=" CG2 THR A 477 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB VAL D 417 " pdb=" CA VAL D 417 " pdb=" CG1 VAL D 417 " pdb=" CG2 VAL D 417 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 3058 not shown) Planarity restraints: 3543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA H 11 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.78e+00 pdb=" C ALA H 11 " -0.051 2.00e-02 2.50e+03 pdb=" O ALA H 11 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA H 12 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 677 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.42e+00 pdb=" N PRO D 678 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO D 678 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 678 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 677 " 0.045 5.00e-02 4.00e+02 6.75e-02 7.30e+00 pdb=" N PRO B 678 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 678 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 678 " 0.037 5.00e-02 4.00e+02 ... (remaining 3540 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.98: 7 1.98 - 2.71: 662 2.71 - 3.44: 27242 3.44 - 4.17: 45485 4.17 - 4.90: 78314 Nonbonded interactions: 151710 Sorted by model distance: nonbonded pdb=" CG2 THR C 535 " pdb=" F2 BEF C 904 " model vdw 1.245 3.410 nonbonded pdb=" F1 BEF B 903 " pdb=" O3B ADP B 905 " model vdw 1.271 2.390 nonbonded pdb=" BE BEF B 903 " pdb=" O3B ADP B 905 " model vdw 1.604 2.420 nonbonded pdb=" CB ALA E 289 " pdb=" CB ALA H 15 " model vdw 1.634 3.880 nonbonded pdb=" CG2 THR C 535 " pdb=" BE BEF C 904 " model vdw 1.696 2.840 ... (remaining 151705 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 209 through 436 or resid 457 through 670)) selection = (chain 'B' and (resid 209 through 436 or resid 457 through 670)) selection = (chain 'C' and (resid 209 through 436 or resid 457 through 670)) selection = (chain 'D' and (resid 209 through 436 or resid 457 through 670)) selection = (chain 'E' and resid 209 through 670) } 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: 0.700 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: 3.830 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 50.500 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 20014 Z= 0.391 Angle : 1.073 15.418 27114 Z= 0.527 Chirality : 0.053 0.300 3061 Planarity : 0.006 0.073 3543 Dihedral : 16.243 176.048 7585 Min Nonbonded Distance : 1.245 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.72 % Favored : 92.08 % Rotamer: Outliers : 0.34 % Allowed : 7.85 % Favored : 91.81 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % 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: -5.58 (0.12), residues: 2513 helix: -5.04 (0.04), residues: 881 sheet: -1.68 (0.31), residues: 235 loop : -3.22 (0.13), residues: 1397 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 484 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 488 average time/residue: 0.3559 time to fit residues: 252.4981 Evaluate side-chains 291 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 289 time to evaluate : 2.164 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1684 time to fit residues: 3.6862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 211 optimal weight: 0.9990 chunk 190 optimal weight: 0.0010 chunk 105 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 128 optimal weight: 0.3980 chunk 101 optimal weight: 3.9990 chunk 196 optimal weight: 8.9990 chunk 76 optimal weight: 0.7980 chunk 119 optimal weight: 7.9990 chunk 146 optimal weight: 0.7980 chunk 227 optimal weight: 0.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 280 ASN D 295 ASN ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 431 GLN ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 612 ASN ** D 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 690 GLN D 782 GLN D 783 GLN ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN E 432 GLN E 612 ASN B 225 GLN B 670 GLN C 280 ASN C 337 GLN ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN C 512 GLN C 638 GLN C 702 GLN C 757 HIS ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 461 ASN A 568 ASN A 622 ASN A 690 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20014 Z= 0.184 Angle : 0.735 9.993 27114 Z= 0.335 Chirality : 0.046 0.275 3061 Planarity : 0.005 0.052 3543 Dihedral : 12.866 175.200 2848 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.32 % Favored : 92.56 % Rotamer: Outliers : 2.14 % Allowed : 16.37 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % 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: -4.41 (0.13), residues: 2513 helix: -3.70 (0.11), residues: 861 sheet: -1.36 (0.31), residues: 255 loop : -2.77 (0.14), residues: 1397 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 321 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 20 residues processed: 351 average time/residue: 0.3255 time to fit residues: 175.6708 Evaluate side-chains 289 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 269 time to evaluate : 2.171 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 20 outliers final: 1 residues processed: 20 average time/residue: 0.1802 time to fit residues: 9.6988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 189 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 228 optimal weight: 0.2980 chunk 246 optimal weight: 9.9990 chunk 203 optimal weight: 6.9990 chunk 226 optimal weight: 5.9990 chunk 77 optimal weight: 0.2980 chunk 183 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 613 GLN B 222 GLN C 350 ASN ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 782 GLN ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20014 Z= 0.197 Angle : 0.695 9.291 27114 Z= 0.319 Chirality : 0.044 0.167 3061 Planarity : 0.004 0.049 3543 Dihedral : 12.342 173.533 2848 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.60 % Favored : 92.28 % Rotamer: Outliers : 2.63 % Allowed : 17.20 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % 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: -3.46 (0.15), residues: 2513 helix: -2.58 (0.14), residues: 885 sheet: -1.23 (0.31), residues: 265 loop : -2.34 (0.16), residues: 1363 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 301 time to evaluate : 2.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 25 residues processed: 336 average time/residue: 0.3164 time to fit residues: 163.8156 Evaluate side-chains 285 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 260 time to evaluate : 2.160 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1901 time to fit residues: 11.6764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 225 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 0.0670 chunk 108 optimal weight: 0.6980 chunk 153 optimal weight: 0.0370 chunk 229 optimal weight: 9.9990 chunk 242 optimal weight: 0.0040 chunk 119 optimal weight: 0.7980 chunk 217 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 overall best weight: 0.3208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN C 782 GLN ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 20014 Z= 0.150 Angle : 0.670 11.010 27114 Z= 0.300 Chirality : 0.043 0.160 3061 Planarity : 0.004 0.044 3543 Dihedral : 12.071 168.856 2848 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.96 % Favored : 92.88 % Rotamer: Outliers : 1.17 % Allowed : 19.49 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.15), residues: 2513 helix: -1.86 (0.16), residues: 876 sheet: -0.68 (0.33), residues: 244 loop : -2.22 (0.16), residues: 1393 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 290 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 300 average time/residue: 0.2996 time to fit residues: 141.3628 Evaluate side-chains 275 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 261 time to evaluate : 2.208 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1735 time to fit residues: 7.6556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 202 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 3 optimal weight: 0.0980 chunk 180 optimal weight: 0.0970 chunk 100 optimal weight: 7.9990 chunk 207 optimal weight: 0.0060 chunk 167 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 217 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 306 ASN ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20014 Z= 0.159 Angle : 0.671 9.227 27114 Z= 0.300 Chirality : 0.044 0.156 3061 Planarity : 0.004 0.045 3543 Dihedral : 11.863 174.099 2848 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.44 % Favored : 92.52 % Rotamer: Outliers : 1.66 % Allowed : 20.22 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.16), residues: 2513 helix: -1.41 (0.17), residues: 890 sheet: -0.73 (0.32), residues: 266 loop : -2.09 (0.16), residues: 1357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 269 time to evaluate : 2.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 16 residues processed: 293 average time/residue: 0.3156 time to fit residues: 144.1595 Evaluate side-chains 271 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 255 time to evaluate : 2.167 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1944 time to fit residues: 9.0150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 81 optimal weight: 0.0570 chunk 218 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 242 optimal weight: 0.4980 chunk 201 optimal weight: 0.0270 chunk 112 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 127 optimal weight: 0.0980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20014 Z= 0.159 Angle : 0.694 10.921 27114 Z= 0.308 Chirality : 0.043 0.152 3061 Planarity : 0.004 0.065 3543 Dihedral : 11.840 177.493 2848 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.44 % Favored : 92.48 % Rotamer: Outliers : 1.32 % Allowed : 20.76 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.16), residues: 2513 helix: -1.09 (0.17), residues: 895 sheet: -0.41 (0.33), residues: 251 loop : -2.02 (0.16), residues: 1367 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 271 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 11 residues processed: 288 average time/residue: 0.2952 time to fit residues: 134.1615 Evaluate side-chains 260 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 249 time to evaluate : 2.252 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1784 time to fit residues: 6.7945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 234 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 204 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 chunk 241 optimal weight: 0.8980 chunk 151 optimal weight: 0.0970 chunk 147 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20014 Z= 0.169 Angle : 0.694 12.065 27114 Z= 0.310 Chirality : 0.044 0.154 3061 Planarity : 0.004 0.054 3543 Dihedral : 11.731 167.775 2848 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.68 % Favored : 92.28 % Rotamer: Outliers : 0.78 % Allowed : 22.03 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.17), residues: 2513 helix: -0.85 (0.18), residues: 910 sheet: -0.38 (0.33), residues: 246 loop : -1.93 (0.16), residues: 1357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 271 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 282 average time/residue: 0.3058 time to fit residues: 135.6458 Evaluate side-chains 260 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 251 time to evaluate : 2.335 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2097 time to fit residues: 6.7521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 149 optimal weight: 0.0770 chunk 96 optimal weight: 0.0020 chunk 144 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 164 optimal weight: 0.2980 chunk 119 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 190 optimal weight: 0.0470 overall best weight: 0.2244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 432 GLN ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20014 Z= 0.158 Angle : 0.705 12.060 27114 Z= 0.315 Chirality : 0.044 0.171 3061 Planarity : 0.004 0.058 3543 Dihedral : 11.595 162.131 2848 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.16 % Favored : 92.80 % Rotamer: Outliers : 0.68 % Allowed : 22.22 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % 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: -1.92 (0.17), residues: 2513 helix: -0.71 (0.18), residues: 896 sheet: -0.37 (0.33), residues: 248 loop : -1.87 (0.16), residues: 1369 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 263 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 268 average time/residue: 0.3018 time to fit residues: 128.0138 Evaluate side-chains 252 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 248 time to evaluate : 2.181 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2612 time to fit residues: 4.7906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 220 optimal weight: 7.9990 chunk 231 optimal weight: 9.9990 chunk 211 optimal weight: 7.9990 chunk 225 optimal weight: 0.3980 chunk 135 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 203 optimal weight: 10.0000 chunk 213 optimal weight: 4.9990 chunk 224 optimal weight: 0.0970 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 GLN ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 782 GLN A 236 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20014 Z= 0.220 Angle : 0.768 15.427 27114 Z= 0.346 Chirality : 0.046 0.309 3061 Planarity : 0.004 0.052 3543 Dihedral : 11.639 165.404 2848 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.83 % Favored : 91.13 % Rotamer: Outliers : 0.54 % Allowed : 22.61 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % 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: -1.74 (0.17), residues: 2513 helix: -0.50 (0.18), residues: 905 sheet: -0.69 (0.31), residues: 268 loop : -1.73 (0.17), residues: 1340 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 276 time to evaluate : 2.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 281 average time/residue: 0.3130 time to fit residues: 137.3597 Evaluate side-chains 253 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 248 time to evaluate : 2.075 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2115 time to fit residues: 5.2784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 148 optimal weight: 0.0570 chunk 238 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 165 optimal weight: 0.7980 chunk 250 optimal weight: 20.0000 chunk 230 optimal weight: 7.9990 chunk 199 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.5576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20014 Z= 0.184 Angle : 0.753 13.127 27114 Z= 0.339 Chirality : 0.045 0.183 3061 Planarity : 0.004 0.073 3543 Dihedral : 11.528 167.705 2848 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.96 % Favored : 93.00 % Rotamer: Outliers : 0.24 % Allowed : 23.49 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % 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: -1.63 (0.17), residues: 2513 helix: -0.44 (0.18), residues: 892 sheet: -0.43 (0.32), residues: 251 loop : -1.67 (0.17), residues: 1370 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 250 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 252 average time/residue: 0.3073 time to fit residues: 122.4663 Evaluate side-chains 235 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 233 time to evaluate : 2.214 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1824 time to fit residues: 3.6098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 158 optimal weight: 5.9990 chunk 212 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 183 optimal weight: 0.0980 chunk 29 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 204 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 394 HIS ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 ASN ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.131189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.103310 restraints weight = 48054.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.106140 restraints weight = 26956.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.107969 restraints weight = 18639.512| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.6256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20014 Z= 0.240 Angle : 0.789 13.314 27114 Z= 0.358 Chirality : 0.046 0.172 3061 Planarity : 0.005 0.149 3543 Dihedral : 11.639 174.560 2848 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.95 % Favored : 91.01 % Rotamer: Outliers : 0.44 % Allowed : 24.07 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % 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: -1.64 (0.17), residues: 2513 helix: -0.51 (0.18), residues: 909 sheet: -0.60 (0.31), residues: 271 loop : -1.61 (0.18), residues: 1333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4029.57 seconds wall clock time: 75 minutes 49.70 seconds (4549.70 seconds total)