Starting phenix.real_space_refine on Mon Mar 18 02:39:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oab_20000/03_2024/6oab_20000_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oab_20000/03_2024/6oab_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_20000/03_2024/6oab_20000.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oab_20000/03_2024/6oab_20000.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oab_20000/03_2024/6oab_20000_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oab_20000/03_2024/6oab_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-dev-5265/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: 10.45, 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: 8.03 Conformation dependent library (CDL) restraints added in 3.8 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: 4.12 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: 5.32 Time building geometry restraints manager: 8.65 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: 0.530 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: 0.010 Extract box with map and model: 3.860 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 51.940 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.220 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 561 HIS 0.004 0.001 HIS C 236 PHE 0.017 0.001 PHE C 462 TYR 0.016 0.001 TYR C 416 ARG 0.005 0.000 ARG E 645 *********************** 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 : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 213 TYR cc_start: 0.8131 (m-10) cc_final: 0.7847 (m-10) REVERT: D 343 ASP cc_start: 0.7048 (p0) cc_final: 0.6787 (p0) REVERT: D 513 TYR cc_start: 0.8574 (m-80) cc_final: 0.8335 (m-10) REVERT: E 225 GLN cc_start: 0.8357 (tm-30) cc_final: 0.7037 (tm-30) REVERT: E 430 MET cc_start: 0.8782 (tmm) cc_final: 0.8261 (tmm) REVERT: E 505 TYR cc_start: 0.7539 (m-10) cc_final: 0.7017 (m-80) REVERT: E 522 LYS cc_start: 0.8087 (tppt) cc_final: 0.7820 (tttt) REVERT: B 231 GLU cc_start: 0.6679 (mm-30) cc_final: 0.6458 (mp0) REVERT: B 402 ASP cc_start: 0.6673 (p0) cc_final: 0.6065 (p0) REVERT: B 470 ASN cc_start: 0.6366 (p0) cc_final: 0.5656 (p0) REVERT: B 649 LEU cc_start: 0.6861 (mt) cc_final: 0.6322 (mp) REVERT: C 264 MET cc_start: 0.7548 (tpp) cc_final: 0.7043 (tpt) REVERT: C 618 MET cc_start: 0.8233 (mmt) cc_final: 0.7914 (mmm) REVERT: A 232 LEU cc_start: 0.6832 (tp) cc_final: 0.6256 (mt) REVERT: A 345 MET cc_start: 0.7636 (mmp) cc_final: 0.7380 (mmm) REVERT: A 407 GLU cc_start: 0.7652 (tp30) cc_final: 0.7266 (pm20) REVERT: A 427 GLU cc_start: 0.7093 (tp30) cc_final: 0.6409 (tm-30) REVERT: A 459 MET cc_start: 0.6657 (tpt) cc_final: 0.5792 (tpp) REVERT: A 463 ARG cc_start: 0.8356 (mmp80) cc_final: 0.7380 (mmt180) REVERT: A 557 LEU cc_start: 0.8093 (tp) cc_final: 0.7841 (tp) REVERT: A 564 GLU cc_start: 0.8500 (mp0) cc_final: 0.8231 (mp0) REVERT: A 587 ASP cc_start: 0.6411 (t0) cc_final: 0.5156 (t70) REVERT: A 659 ASP cc_start: 0.6544 (p0) cc_final: 0.5501 (p0) outliers start: 7 outliers final: 2 residues processed: 488 average time/residue: 0.3554 time to fit residues: 250.9552 Evaluate side-chains 300 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 298 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain C residue 655 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 211 optimal weight: 3.9990 chunk 190 optimal weight: 0.0000 chunk 105 optimal weight: 7.9990 chunk 64 optimal weight: 0.0370 chunk 128 optimal weight: 0.6980 chunk 101 optimal weight: 0.1980 chunk 196 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 227 optimal weight: 0.3980 overall best weight: 0.2662 ------------------------------------------------------------------------------- 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 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 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: 0.6874 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20014 Z= 0.175 Angle : 0.727 10.176 27114 Z= 0.330 Chirality : 0.046 0.284 3061 Planarity : 0.005 0.051 3543 Dihedral : 12.861 176.267 2850 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.04 % Favored : 92.84 % Rotamer: Outliers : 2.05 % Allowed : 16.18 % Favored : 81.77 % 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: -4.45 (0.13), residues: 2513 helix: -3.71 (0.11), residues: 864 sheet: -1.36 (0.30), residues: 256 loop : -2.81 (0.14), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 486 HIS 0.023 0.001 HIS C 394 PHE 0.026 0.001 PHE A 549 TYR 0.017 0.001 TYR A 254 ARG 0.008 0.000 ARG A 372 *********************** 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 367 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 325 time to evaluate : 2.200 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: D 213 TYR cc_start: 0.8113 (m-10) cc_final: 0.7899 (m-10) REVERT: D 214 ASP cc_start: 0.8246 (p0) cc_final: 0.8006 (p0) REVERT: D 470 ASN cc_start: 0.6126 (t0) cc_final: 0.5894 (t0) REVERT: D 513 TYR cc_start: 0.8621 (m-80) cc_final: 0.8353 (m-10) REVERT: D 762 MET cc_start: 0.4997 (mmp) cc_final: 0.4538 (ptp) REVERT: E 430 MET cc_start: 0.9004 (tmm) cc_final: 0.8516 (tmm) REVERT: E 522 LYS cc_start: 0.8050 (tppt) cc_final: 0.7740 (mtmt) REVERT: B 288 MET cc_start: 0.7887 (mmt) cc_final: 0.7527 (mmm) REVERT: B 402 ASP cc_start: 0.6852 (p0) cc_final: 0.6271 (p0) REVERT: B 439 LEU cc_start: 0.3643 (OUTLIER) cc_final: 0.3188 (tp) REVERT: B 470 ASN cc_start: 0.6815 (p0) cc_final: 0.6438 (p0) REVERT: B 621 MET cc_start: 0.6506 (mmm) cc_final: 0.5714 (mmm) REVERT: B 649 LEU cc_start: 0.7046 (mt) cc_final: 0.6437 (mp) REVERT: C 264 MET cc_start: 0.7535 (tpp) cc_final: 0.7002 (tpt) REVERT: C 370 PHE cc_start: 0.7795 (t80) cc_final: 0.7573 (t80) REVERT: C 459 MET cc_start: 0.7635 (mmm) cc_final: 0.7295 (tpp) REVERT: A 232 LEU cc_start: 0.6770 (tp) cc_final: 0.6148 (mt) REVERT: A 271 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: A 288 MET cc_start: 0.4418 (mpp) cc_final: 0.3153 (tmm) REVERT: A 427 GLU cc_start: 0.7043 (tp30) cc_final: 0.6747 (pt0) REVERT: A 459 MET cc_start: 0.7014 (tpt) cc_final: 0.6656 (tpp) REVERT: A 557 LEU cc_start: 0.8178 (tp) cc_final: 0.7948 (tp) REVERT: A 558 LEU cc_start: 0.8093 (tp) cc_final: 0.7644 (tp) REVERT: A 564 GLU cc_start: 0.8560 (mp0) cc_final: 0.8334 (mp0) REVERT: A 585 PHE cc_start: 0.7349 (t80) cc_final: 0.7147 (t80) REVERT: A 659 ASP cc_start: 0.5646 (p0) cc_final: 0.5190 (p0) outliers start: 42 outliers final: 21 residues processed: 354 average time/residue: 0.3217 time to fit residues: 175.2403 Evaluate side-chains 310 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 287 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 464 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 126 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 189 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 228 optimal weight: 5.9990 chunk 246 optimal weight: 8.9990 chunk 203 optimal weight: 5.9990 chunk 226 optimal weight: 0.9990 chunk 77 optimal weight: 0.1980 chunk 183 optimal weight: 1.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- 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 613 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 ASN C 782 GLN ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 20014 Z= 0.249 Angle : 0.729 9.906 27114 Z= 0.339 Chirality : 0.046 0.180 3061 Planarity : 0.005 0.050 3543 Dihedral : 12.382 169.941 2850 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.72 % Favored : 92.12 % Rotamer: Outliers : 3.46 % Allowed : 16.76 % Favored : 79.78 % 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: -3.47 (0.15), residues: 2513 helix: -2.64 (0.14), residues: 912 sheet: -1.06 (0.32), residues: 250 loop : -2.30 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 486 HIS 0.022 0.001 HIS C 394 PHE 0.014 0.002 PHE A 549 TYR 0.024 0.002 TYR C 254 ARG 0.012 0.001 ARG A 463 *********************** 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 386 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 315 time to evaluate : 2.221 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: D 214 ASP cc_start: 0.8277 (p0) cc_final: 0.8075 (p0) REVERT: D 253 MET cc_start: 0.7387 (pmm) cc_final: 0.7044 (ptp) REVERT: D 513 TYR cc_start: 0.8745 (m-80) cc_final: 0.8462 (m-10) REVERT: D 762 MET cc_start: 0.5103 (mmp) cc_final: 0.4492 (ptp) REVERT: E 359 ARG cc_start: 0.6720 (mtm-85) cc_final: 0.6276 (ptt-90) REVERT: E 430 MET cc_start: 0.8854 (tmm) cc_final: 0.8361 (tmm) REVERT: E 560 MET cc_start: 0.6852 (mmm) cc_final: 0.6615 (mmm) REVERT: E 572 ILE cc_start: 0.8622 (tp) cc_final: 0.8364 (tp) REVERT: B 387 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.4647 (ttm170) REVERT: B 402 ASP cc_start: 0.7067 (p0) cc_final: 0.6490 (p0) REVERT: B 424 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9051 (tp) REVERT: B 439 LEU cc_start: 0.3650 (OUTLIER) cc_final: 0.3411 (tp) REVERT: B 470 ASN cc_start: 0.7201 (p0) cc_final: 0.6872 (p0) REVERT: B 621 MET cc_start: 0.6796 (mmm) cc_final: 0.6132 (mmm) REVERT: C 301 GLU cc_start: 0.8434 (pp20) cc_final: 0.8212 (pp20) REVERT: C 459 MET cc_start: 0.7894 (mmm) cc_final: 0.7394 (tpp) REVERT: A 232 LEU cc_start: 0.6790 (tp) cc_final: 0.6252 (mt) REVERT: A 253 MET cc_start: 0.2721 (ppp) cc_final: 0.2449 (ppp) REVERT: A 264 MET cc_start: 0.7307 (mmm) cc_final: 0.7079 (mmm) REVERT: A 403 ASP cc_start: 0.7171 (p0) cc_final: 0.6955 (p0) REVERT: A 427 GLU cc_start: 0.7318 (tp30) cc_final: 0.6812 (pt0) REVERT: A 527 TYR cc_start: 0.6689 (p90) cc_final: 0.6211 (p90) REVERT: A 537 LEU cc_start: 0.8111 (tp) cc_final: 0.7603 (mt) REVERT: A 659 ASP cc_start: 0.6232 (p0) cc_final: 0.5633 (p0) outliers start: 71 outliers final: 35 residues processed: 369 average time/residue: 0.3008 time to fit residues: 170.5119 Evaluate side-chains 302 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 264 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 488 ASP Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 495 ILE Chi-restraints excluded: chain E residue 587 ASP Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 387 ARG Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 460 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 225 optimal weight: 0.7980 chunk 171 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 229 optimal weight: 10.0000 chunk 242 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 217 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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** ** E 225 GLN ** 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: 0.7395 moved from start: 0.4263 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= 0.201 Angle : 0.710 13.157 27114 Z= 0.320 Chirality : 0.045 0.334 3061 Planarity : 0.004 0.045 3543 Dihedral : 12.109 177.808 2848 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.08 % Favored : 92.76 % Rotamer: Outliers : 2.73 % Allowed : 19.54 % Favored : 77.73 % 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: -2.82 (0.16), residues: 2513 helix: -1.80 (0.16), residues: 897 sheet: -1.06 (0.29), residues: 284 loop : -2.11 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 486 HIS 0.005 0.001 HIS C 394 PHE 0.016 0.001 PHE D 275 TYR 0.016 0.001 TYR B 254 ARG 0.006 0.000 ARG E 227 *********************** 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 338 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 282 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 280 ASN cc_start: 0.7458 (m-40) cc_final: 0.6778 (m-40) REVERT: D 316 ILE cc_start: 0.7932 (mm) cc_final: 0.7507 (mm) REVERT: D 513 TYR cc_start: 0.8770 (m-80) cc_final: 0.8415 (m-10) REVERT: D 590 ASP cc_start: 0.6305 (t0) cc_final: 0.6001 (t0) REVERT: D 762 MET cc_start: 0.5236 (mmp) cc_final: 0.4963 (ptp) REVERT: E 430 MET cc_start: 0.8916 (tmm) cc_final: 0.8452 (tmm) REVERT: E 572 ILE cc_start: 0.8598 (tp) cc_final: 0.8323 (tp) REVERT: E 574 ASP cc_start: 0.8457 (p0) cc_final: 0.8252 (p0) REVERT: B 364 ASP cc_start: 0.6360 (OUTLIER) cc_final: 0.5990 (t0) REVERT: B 387 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.4769 (ttm170) REVERT: B 402 ASP cc_start: 0.6987 (p0) cc_final: 0.6444 (p0) REVERT: B 439 LEU cc_start: 0.3543 (OUTLIER) cc_final: 0.3061 (tp) REVERT: C 301 GLU cc_start: 0.8404 (pp20) cc_final: 0.8189 (pp20) REVERT: C 498 GLU cc_start: 0.7852 (tp30) cc_final: 0.7589 (tp30) REVERT: C 618 MET cc_start: 0.8515 (mmt) cc_final: 0.8291 (mmm) REVERT: A 288 MET cc_start: 0.4604 (mpp) cc_final: 0.3275 (tmm) REVERT: A 427 GLU cc_start: 0.7347 (tp30) cc_final: 0.6852 (pt0) REVERT: A 430 MET cc_start: 0.8330 (mmm) cc_final: 0.7824 (mmm) REVERT: A 459 MET cc_start: 0.7076 (tpt) cc_final: 0.6869 (tpp) REVERT: A 659 ASP cc_start: 0.6449 (p0) cc_final: 0.5666 (p0) REVERT: A 660 GLU cc_start: 0.6377 (pm20) cc_final: 0.5979 (pm20) outliers start: 56 outliers final: 33 residues processed: 324 average time/residue: 0.3008 time to fit residues: 152.3151 Evaluate side-chains 284 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 248 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 488 ASP Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 548 ASN Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 387 ARG Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 468 ASN Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 753 ILE Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 532 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 202 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 3 optimal weight: 0.4980 chunk 180 optimal weight: 0.0050 chunk 100 optimal weight: 0.0270 chunk 207 optimal weight: 0.0970 chunk 167 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 217 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 overall best weight: 0.3252 ------------------------------------------------------------------------------- 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** B 414 HIS ** 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: 0.7364 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 20014 Z= 0.162 Angle : 0.695 13.295 27114 Z= 0.310 Chirality : 0.045 0.316 3061 Planarity : 0.004 0.046 3543 Dihedral : 11.969 173.409 2848 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.36 % Favored : 92.56 % Rotamer: Outliers : 3.36 % Allowed : 20.03 % Favored : 76.61 % 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: -2.51 (0.16), residues: 2513 helix: -1.39 (0.17), residues: 905 sheet: -0.86 (0.30), residues: 280 loop : -2.06 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 486 HIS 0.003 0.000 HIS C 394 PHE 0.014 0.001 PHE A 549 TYR 0.019 0.001 TYR A 254 ARG 0.004 0.000 ARG D 672 *********************** 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 341 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 272 time to evaluate : 2.315 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: D 215 ASP cc_start: 0.8050 (m-30) cc_final: 0.7462 (t0) REVERT: D 264 MET cc_start: 0.7060 (mtt) cc_final: 0.6792 (mtt) REVERT: D 283 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6940 (mt-10) REVERT: D 513 TYR cc_start: 0.8751 (m-80) cc_final: 0.8385 (m-10) REVERT: D 590 ASP cc_start: 0.6340 (t0) cc_final: 0.6037 (t0) REVERT: D 762 MET cc_start: 0.5198 (mmp) cc_final: 0.4970 (ptp) REVERT: E 225 GLN cc_start: 0.8315 (pp30) cc_final: 0.7533 (pp30) REVERT: E 229 MET cc_start: 0.8635 (tmm) cc_final: 0.8358 (tmm) REVERT: E 430 MET cc_start: 0.8903 (tmm) cc_final: 0.8439 (tmm) REVERT: E 572 ILE cc_start: 0.8533 (tp) cc_final: 0.8260 (tp) REVERT: B 293 GLU cc_start: 0.7225 (mp0) cc_final: 0.6105 (mp0) REVERT: B 387 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.4651 (ttm170) REVERT: B 402 ASP cc_start: 0.6884 (p0) cc_final: 0.6341 (p0) REVERT: B 439 LEU cc_start: 0.3386 (OUTLIER) cc_final: 0.2926 (tp) REVERT: B 557 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8677 (pp) REVERT: C 301 GLU cc_start: 0.8391 (pp20) cc_final: 0.8148 (pp20) REVERT: C 618 MET cc_start: 0.8410 (mmt) cc_final: 0.8172 (mmm) REVERT: A 271 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: A 288 MET cc_start: 0.4686 (mpp) cc_final: 0.3328 (tmm) REVERT: A 427 GLU cc_start: 0.7432 (tp30) cc_final: 0.6982 (pt0) REVERT: A 430 MET cc_start: 0.8318 (mmm) cc_final: 0.7863 (mmm) REVERT: A 659 ASP cc_start: 0.6449 (p0) cc_final: 0.5578 (p0) REVERT: A 660 GLU cc_start: 0.6321 (pm20) cc_final: 0.5939 (pm20) outliers start: 69 outliers final: 44 residues processed: 323 average time/residue: 0.2849 time to fit residues: 145.1829 Evaluate side-chains 300 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 252 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 488 ASP Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 548 ASN Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 670 GLN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 387 ARG Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 532 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 81 optimal weight: 3.9990 chunk 218 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 242 optimal weight: 0.6980 chunk 201 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 127 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** C 432 GLN ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.4776 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= 0.167 Angle : 0.682 13.337 27114 Z= 0.306 Chirality : 0.044 0.314 3061 Planarity : 0.004 0.056 3543 Dihedral : 11.870 161.951 2848 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.80 % Favored : 92.16 % Rotamer: Outliers : 3.12 % Allowed : 20.71 % Favored : 76.17 % 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: -2.17 (0.16), residues: 2513 helix: -0.97 (0.17), residues: 910 sheet: -0.73 (0.31), residues: 280 loop : -1.95 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 486 HIS 0.003 0.000 HIS D 757 PHE 0.012 0.001 PHE E 549 TYR 0.014 0.001 TYR A 254 ARG 0.008 0.000 ARG D 775 *********************** 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 330 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 266 time to evaluate : 2.229 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: D 215 ASP cc_start: 0.7950 (m-30) cc_final: 0.7444 (t0) REVERT: D 280 ASN cc_start: 0.7047 (m-40) cc_final: 0.5788 (m-40) REVERT: D 513 TYR cc_start: 0.8755 (m-80) cc_final: 0.8402 (m-10) REVERT: D 560 MET cc_start: 0.7777 (ptp) cc_final: 0.7227 (ptp) REVERT: D 590 ASP cc_start: 0.6381 (t0) cc_final: 0.6154 (t0) REVERT: E 225 GLN cc_start: 0.8341 (pp30) cc_final: 0.7673 (pp30) REVERT: E 229 MET cc_start: 0.8657 (tmm) cc_final: 0.8312 (tmm) REVERT: E 430 MET cc_start: 0.8877 (tmm) cc_final: 0.8446 (tmm) REVERT: E 572 ILE cc_start: 0.8495 (tp) cc_final: 0.8234 (tp) REVERT: E 621 MET cc_start: 0.8259 (tpp) cc_final: 0.8004 (mmt) REVERT: B 232 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8373 (mm) REVERT: B 293 GLU cc_start: 0.7393 (mp0) cc_final: 0.6251 (mp0) REVERT: B 387 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.4782 (ttm170) REVERT: B 402 ASP cc_start: 0.7029 (p0) cc_final: 0.6568 (p0) REVERT: B 439 LEU cc_start: 0.3523 (OUTLIER) cc_final: 0.2786 (tp) REVERT: C 301 GLU cc_start: 0.8410 (pp20) cc_final: 0.8154 (pp20) REVERT: C 618 MET cc_start: 0.8507 (mmt) cc_final: 0.8280 (mmm) REVERT: A 271 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: A 288 MET cc_start: 0.4656 (mpp) cc_final: 0.3454 (tmm) REVERT: A 427 GLU cc_start: 0.7357 (tp30) cc_final: 0.6894 (pt0) REVERT: A 430 MET cc_start: 0.8367 (mmm) cc_final: 0.7930 (mmm) REVERT: A 527 TYR cc_start: 0.7124 (p90) cc_final: 0.6845 (p90) REVERT: A 659 ASP cc_start: 0.6691 (p0) cc_final: 0.6025 (p0) outliers start: 64 outliers final: 41 residues processed: 315 average time/residue: 0.2807 time to fit residues: 140.8192 Evaluate side-chains 298 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 253 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 488 ASP Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 548 ASN Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 387 ARG Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 468 ASN Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 461 ASN Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 753 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 541 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 234 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 177 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 241 optimal weight: 0.0010 chunk 151 optimal weight: 0.5980 chunk 147 optimal weight: 0.5980 chunk 111 optimal weight: 10.0000 overall best weight: 1.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 394 HIS D 431 GLN ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 ASN D 651 GLN A 236 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.5984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20014 Z= 0.271 Angle : 0.788 15.851 27114 Z= 0.362 Chirality : 0.047 0.354 3061 Planarity : 0.005 0.078 3543 Dihedral : 12.002 171.057 2848 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.15 % Favored : 90.81 % Rotamer: Outliers : 3.70 % Allowed : 22.03 % Favored : 74.27 % 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: -2.09 (0.17), residues: 2513 helix: -0.91 (0.17), residues: 941 sheet: -0.86 (0.30), residues: 292 loop : -1.87 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 486 HIS 0.016 0.001 HIS C 394 PHE 0.015 0.001 PHE D 758 TYR 0.037 0.002 TYR A 505 ARG 0.008 0.001 ARG D 775 *********************** 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 342 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 266 time to evaluate : 2.414 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: D 215 ASP cc_start: 0.7966 (m-30) cc_final: 0.7509 (t0) REVERT: D 216 ILE cc_start: 0.8599 (tp) cc_final: 0.8167 (tp) REVERT: D 513 TYR cc_start: 0.8809 (m-80) cc_final: 0.8482 (m-10) REVERT: D 615 LEU cc_start: 0.9147 (mt) cc_final: 0.8812 (mp) REVERT: E 222 GLN cc_start: 0.8549 (mp10) cc_final: 0.8211 (mp10) REVERT: E 229 MET cc_start: 0.8882 (tmm) cc_final: 0.8493 (tmm) REVERT: E 316 ILE cc_start: 0.6804 (OUTLIER) cc_final: 0.6439 (mt) REVERT: E 430 MET cc_start: 0.8946 (tmm) cc_final: 0.8469 (tmm) REVERT: E 572 ILE cc_start: 0.8574 (tp) cc_final: 0.8271 (tp) REVERT: E 621 MET cc_start: 0.8367 (tpp) cc_final: 0.8066 (mmt) REVERT: B 231 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7022 (mt-10) REVERT: B 232 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8448 (mm) REVERT: B 293 GLU cc_start: 0.8071 (mp0) cc_final: 0.6850 (mp0) REVERT: B 387 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.4860 (ttm170) REVERT: B 402 ASP cc_start: 0.7063 (p0) cc_final: 0.6734 (p0) REVERT: B 495 ILE cc_start: 0.8150 (mt) cc_final: 0.7932 (mt) REVERT: C 301 GLU cc_start: 0.8433 (pp20) cc_final: 0.8175 (pp20) REVERT: C 560 MET cc_start: 0.8591 (ppp) cc_final: 0.8075 (ppp) REVERT: C 766 LYS cc_start: 0.7853 (mmtt) cc_final: 0.7112 (mmtt) REVERT: A 271 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.6763 (mp0) REVERT: A 288 MET cc_start: 0.4773 (mpp) cc_final: 0.3704 (tmm) REVERT: A 430 MET cc_start: 0.8579 (mmm) cc_final: 0.8135 (mmm) REVERT: A 659 ASP cc_start: 0.7216 (p0) cc_final: 0.6540 (p0) outliers start: 76 outliers final: 43 residues processed: 321 average time/residue: 0.3069 time to fit residues: 153.5718 Evaluate side-chains 285 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 238 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 624 LYS Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 316 ILE Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 488 ASP Chi-restraints excluded: chain E residue 548 ASN Chi-restraints excluded: chain E residue 587 ASP Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 387 ARG Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 468 ASN Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 461 ASN Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 753 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 541 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 149 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 144 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 153 optimal weight: 0.0870 chunk 164 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 190 optimal weight: 2.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- 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 432 GLN B 414 HIS A 236 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.6524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20014 Z= 0.249 Angle : 0.772 16.481 27114 Z= 0.351 Chirality : 0.046 0.337 3061 Planarity : 0.004 0.076 3543 Dihedral : 12.263 176.702 2848 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.76 % Favored : 92.16 % Rotamer: Outliers : 3.02 % Allowed : 22.86 % Favored : 74.12 % 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: -1.92 (0.17), residues: 2513 helix: -0.76 (0.17), residues: 926 sheet: -0.76 (0.31), residues: 272 loop : -1.76 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 486 HIS 0.028 0.001 HIS C 394 PHE 0.016 0.001 PHE E 277 TYR 0.028 0.001 TYR A 505 ARG 0.007 0.000 ARG D 775 *********************** 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 317 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 255 time to evaluate : 2.403 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: D 215 ASP cc_start: 0.8143 (m-30) cc_final: 0.7516 (t0) REVERT: D 216 ILE cc_start: 0.8672 (tp) cc_final: 0.8155 (tp) REVERT: D 345 MET cc_start: 0.6438 (tpp) cc_final: 0.6181 (mmt) REVERT: D 513 TYR cc_start: 0.8835 (m-80) cc_final: 0.8454 (m-10) REVERT: D 615 LEU cc_start: 0.9180 (mt) cc_final: 0.8854 (mp) REVERT: E 222 GLN cc_start: 0.8532 (mp10) cc_final: 0.8312 (mp10) REVERT: E 229 MET cc_start: 0.8851 (tmm) cc_final: 0.8435 (tmm) REVERT: E 249 ARG cc_start: 0.7800 (mmp80) cc_final: 0.7579 (mmp80) REVERT: E 430 MET cc_start: 0.8965 (tmm) cc_final: 0.8467 (tmm) REVERT: E 572 ILE cc_start: 0.8516 (tp) cc_final: 0.8249 (tp) REVERT: E 621 MET cc_start: 0.8394 (tpp) cc_final: 0.8130 (mmt) REVERT: B 231 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7203 (mt-10) REVERT: B 232 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8473 (mm) REVERT: B 293 GLU cc_start: 0.8195 (mp0) cc_final: 0.6967 (mp0) REVERT: B 387 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.4986 (ttm170) REVERT: B 402 ASP cc_start: 0.6949 (p0) cc_final: 0.6668 (p0) REVERT: C 288 MET cc_start: 0.8002 (mmm) cc_final: 0.7739 (mmm) REVERT: C 301 GLU cc_start: 0.8339 (pp20) cc_final: 0.8069 (pp20) REVERT: C 345 MET cc_start: 0.7588 (tpp) cc_final: 0.7330 (tpt) REVERT: C 460 ASP cc_start: 0.8057 (p0) cc_final: 0.7839 (p0) REVERT: C 560 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8141 (ppp) REVERT: A 288 MET cc_start: 0.4801 (mpp) cc_final: 0.3862 (tmm) REVERT: A 430 MET cc_start: 0.8736 (mmm) cc_final: 0.8274 (mmm) REVERT: A 574 ASP cc_start: 0.7321 (t0) cc_final: 0.6970 (m-30) REVERT: A 659 ASP cc_start: 0.7344 (p0) cc_final: 0.6551 (p0) outliers start: 62 outliers final: 41 residues processed: 304 average time/residue: 0.3074 time to fit residues: 144.5616 Evaluate side-chains 281 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 237 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 624 LYS Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 488 ASP Chi-restraints excluded: chain E residue 548 ASN Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 387 ARG Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 468 ASN Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 461 ASN Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 560 MET Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 753 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 545 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 220 optimal weight: 8.9990 chunk 231 optimal weight: 0.9980 chunk 211 optimal weight: 0.0040 chunk 225 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 177 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 203 optimal weight: 9.9990 chunk 213 optimal weight: 10.0000 chunk 224 optimal weight: 1.9990 overall best weight: 1.7596 ------------------------------------------------------------------------------- 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** B 414 HIS A 236 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.6953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20014 Z= 0.251 Angle : 0.785 19.557 27114 Z= 0.358 Chirality : 0.046 0.339 3061 Planarity : 0.004 0.058 3543 Dihedral : 12.346 178.896 2848 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.87 % Favored : 91.05 % Rotamer: Outliers : 2.83 % Allowed : 23.44 % Favored : 73.73 % 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: -1.87 (0.17), residues: 2513 helix: -0.74 (0.17), residues: 927 sheet: -0.71 (0.30), residues: 272 loop : -1.73 (0.18), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 486 HIS 0.017 0.001 HIS C 394 PHE 0.015 0.001 PHE E 312 TYR 0.024 0.001 TYR A 505 ARG 0.009 0.000 ARG B 249 *********************** 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 309 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 251 time to evaluate : 2.099 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: D 215 ASP cc_start: 0.8204 (m-30) cc_final: 0.7608 (t0) REVERT: D 216 ILE cc_start: 0.8725 (tp) cc_final: 0.8227 (tp) REVERT: D 345 MET cc_start: 0.6446 (tpp) cc_final: 0.6151 (mmt) REVERT: D 513 TYR cc_start: 0.8841 (m-80) cc_final: 0.8462 (m-10) REVERT: D 615 LEU cc_start: 0.9177 (mt) cc_final: 0.8887 (mp) REVERT: E 222 GLN cc_start: 0.8585 (mp10) cc_final: 0.8237 (mp10) REVERT: E 229 MET cc_start: 0.8899 (tmm) cc_final: 0.8406 (tmm) REVERT: E 430 MET cc_start: 0.8993 (tmm) cc_final: 0.8504 (tmm) REVERT: E 459 MET cc_start: 0.7457 (tpp) cc_final: 0.6906 (tpp) REVERT: E 572 ILE cc_start: 0.8553 (tp) cc_final: 0.8268 (tp) REVERT: E 621 MET cc_start: 0.8391 (tpp) cc_final: 0.8143 (mmt) REVERT: B 293 GLU cc_start: 0.8356 (mp0) cc_final: 0.7208 (mp0) REVERT: B 387 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.5069 (ttm170) REVERT: B 402 ASP cc_start: 0.6848 (p0) cc_final: 0.6583 (p0) REVERT: B 430 MET cc_start: 0.8883 (mmm) cc_final: 0.8660 (mmm) REVERT: C 288 MET cc_start: 0.8013 (mmm) cc_final: 0.7751 (mmm) REVERT: C 301 GLU cc_start: 0.8264 (pp20) cc_final: 0.8019 (pp20) REVERT: C 560 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8259 (ptm) REVERT: C 766 LYS cc_start: 0.7901 (mmtt) cc_final: 0.7133 (mmtt) REVERT: A 223 MET cc_start: 0.3944 (mmm) cc_final: 0.3738 (tpt) REVERT: A 288 MET cc_start: 0.4880 (mpp) cc_final: 0.4274 (tmm) REVERT: A 430 MET cc_start: 0.8798 (mmm) cc_final: 0.8354 (mmm) REVERT: A 527 TYR cc_start: 0.7914 (p90) cc_final: 0.7634 (p90) REVERT: A 574 ASP cc_start: 0.7200 (t0) cc_final: 0.6849 (m-30) REVERT: A 659 ASP cc_start: 0.7500 (p0) cc_final: 0.6824 (p0) outliers start: 58 outliers final: 45 residues processed: 293 average time/residue: 0.2983 time to fit residues: 134.9167 Evaluate side-chains 283 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 236 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 488 ASP Chi-restraints excluded: chain E residue 548 ASN Chi-restraints excluded: chain E residue 587 ASP Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 387 ARG Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 468 ASN Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 461 ASN Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 560 MET Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 753 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 545 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 148 optimal weight: 4.9990 chunk 238 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 165 optimal weight: 0.0970 chunk 250 optimal weight: 20.0000 chunk 230 optimal weight: 0.0020 chunk 199 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 chunk 153 optimal weight: 0.7980 chunk 122 optimal weight: 0.3980 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 432 GLN D 461 ASN E 612 ASN B 414 HIS A 236 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.7010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20014 Z= 0.182 Angle : 0.756 15.261 27114 Z= 0.341 Chirality : 0.045 0.307 3061 Planarity : 0.004 0.064 3543 Dihedral : 12.236 179.499 2848 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.80 % Favored : 92.12 % Rotamer: Outliers : 2.14 % Allowed : 24.56 % Favored : 73.29 % 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: -1.76 (0.17), residues: 2513 helix: -0.62 (0.18), residues: 916 sheet: -0.64 (0.31), residues: 276 loop : -1.69 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 486 HIS 0.013 0.001 HIS C 394 PHE 0.013 0.001 PHE E 277 TYR 0.028 0.001 TYR A 505 ARG 0.009 0.000 ARG D 635 ********************** 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 304 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 260 time to evaluate : 2.400 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: D 215 ASP cc_start: 0.8040 (m-30) cc_final: 0.7554 (t0) REVERT: D 216 ILE cc_start: 0.8611 (tp) cc_final: 0.8328 (tp) REVERT: D 345 MET cc_start: 0.6522 (tpp) cc_final: 0.6251 (mmt) REVERT: D 513 TYR cc_start: 0.8746 (m-80) cc_final: 0.8297 (m-80) REVERT: D 615 LEU cc_start: 0.9115 (mt) cc_final: 0.8821 (mp) REVERT: D 616 THR cc_start: 0.9547 (t) cc_final: 0.9317 (m) REVERT: E 216 ILE cc_start: 0.6594 (pt) cc_final: 0.6391 (pt) REVERT: E 222 GLN cc_start: 0.8351 (mp10) cc_final: 0.7877 (mp10) REVERT: E 223 MET cc_start: 0.6418 (mpp) cc_final: 0.5433 (mmt) REVERT: E 229 MET cc_start: 0.8790 (tmm) cc_final: 0.8582 (tmm) REVERT: E 264 MET cc_start: 0.7828 (mmt) cc_final: 0.6942 (mmt) REVERT: E 430 MET cc_start: 0.9019 (tmm) cc_final: 0.8523 (tmm) REVERT: E 459 MET cc_start: 0.7394 (tpp) cc_final: 0.6966 (tpp) REVERT: E 572 ILE cc_start: 0.8585 (tp) cc_final: 0.8323 (tp) REVERT: E 621 MET cc_start: 0.8312 (tpp) cc_final: 0.8071 (mmt) REVERT: B 402 ASP cc_start: 0.7023 (p0) cc_final: 0.6732 (p0) REVERT: B 430 MET cc_start: 0.8891 (mmm) cc_final: 0.8456 (mmm) REVERT: C 249 ARG cc_start: 0.7403 (mmp80) cc_final: 0.6707 (mmp-170) REVERT: C 301 GLU cc_start: 0.8164 (pp20) cc_final: 0.7956 (pp20) REVERT: C 560 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8185 (ptm) REVERT: A 223 MET cc_start: 0.3886 (mmm) cc_final: 0.3622 (tpt) REVERT: A 288 MET cc_start: 0.4750 (mpp) cc_final: 0.4269 (tmm) REVERT: A 430 MET cc_start: 0.8767 (mmm) cc_final: 0.8275 (mmm) REVERT: A 527 TYR cc_start: 0.7908 (p90) cc_final: 0.7662 (p90) REVERT: A 574 ASP cc_start: 0.7147 (t0) cc_final: 0.6829 (m-30) REVERT: A 659 ASP cc_start: 0.7469 (p0) cc_final: 0.6792 (p0) outliers start: 44 outliers final: 35 residues processed: 290 average time/residue: 0.3018 time to fit residues: 135.8664 Evaluate side-chains 274 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 238 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 548 ASN Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 461 ASN Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 560 MET Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 753 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 545 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 158 optimal weight: 2.9990 chunk 212 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 199 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 204 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 HIS A 236 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.126241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.098660 restraints weight = 47092.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.101520 restraints weight = 25247.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.103325 restraints weight = 16940.680| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.7296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20014 Z= 0.210 Angle : 0.767 15.749 27114 Z= 0.345 Chirality : 0.046 0.319 3061 Planarity : 0.004 0.055 3543 Dihedral : 12.156 176.007 2848 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.87 % Favored : 91.05 % Rotamer: Outliers : 2.34 % Allowed : 25.10 % Favored : 72.56 % 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: -0.59 (0.17), residues: 925 sheet: -0.63 (0.31), residues: 269 loop : -1.68 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 486 HIS 0.012 0.001 HIS C 394 PHE 0.016 0.001 PHE E 277 TYR 0.027 0.001 TYR A 505 ARG 0.009 0.000 ARG D 249 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3995.28 seconds wall clock time: 74 minutes 6.29 seconds (4446.29 seconds total)