Starting phenix.real_space_refine (version: dev) on Thu Feb 23 06:28:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oaa_0666/02_2023/6oaa_0666_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oaa_0666/02_2023/6oaa_0666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oaa_0666/02_2023/6oaa_0666.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oaa_0666/02_2023/6oaa_0666.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oaa_0666/02_2023/6oaa_0666_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oaa_0666/02_2023/6oaa_0666_neut_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.092 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 Process input model Symmetric amino acids flipped Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 214": "OD1" <-> "OD2" 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 GLU 283": "OE1" <-> "OE2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "B PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 301": "OE1" <-> "OE2" Residue "B GLU 302": "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 331": "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 ARG 372": "NH1" <-> "NH2" Residue "B ASP 374": "OD1" <-> "OD2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B ASP 405": "OD1" <-> "OD2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B ASP 443": "OD1" <-> "OD2" Residue "B GLU 446": "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 480": "OE1" <-> "OE2" Residue "B ASP 493": "OD1" <-> "OD2" Residue "B TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 564": "OE1" <-> "OE2" Residue "B GLU 566": "OE1" <-> "OE2" Residue "B PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 587": "OD1" <-> "OD2" Residue "B ARG 596": "NH1" <-> "NH2" Residue "B ARG 648": "NH1" <-> "NH2" Residue "B ASP 696": "OD1" <-> "OD2" Residue "B ARG 703": "NH1" <-> "NH2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 717": "NH1" <-> "NH2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C ARG 220": "NH1" <-> "NH2" Residue "C ARG 227": "NH1" <-> "NH2" Residue "C ARG 266": "NH1" <-> "NH2" Residue "C PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "C PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 302": "OE1" <-> "OE2" 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 ARG 392": "NH1" <-> "NH2" Residue "C TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 434": "NH1" <-> "NH2" Residue "C ASP 460": "OD1" <-> "OD2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 487": "OD1" <-> "OD2" Residue "C ASP 493": "OD1" <-> "OD2" Residue "C GLU 504": "OE1" <-> "OE2" Residue "C PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 564": "OE1" <-> "OE2" Residue "C GLU 566": "OE1" <-> "OE2" Residue "C ASP 571": "OD1" <-> "OD2" Residue "C ARG 577": "NH1" <-> "NH2" Residue "C GLU 588": "OE1" <-> "OE2" Residue "C ARG 635": "NH1" <-> "NH2" Residue "C ASP 640": "OD1" <-> "OD2" Residue "C ARG 648": "NH1" <-> "NH2" Residue "C ARG 663": "NH1" <-> "NH2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 717": "NH1" <-> "NH2" Residue "C PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C ARG 776": "NH1" <-> "NH2" Residue "C TYR 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 220": "NH1" <-> "NH2" Residue "D ARG 227": "NH1" <-> "NH2" Residue "D TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 297": "NH1" <-> "NH2" Residue "D GLU 304": "OE1" <-> "OE2" Residue "D GLU 315": "OE1" <-> "OE2" Residue "D ASP 317": "OD1" <-> "OD2" Residue "D ASP 324": "OD1" <-> "OD2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D GLU 331": "OE1" <-> "OE2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 348": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D ARG 372": "NH1" <-> "NH2" Residue "D ASP 374": "OD1" <-> "OD2" Residue "D GLU 389": "OE1" <-> "OE2" Residue "D ARG 392": "NH1" <-> "NH2" Residue "D ASP 405": "OD1" <-> "OD2" Residue "D TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 434": "NH1" <-> "NH2" Residue "D GLU 435": "OE1" <-> "OE2" Residue "D PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 494": "OE1" <-> "OE2" Residue "D GLU 497": "OE1" <-> "OE2" Residue "D GLU 501": "OE1" <-> "OE2" Residue "D GLU 544": "OE1" <-> "OE2" Residue "D TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 564": "OE1" <-> "OE2" Residue "D ASP 571": "OD1" <-> "OD2" Residue "D PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 574": "OD1" <-> "OD2" Residue "D ASP 587": "OD1" <-> "OD2" Residue "D GLU 588": "OE1" <-> "OE2" Residue "D ARG 596": "NH1" <-> "NH2" Residue "D ASP 602": "OD1" <-> "OD2" Residue "D GLU 617": "OE1" <-> "OE2" Residue "D ARG 645": "NH1" <-> "NH2" Residue "D ARG 648": "NH1" <-> "NH2" Residue "D GLU 660": "OE1" <-> "OE2" Residue "D ASP 696": "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 GLU 773": "OE1" <-> "OE2" Residue "D ARG 776": "NH1" <-> "NH2" Residue "D ARG 788": "NH1" <-> "NH2" Residue "E ARG 220": "NH1" <-> "NH2" Residue "E TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 283": "OE1" <-> "OE2" Residue "E GLU 293": "OE1" <-> "OE2" Residue "E ARG 297": "NH1" <-> "NH2" Residue "E PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 301": "OE1" <-> "OE2" Residue "E ASP 317": "OD1" <-> "OD2" Residue "E ARG 323": "NH1" <-> "NH2" Residue "E GLU 329": "OE1" <-> "OE2" Residue "E GLU 331": "OE1" <-> "OE2" Residue "E ARG 332": "NH1" <-> "NH2" Residue "E ASP 343": "OD1" <-> "OD2" Residue "E ARG 348": "NH1" <-> "NH2" Residue "E ASP 364": "OD1" <-> "OD2" 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 ARG 392": "NH1" <-> "NH2" Residue "E GLU 407": "OE1" <-> "OE2" Residue "E TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 420": "OD1" <-> "OD2" Residue "E ARG 434": "NH1" <-> "NH2" Residue "E PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 494": "OE1" <-> "OE2" Residue "E GLU 504": "OE1" <-> "OE2" Residue "E ASP 511": "OD1" <-> "OD2" Residue "E PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 556": "OE1" <-> "OE2" Residue "E GLU 564": "OE1" <-> "OE2" Residue "E PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 574": "OD1" <-> "OD2" Residue "E ARG 577": "NH1" <-> "NH2" Residue "E PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 596": "NH1" <-> "NH2" Residue "E ASP 602": "OD1" <-> "OD2" Residue "E ARG 645": "NH1" <-> "NH2" Residue "E ARG 648": "NH1" <-> "NH2" Residue "E ASP 659": "OD1" <-> "OD2" Residue "E GLU 660": "OE1" <-> "OE2" Residue "G ASP 119": "OD1" <-> "OD2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G ASP 126": "OD1" <-> "OD2" Residue "G GLU 157": "OE1" <-> "OE2" Residue "G GLU 160": "OE1" <-> "OE2" Residue "G TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 203": "NH1" <-> "NH2" Residue "G PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 243": "OE1" <-> "OE2" Residue "G TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 271": "OD1" <-> "OD2" Residue "G GLU 282": "OE1" <-> "OE2" Residue "G ASP 291": "OD1" <-> "OD2" Residue "G ASP 294": "OD1" <-> "OD2" Residue "G ARG 312": "NH1" <-> "NH2" Residue "G ARG 321": "NH1" <-> "NH2" Residue "G PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 328": "OD1" <-> "OD2" Residue "G ASP 346": "OD1" <-> "OD2" Residue "G PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 364": "NH1" <-> "NH2" Residue "G GLU 373": "OE1" <-> "OE2" Residue "G PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 432": "NH1" <-> "NH2" Residue "G TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 460": "OD1" <-> "OD2" Residue "G PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 503": "OE1" <-> "OE2" Residue "G ASP 516": "OD1" <-> "OD2" Residue "G TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 549": "OE1" <-> "OE2" Residue "H PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 16": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 19546 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 3897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3897 Classifications: {'peptide': 509} Link IDs: {'PCIS': 1, 'PTRANS': 26, '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: "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: "G" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3432 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 407} Chain breaks: 2 Chain: "H" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "B" 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: "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: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Unusual residues: {'BEF': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 108 Unusual residues: {'ADP': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 10.14, per 1000 atoms: 0.52 Number of scatterers: 19546 At special positions: 0 Unit cell: (140.3, 128.8, 164.45, 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 16 15.00 F 18 9.00 O 3810 8.00 N 3381 7.00 C 12228 6.00 Be 6 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 Atom "HETATM19363 O3A ADP B 904 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=19, symmetry=0 Number of additional bonds: simple=19, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.89 Conformation dependent library (CDL) restraints added in 3.2 seconds 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4620 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 99 helices and 9 sheets defined 32.2% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'B' and resid 220 through 227 removed outlier: 4.457A pdb=" N GLN B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 235 No H-bonds generated for 'chain 'B' and resid 232 through 235' Processing helix chain 'B' and resid 262 through 271 removed outlier: 3.747A pdb=" N ARG B 266 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN B 270 " --> pdb=" O ARG B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 Processing helix chain 'B' and resid 330 through 344 removed outlier: 3.618A pdb=" N VAL B 334 " --> pdb=" O GLU B 331 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL B 335 " --> pdb=" O ARG B 332 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 338 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 339 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU B 341 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET B 342 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP B 343 " --> pdb=" O THR B 340 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY B 344 " --> pdb=" O LEU B 341 " (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 368 Processing helix chain 'B' and resid 387 through 394 removed outlier: 3.702A pdb=" N ILE B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 412 removed outlier: 3.742A pdb=" N ALA B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 435 removed outlier: 3.559A pdb=" N GLU B 427 " --> pdb=" O SER B 423 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN B 432 " --> pdb=" O ALA B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 467 Processing helix chain 'B' and resid 475 through 477 No H-bonds generated for 'chain 'B' and resid 475 through 477' Processing helix chain 'B' and resid 495 through 508 removed outlier: 3.600A pdb=" N THR B 502 " --> pdb=" O GLU B 498 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B 503 " --> pdb=" O LEU B 499 " (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 540 Processing helix chain 'B' and resid 564 through 567 No H-bonds generated for 'chain 'B' and resid 564 through 567' Processing helix chain 'B' and resid 572 through 578 Processing helix chain 'B' and resid 589 through 596 removed outlier: 3.852A pdb=" N ALA B 593 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N LYS B 594 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA B 595 " --> pdb=" O ILE B 592 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG B 596 " --> pdb=" O ALA B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 619 removed outlier: 3.549A pdb=" N GLN B 613 " --> pdb=" O ARG B 609 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 614 " --> pdb=" O VAL B 610 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR B 616 " --> pdb=" O ASN B 612 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 617 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET B 618 " --> pdb=" O LEU B 614 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP B 619 " --> pdb=" O LEU B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 670 removed outlier: 4.110A pdb=" N SER B 665 " --> pdb=" O ASN B 661 " (cutoff:3.500A) removed outlier: 3.506A 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: 3.715A pdb=" N LEU B 698 " --> pdb=" O GLY B 694 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 700 " --> pdb=" O ASP B 696 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER B 712 " --> pdb=" O ALA B 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 230 removed outlier: 3.803A pdb=" N GLN C 225 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE C 226 " --> pdb=" O GLN C 222 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N MET C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 3.612A 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 294 through 303 removed outlier: 3.702A pdb=" N ALA C 299 " --> pdb=" O ASN C 295 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 342 removed outlier: 3.570A pdb=" N VAL C 335 " --> pdb=" O GLU C 331 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR C 340 " --> pdb=" O SER C 336 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 368 Processing helix chain 'C' and resid 388 through 395 Processing helix chain 'C' and resid 406 through 411 removed outlier: 3.710A pdb=" N ALA C 411 " --> pdb=" O GLU C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 436 removed outlier: 3.620A pdb=" N CYS C 425 " --> pdb=" O ILE C 421 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA C 429 " --> pdb=" O CYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 465 Processing helix chain 'C' and resid 493 through 508 removed outlier: 3.552A pdb=" N THR C 502 " --> pdb=" O GLU C 498 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL C 503 " --> pdb=" O LEU C 499 " (cutoff:3.500A) removed outlier: 3.533A 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 510 through 516 removed outlier: 3.542A pdb=" N THR C 514 " --> pdb=" O PRO C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 541 No H-bonds generated for 'chain 'C' and resid 538 through 541' Processing helix chain 'C' and resid 564 through 578 removed outlier: 4.633A pdb=" N ILE C 569 " --> pdb=" O SER C 565 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG C 570 " --> pdb=" O GLU C 566 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 572 " --> pdb=" O ASN C 568 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP C 574 " --> pdb=" O ARG C 570 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS C 575 " --> pdb=" O ASP C 571 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C 576 " --> pdb=" O ILE C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 618 removed outlier: 3.691A pdb=" N LEU C 614 " --> pdb=" O VAL C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 671 removed outlier: 3.989A pdb=" N ASN C 668 " --> pdb=" O LEU C 664 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA C 669 " --> pdb=" O SER C 665 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 671 " --> pdb=" O LEU C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 687 Processing helix chain 'C' and resid 694 through 710 removed outlier: 3.724A pdb=" N ILE C 700 " --> pdb=" O ASP C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 759 Processing helix chain 'C' and resid 771 through 778 removed outlier: 3.565A pdb=" N ARG C 775 " --> pdb=" O ASP C 771 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG C 776 " --> pdb=" O ALA C 772 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR C 777 " --> pdb=" O GLU C 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 230 removed outlier: 3.765A pdb=" N GLN D 225 " --> pdb=" O LYS D 221 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE D 226 " --> pdb=" O GLN D 222 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET D 229 " --> pdb=" O GLN D 225 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL D 230 " --> pdb=" O ILE D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 235 No H-bonds generated for 'chain 'D' and resid 232 through 235' Processing helix chain 'D' and resid 264 through 267 No H-bonds generated for 'chain 'D' and resid 264 through 267' Processing helix chain 'D' and resid 294 through 301 Processing helix chain 'D' and resid 329 through 340 removed outlier: 3.821A pdb=" N ARG D 333 " --> pdb=" O GLU D 329 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL D 335 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 367 No H-bonds generated for 'chain 'D' and resid 365 through 367' Processing helix chain 'D' and resid 388 through 391 No H-bonds generated for 'chain 'D' and resid 388 through 391' Processing helix chain 'D' and resid 408 through 411 removed outlier: 3.682A pdb=" N ALA D 411 " --> pdb=" O ALA D 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 408 through 411' Processing helix chain 'D' and resid 419 through 435 removed outlier: 3.627A pdb=" N GLU D 435 " --> pdb=" O GLN D 431 " (cutoff:3.500A) 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: 3.557A pdb=" N THR D 502 " --> pdb=" O GLU D 498 " (cutoff:3.500A) removed outlier: 3.677A 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 Processing helix chain 'D' and resid 534 through 544 removed outlier: 3.897A pdb=" N ALA D 538 " --> pdb=" O LYS D 534 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS D 539 " --> pdb=" O THR D 535 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR D 543 " --> pdb=" O LYS D 539 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU D 544 " --> pdb=" O ALA D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 579 Processing helix chain 'D' and resid 589 through 593 Processing helix chain 'D' and resid 609 through 615 removed outlier: 3.687A pdb=" N LEU D 614 " --> pdb=" O VAL D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 638 No H-bonds generated for 'chain 'D' and resid 636 through 638' Processing helix chain 'D' and resid 662 through 670 removed outlier: 3.703A pdb=" N ILE D 666 " --> pdb=" O ALA D 662 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 667 " --> pdb=" O ARG D 663 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN D 668 " --> pdb=" O LEU D 664 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA D 669 " --> pdb=" O SER D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 688 removed outlier: 3.550A pdb=" N ALA D 688 " --> pdb=" O ALA D 684 " (cutoff:3.500A) 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 713 through 715 No H-bonds generated for 'chain 'D' and resid 713 through 715' Processing helix chain 'D' and resid 771 through 779 removed outlier: 3.885A pdb=" N ARG D 775 " --> pdb=" O ASP D 771 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG D 776 " --> pdb=" O ALA D 772 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR D 777 " --> pdb=" O GLU D 773 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D 779 " --> pdb=" O ARG D 775 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 227 Processing helix chain 'E' and resid 231 through 235 Processing helix chain 'E' and resid 262 through 272 removed outlier: 3.537A pdb=" N ARG E 266 " --> pdb=" O THR E 262 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA E 267 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 295 No H-bonds generated for 'chain 'E' and resid 292 through 295' Processing helix chain 'E' and resid 297 through 302 Processing helix chain 'E' and resid 329 through 342 removed outlier: 3.633A pdb=" N VAL E 334 " --> pdb=" O VAL E 330 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL E 335 " --> pdb=" O GLU E 331 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU E 341 " --> pdb=" O GLN E 337 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N MET E 342 " --> pdb=" O LEU E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 367 No H-bonds generated for 'chain 'E' and resid 365 through 367' Processing helix chain 'E' and resid 388 through 394 removed outlier: 3.507A pdb=" N ILE E 393 " --> pdb=" O GLU E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 412 removed outlier: 3.507A pdb=" N ALA E 411 " --> pdb=" O GLU E 407 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 435 removed outlier: 3.586A pdb=" N CYS E 425 " --> pdb=" O ILE E 421 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN E 432 " --> pdb=" O ALA E 428 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE E 433 " --> pdb=" O ALA E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 467 removed outlier: 3.968A pdb=" N GLY E 467 " --> pdb=" O ARG E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 493 through 502 removed outlier: 3.854A pdb=" N GLU E 497 " --> pdb=" O ASP E 493 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLU E 498 " --> pdb=" O GLU E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 516 removed outlier: 3.763A pdb=" N THR E 514 " --> pdb=" O PRO E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 534 through 544 removed outlier: 3.619A pdb=" N ALA E 538 " --> pdb=" O LYS E 534 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL E 541 " --> pdb=" O LEU E 537 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA E 542 " --> pdb=" O ALA E 538 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU E 544 " --> pdb=" O ALA E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 564 through 578 removed outlier: 4.448A pdb=" N ILE E 569 " --> pdb=" O SER E 565 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG E 570 " --> pdb=" O GLU E 566 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE E 572 " --> pdb=" O ASN E 568 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE E 573 " --> pdb=" O ILE E 569 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP E 574 " --> pdb=" O ARG E 570 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS E 575 " --> pdb=" O ASP E 571 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA E 576 " --> pdb=" O ILE E 572 " (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 616 Processing helix chain 'E' and resid 660 through 667 removed outlier: 3.544A pdb=" N LEU E 664 " --> pdb=" O GLU E 660 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER E 665 " --> pdb=" O ASN E 661 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE E 666 " --> pdb=" O ALA E 662 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 124 removed outlier: 3.747A pdb=" N LEU G 122 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU G 123 " --> pdb=" O ASP G 119 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS G 124 " --> pdb=" O GLU G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 159 No H-bonds generated for 'chain 'G' and resid 156 through 159' Processing helix chain 'G' and resid 170 through 175 removed outlier: 3.681A pdb=" N LYS G 175 " --> pdb=" O SER G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 219 No H-bonds generated for 'chain 'G' and resid 217 through 219' Processing helix chain 'G' and resid 242 through 255 removed outlier: 3.503A pdb=" N ALA G 251 " --> pdb=" O GLU G 247 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TRP G 252 " --> pdb=" O PHE G 248 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR G 255 " --> pdb=" O ALA G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 304 No H-bonds generated for 'chain 'G' and resid 301 through 304' Processing helix chain 'G' and resid 306 through 312 removed outlier: 3.709A pdb=" N ILE G 310 " --> pdb=" O GLU G 306 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP G 311 " --> pdb=" O MET G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 363 removed outlier: 3.871A pdb=" N ILE G 356 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N MET G 357 " --> pdb=" O LEU G 353 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS G 361 " --> pdb=" O MET G 357 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN G 362 " --> pdb=" O ALA G 358 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR G 363 " --> pdb=" O ALA G 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 501 through 507 removed outlier: 3.649A pdb=" N LYS G 505 " --> pdb=" O TYR G 501 " (cutoff:3.500A) Processing helix chain 'G' and resid 518 through 524 removed outlier: 3.733A pdb=" N GLU G 522 " --> pdb=" O ASN G 518 " (cutoff:3.500A) Processing helix chain 'G' and resid 527 through 535 removed outlier: 3.609A pdb=" N LEU G 531 " --> pdb=" O PHE G 527 " (cutoff:3.500A) Processing helix chain 'G' and resid 541 through 549 Processing helix chain 'G' and resid 557 through 564 removed outlier: 3.556A pdb=" N LEU G 561 " --> pdb=" O GLU G 557 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS G 562 " --> pdb=" O GLU G 558 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU G 563 " --> pdb=" O SER G 559 " (cutoff:3.500A) Processing helix chain 'G' and resid 567 through 578 removed outlier: 3.753A pdb=" N THR G 571 " --> pdb=" O ALA G 567 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU G 572 " --> pdb=" O GLY G 568 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL G 573 " --> pdb=" O TRP G 569 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU G 578 " --> pdb=" O MET G 574 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 29 Processing sheet with id= A, first strand: chain 'B' and resid 277 through 279 removed outlier: 4.023A pdb=" N PHE B 312 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA B 356 " --> pdb=" O ILE B 313 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 651 through 655 removed outlier: 3.620A pdb=" N LEU B 525 " --> pdb=" O GLN B 651 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR B 527 " --> pdb=" O ILE B 653 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 655 " --> pdb=" O TYR B 527 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 275 through 279 removed outlier: 6.738A pdb=" N VAL C 352 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE C 313 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE C 354 " --> pdb=" O ILE C 313 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 651 through 653 removed outlier: 3.679A pdb=" N ILE C 653 " --> pdb=" O LEU C 525 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR C 582 " --> pdb=" O PHE C 628 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE C 630 " --> pdb=" O THR C 582 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C 584 " --> pdb=" O ILE C 630 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N ALA C 632 " --> pdb=" O VAL C 584 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU C 586 " --> pdb=" O ALA C 632 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ASN C 548 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N PHE C 585 " --> pdb=" O ASN C 548 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE C 550 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASP C 587 " --> pdb=" O ILE C 550 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C 552 " --> pdb=" O ASP C 587 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 353 through 356 removed outlier: 3.515A pdb=" N MET D 253 " --> pdb=" O ALA D 355 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL D 377 " --> pdb=" O TYR D 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 524 through 526 removed outlier: 6.708A pdb=" N THR D 582 " --> pdb=" O PHE D 628 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ILE D 630 " --> pdb=" O THR D 582 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL D 584 " --> pdb=" O ILE D 630 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ALA D 632 " --> pdb=" O VAL D 584 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU D 586 " --> pdb=" O ALA D 632 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN D 548 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N PHE D 585 " --> pdb=" O ASN D 548 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE D 550 " --> pdb=" O PHE D 585 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ASP D 587 " --> pdb=" O ILE D 550 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL D 552 " --> pdb=" O ASP D 587 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 353 through 357 removed outlier: 3.526A pdb=" N VAL E 251 " --> pdb=" O VAL E 353 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ARG E 375 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N TYR E 254 " --> pdb=" O ARG E 375 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL E 377 " --> pdb=" O TYR E 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 651 through 654 removed outlier: 3.864A pdb=" N GLN E 651 " --> pdb=" O GLY E 523 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE E 653 " --> pdb=" O LEU E 525 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR E 527 " --> pdb=" O ILE E 653 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N VAL E 524 " --> pdb=" O VAL E 627 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL E 629 " --> pdb=" O VAL E 524 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N PHE E 526 " --> pdb=" O VAL E 629 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLY E 631 " --> pdb=" O PHE E 526 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR E 582 " --> pdb=" O PHE E 628 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ILE E 630 " --> pdb=" O THR E 582 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL E 584 " --> pdb=" O ILE E 630 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ALA E 632 " --> pdb=" O VAL E 584 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU E 586 " --> pdb=" O ALA E 632 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASN E 548 " --> pdb=" O VAL E 583 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N PHE E 585 " --> pdb=" O ASN E 548 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ILE E 550 " --> pdb=" O PHE E 585 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 236 through 238 removed outlier: 4.094A pdb=" N HIS G 236 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY G 276 " --> pdb=" O TYR G 270 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TYR G 264 " --> pdb=" O GLU G 282 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE G 284 " --> pdb=" O TYR G 262 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TYR G 262 " --> pdb=" O ILE G 284 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY G 323 " --> pdb=" O MET G 263 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLY G 265 " --> pdb=" O ARG G 321 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ARG G 321 " --> pdb=" O GLY G 265 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL G 382 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N PHE G 326 " --> pdb=" O VAL G 382 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N CYS G 384 " --> pdb=" O PHE G 326 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 930 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: 5.28 Time building geometry restraints manager: 7.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 3401 1.29 - 1.43: 4664 1.43 - 1.56: 11641 1.56 - 1.70: 26 1.70 - 1.83: 161 Bond restraints: 19893 Sorted by residual: bond pdb=" C ALA D 269 " pdb=" O ALA D 269 " ideal model delta sigma weight residual 1.235 1.160 0.075 1.26e-02 6.30e+03 3.53e+01 bond pdb=" C4 ADP E 903 " pdb=" C5 ADP E 903 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C4 ADP B 904 " pdb=" C5 ADP B 904 " 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 C 903 " pdb=" C5 ADP C 903 " 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 E 904 " pdb=" C5 ADP E 904 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.94e+01 ... (remaining 19888 not shown) Histogram of bond angle deviations from ideal: 98.23 - 105.48: 516 105.48 - 112.73: 10168 112.73 - 119.98: 7550 119.98 - 127.23: 8476 127.23 - 134.48: 221 Bond angle restraints: 26931 Sorted by residual: angle pdb=" C LEU D 239 " pdb=" N PHE D 240 " pdb=" CA PHE D 240 " ideal model delta sigma weight residual 120.58 107.60 12.98 1.71e+00 3.42e-01 5.76e+01 angle pdb=" C VAL D 268 " pdb=" CA VAL D 268 " pdb=" CB VAL D 268 " ideal model delta sigma weight residual 111.29 122.55 -11.26 1.64e+00 3.72e-01 4.71e+01 angle pdb=" C ALA D 267 " pdb=" N VAL D 268 " pdb=" CA VAL D 268 " ideal model delta sigma weight residual 121.97 109.94 12.03 1.80e+00 3.09e-01 4.47e+01 angle pdb=" CA PHE D 240 " pdb=" CB PHE D 240 " pdb=" CG PHE D 240 " ideal model delta sigma weight residual 113.80 107.24 6.56 1.00e+00 1.00e+00 4.31e+01 angle pdb=" C LYS E 594 " pdb=" N ALA E 595 " pdb=" CA ALA E 595 " ideal model delta sigma weight residual 121.54 133.74 -12.20 1.91e+00 2.74e-01 4.08e+01 ... (remaining 26926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.43: 11646 30.43 - 60.86: 442 60.86 - 91.29: 41 91.29 - 121.72: 11 121.72 - 152.15: 12 Dihedral angle restraints: 12152 sinusoidal: 4989 harmonic: 7163 Sorted by residual: dihedral pdb=" CA ALA B 580 " pdb=" C ALA B 580 " pdb=" N PRO B 581 " pdb=" CA PRO B 581 " ideal model delta harmonic sigma weight residual -180.00 -127.23 -52.77 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CA ARG E 596 " pdb=" C ARG E 596 " pdb=" N GLY E 597 " pdb=" CA GLY E 597 " ideal model delta harmonic sigma weight residual 180.00 -135.70 -44.30 0 5.00e+00 4.00e-02 7.85e+01 dihedral pdb=" CA ALA E 595 " pdb=" C ALA E 595 " pdb=" N ARG E 596 " pdb=" CA ARG E 596 " ideal model delta harmonic sigma weight residual 180.00 139.76 40.24 0 5.00e+00 4.00e-02 6.48e+01 ... (remaining 12149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2684 0.086 - 0.172: 294 0.172 - 0.257: 27 0.257 - 0.343: 2 0.343 - 0.429: 2 Chirality restraints: 3009 Sorted by residual: chirality pdb=" CB ILE E 216 " pdb=" CA ILE E 216 " pdb=" CG1 ILE E 216 " pdb=" CG2 ILE E 216 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.60e+00 chirality pdb=" CB ILE C 666 " pdb=" CA ILE C 666 " pdb=" CG1 ILE C 666 " pdb=" CG2 ILE C 666 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB THR H 7 " pdb=" CA THR H 7 " pdb=" OG1 THR H 7 " pdb=" CG2 THR H 7 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 3006 not shown) Planarity restraints: 3512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 269 " -0.020 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C ALA D 269 " 0.069 2.00e-02 2.50e+03 pdb=" O ALA D 269 " -0.028 2.00e-02 2.50e+03 pdb=" N ASN D 270 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO H 37 " 0.064 5.00e-02 4.00e+02 9.72e-02 1.51e+01 pdb=" N PRO H 38 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO H 38 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO H 38 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 232 " -0.048 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO E 233 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO E 233 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 233 " -0.040 5.00e-02 4.00e+02 ... (remaining 3509 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.03: 20 2.03 - 2.75: 2264 2.75 - 3.47: 27285 3.47 - 4.18: 45609 4.18 - 4.90: 76715 Nonbonded interactions: 151893 Sorted by model distance: nonbonded pdb=" CG2 THR C 535 " pdb=" F2 BEF C 902 " model vdw 1.317 3.410 nonbonded pdb=" CG2 THR D 535 " pdb=" F3 BEF D 902 " model vdw 1.369 3.410 nonbonded pdb=" O PRO B 257 " pdb=" O1B ADP B 904 " model vdw 1.386 3.040 nonbonded pdb=" OD1 ASP G 395 " pdb=" CD1 LEU H 43 " model vdw 1.504 3.460 nonbonded pdb=" OG1 THR C 262 " pdb=" O3A ADP C 903 " model vdw 1.539 2.440 ... (remaining 151888 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 '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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 16 5.49 5 S 87 5.16 5 Be 6 3.05 5 C 12228 2.51 5 N 3381 2.21 5 O 3810 1.98 5 F 18 1.80 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.450 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: 4.330 Check model and map are aligned: 0.280 Process input model: 48.190 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.190 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 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 0.110 19893 Z= 0.369 Angle : 1.064 13.250 26931 Z= 0.535 Chirality : 0.055 0.429 3009 Planarity : 0.006 0.097 3512 Dihedral : 16.651 152.147 7532 Min Nonbonded Distance : 1.317 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.27 % Favored : 91.45 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 1.56 % Twisted General : 0.21 % 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: -5.52 (0.12), residues: 2468 helix: -4.96 (0.05), residues: 838 sheet: -2.12 (0.29), residues: 262 loop : -3.17 (0.13), residues: 1368 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 586 time to evaluate : 2.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 592 average time/residue: 0.3939 time to fit residues: 331.6291 Evaluate side-chains 350 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 346 time to evaluate : 2.071 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.1969 time to fit residues: 4.6246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 223 optimal weight: 20.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 270 ASN B 394 HIS C 280 ASN C 337 GLN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 ASN C 638 GLN C 757 HIS ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 568 ASN ** D 757 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 GLN ** E 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 ASN G 166 HIS G 170 HIS G 201 ASN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 GLN G 240 GLN G 272 ASN G 313 GLN G 315 GLN ** G 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 19893 Z= 0.212 Angle : 0.761 10.430 26931 Z= 0.361 Chirality : 0.047 0.283 3009 Planarity : 0.006 0.085 3512 Dihedral : 12.436 172.098 2774 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.06 % Favored : 91.86 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 1.56 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.44 (0.13), residues: 2468 helix: -3.56 (0.11), residues: 893 sheet: -1.67 (0.30), residues: 254 loop : -2.78 (0.15), residues: 1321 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 409 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 412 average time/residue: 0.3573 time to fit residues: 216.0435 Evaluate side-chains 281 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 280 time to evaluate : 2.289 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1726 time to fit residues: 3.5766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 185 optimal weight: 8.9990 chunk 152 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 223 optimal weight: 0.6980 chunk 241 optimal weight: 20.0000 chunk 199 optimal weight: 20.0000 chunk 221 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 634 ASN ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN C 509 HIS C 613 GLN C 782 GLN ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 GLN ** D 757 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 ASN ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 GLN G 313 GLN G 400 GLN ** G 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 526 ASN H 2 GLN H 31 GLN ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 19893 Z= 0.308 Angle : 0.805 11.193 26931 Z= 0.385 Chirality : 0.048 0.221 3009 Planarity : 0.006 0.103 3512 Dihedral : 12.423 171.793 2774 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.12 % Favored : 90.80 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 1.56 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.15), residues: 2468 helix: -2.21 (0.15), residues: 901 sheet: -1.57 (0.31), residues: 256 loop : -2.45 (0.16), residues: 1311 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 370 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 373 average time/residue: 0.3405 time to fit residues: 190.9757 Evaluate side-chains 286 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 284 time to evaluate : 2.166 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1694 time to fit residues: 3.9091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 106 optimal weight: 0.0170 chunk 150 optimal weight: 10.0000 chunk 224 optimal weight: 6.9990 chunk 237 optimal weight: 10.0000 chunk 117 optimal weight: 0.5980 chunk 212 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.3224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 ASN ** C 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 HIS ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 612 ASN E 613 GLN G 246 ASN ** G 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 502 GLN H 2 GLN ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 19893 Z= 0.265 Angle : 0.766 13.234 26931 Z= 0.362 Chirality : 0.047 0.241 3009 Planarity : 0.005 0.098 3512 Dihedral : 12.487 176.508 2774 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.28 % Favored : 90.64 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 1.56 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.16), residues: 2468 helix: -1.60 (0.16), residues: 906 sheet: -1.36 (0.30), residues: 263 loop : -2.34 (0.16), residues: 1299 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 2.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.3309 time to fit residues: 180.4802 Evaluate side-chains 271 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 2.245 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 198 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 177 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 202 optimal weight: 7.9990 chunk 164 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 213 optimal weight: 20.0000 chunk 60 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 394 HIS ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 613 GLN G 315 GLN ** G 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 19893 Z= 0.209 Angle : 0.739 13.091 26931 Z= 0.343 Chirality : 0.046 0.281 3009 Planarity : 0.005 0.089 3512 Dihedral : 12.408 179.268 2774 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.28 % Favored : 90.64 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 1.56 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.16), residues: 2468 helix: -1.29 (0.17), residues: 899 sheet: -1.32 (0.31), residues: 263 loop : -2.25 (0.16), residues: 1306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 2.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.3261 time to fit residues: 177.1834 Evaluate side-chains 264 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 2.317 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 2.9990 chunk 214 optimal weight: 8.9990 chunk 47 optimal weight: 0.0980 chunk 139 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 238 optimal weight: 20.0000 chunk 197 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 19 optimal weight: 0.0070 chunk 78 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 470 ASN ** C 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 HIS ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 613 GLN G 206 ASN G 240 GLN G 246 ASN ** G 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 19893 Z= 0.196 Angle : 0.738 15.967 26931 Z= 0.343 Chirality : 0.046 0.288 3009 Planarity : 0.005 0.084 3512 Dihedral : 12.287 176.966 2774 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.28 % Favored : 90.64 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 0.78 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.16), residues: 2468 helix: -1.07 (0.17), residues: 898 sheet: -1.26 (0.31), residues: 264 loop : -2.18 (0.17), residues: 1306 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 348 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 349 average time/residue: 0.3198 time to fit residues: 171.3900 Evaluate side-chains 268 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 267 time to evaluate : 2.308 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1925 time to fit residues: 3.4777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 173 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 237 optimal weight: 0.9990 chunk 148 optimal weight: 20.0000 chunk 144 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 HIS ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 613 GLN G 240 GLN ** G 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 ASN G 499 GLN H 2 GLN ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 19893 Z= 0.204 Angle : 0.736 18.650 26931 Z= 0.340 Chirality : 0.046 0.215 3009 Planarity : 0.005 0.085 3512 Dihedral : 12.189 173.118 2774 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.89 % Favored : 90.03 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.16), residues: 2468 helix: -0.91 (0.17), residues: 919 sheet: -1.14 (0.31), residues: 263 loop : -2.21 (0.17), residues: 1286 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 2.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.3154 time to fit residues: 169.1384 Evaluate side-chains 265 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 2.268 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 141 optimal weight: 0.0010 chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 45 optimal weight: 0.2980 chunk 150 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 186 optimal weight: 0.0370 overall best weight: 0.6266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 470 ASN ** B 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 613 GLN G 272 ASN ** G 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 526 ASN H 2 GLN ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 19893 Z= 0.169 Angle : 0.722 16.778 26931 Z= 0.332 Chirality : 0.045 0.231 3009 Planarity : 0.005 0.083 3512 Dihedral : 11.970 166.451 2774 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.91 % Favored : 91.00 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.16), residues: 2468 helix: -0.74 (0.17), residues: 904 sheet: -1.07 (0.32), residues: 257 loop : -2.17 (0.17), residues: 1307 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 345 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 347 average time/residue: 0.3140 time to fit residues: 169.3398 Evaluate side-chains 273 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 272 time to evaluate : 2.339 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1742 time to fit residues: 3.4863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 215 optimal weight: 0.6980 chunk 227 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 220 optimal weight: 5.9990 chunk 132 optimal weight: 0.0870 chunk 96 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 67 optimal weight: 0.0770 chunk 199 optimal weight: 20.0000 chunk 208 optimal weight: 9.9990 chunk 145 optimal weight: 0.9980 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 626 ASN ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 ASN ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 613 GLN ** G 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 19893 Z= 0.179 Angle : 0.731 16.670 26931 Z= 0.336 Chirality : 0.045 0.229 3009 Planarity : 0.005 0.081 3512 Dihedral : 11.871 164.650 2774 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.52 % Favored : 90.40 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.16), residues: 2468 helix: -0.62 (0.18), residues: 892 sheet: -0.95 (0.32), residues: 255 loop : -2.17 (0.16), residues: 1321 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.3235 time to fit residues: 166.4967 Evaluate side-chains 259 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 2.165 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 233 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 162 optimal weight: 0.0570 chunk 245 optimal weight: 0.0870 chunk 225 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 119 optimal weight: 0.0010 chunk 155 optimal weight: 2.9990 overall best weight: 1.0286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 470 ASN ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 ASN ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 240 GLN ** G 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.5552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 19893 Z= 0.187 Angle : 0.731 15.748 26931 Z= 0.337 Chirality : 0.046 0.221 3009 Planarity : 0.005 0.081 3512 Dihedral : 11.774 164.005 2774 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.32 % Favored : 90.60 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.16), residues: 2468 helix: -0.52 (0.18), residues: 892 sheet: -1.00 (0.31), residues: 257 loop : -2.18 (0.16), residues: 1319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 327 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 outliers start: 1 outliers final: 1 residues processed: 328 average time/residue: 0.3115 time to fit residues: 158.9658 Evaluate side-chains 258 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 257 time to evaluate : 2.311 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1817 time to fit residues: 3.5177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 200 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 36 optimal weight: 0.6980 chunk 171 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 HIS ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 ASN ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 613 GLN ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 240 GLN G 526 ASN H 2 GLN ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.147450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.120441 restraints weight = 45560.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.120492 restraints weight = 33186.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.120986 restraints weight = 25417.746| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.5724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 19893 Z= 0.198 Angle : 0.735 14.805 26931 Z= 0.341 Chirality : 0.046 0.217 3009 Planarity : 0.005 0.080 3512 Dihedral : 11.753 163.156 2774 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.68 % Favored : 90.24 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.16), residues: 2468 helix: -0.51 (0.18), residues: 898 sheet: -1.08 (0.31), residues: 259 loop : -2.22 (0.16), residues: 1311 =============================================================================== Job complete usr+sys time: 4037.17 seconds wall clock time: 73 minutes 43.81 seconds (4423.81 seconds total)