Starting phenix.real_space_refine (version: dev) on Fri Feb 24 09:19:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0c_22591/02_2023/7k0c_22591.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0c_22591/02_2023/7k0c_22591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0c_22591/02_2023/7k0c_22591.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0c_22591/02_2023/7k0c_22591.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0c_22591/02_2023/7k0c_22591.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0c_22591/02_2023/7k0c_22591.pdb" } resolution = 3.3 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= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C GLU 330": "OE1" <-> "OE2" Residue "C GLU 436": "OE1" <-> "OE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "B GLU 541": "OE1" <-> "OE2" Residue "K PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 527": "OE1" <-> "OE2" Residue "I GLU 462": "OE1" <-> "OE2" Residue "I GLU 498": "OE1" <-> "OE2" Residue "J GLU 415": "OE1" <-> "OE2" Residue "J GLU 532": "OE1" <-> "OE2" Residue "E GLU 410": "OE1" <-> "OE2" Residue "H GLU 422": "OE1" <-> "OE2" Residue "H ARG 451": "NH1" <-> "NH2" Residue "D ARG 5": "NH1" <-> "NH2" Residue "D ARG 47": "NH1" <-> "NH2" Residue "D ARG 58": "NH1" <-> "NH2" Residue "D ASP 132": "OD1" <-> "OD2" Residue "G GLU 398": "OE1" <-> "OE2" Residue "G GLU 526": "OE1" <-> "OE2" Residue "G GLU 549": "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: 22540 Number of models: 1 Model: "" Number of chains: 13 Chain: "C" Number of atoms: 4109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4109 Classifications: {'peptide': 534} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 25, 'TRANS': 508} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1764 Classifications: {'peptide': 227} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 208} Chain: "B" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1764 Classifications: {'peptide': 227} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 208} Chain: "K" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 206} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1737 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "J" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1723 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 202} Chain breaks: 1 Chain: "E" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1742 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1785 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 211} Chain breaks: 1 Chain: "D" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 838 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 7, 'TRANS': 96} Chain breaks: 2 Chain: "G" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 211} Chain breaks: 1 Chain: "F" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1773 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 209} Chain breaks: 1 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.62, per 1000 atoms: 0.56 Number of scatterers: 22540 At special positions: 0 Unit cell: (177.6, 195.6, 128.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 4399 8.00 N 3833 7.00 C 14198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.04 Simple disulfide: pdb=" SG CYS C 38 " - pdb=" SG CYS C 46 " distance=2.04 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 202 " distance=2.03 Simple disulfide: pdb=" SG CYS C 239 " - pdb=" SG CYS C 307 " distance=2.04 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 261 " distance=2.03 Simple disulfide: pdb=" SG CYS C 464 " - pdb=" SG CYS C 526 " distance=2.05 Simple disulfide: pdb=" SG CYS C 468 " - pdb=" SG CYS F 414 " distance=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 426 " distance=2.04 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 536 " distance=2.04 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 414 " - pdb=" SG CYS K 414 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 536 " distance=2.04 Simple disulfide: pdb=" SG CYS K 367 " - pdb=" SG CYS K 426 " distance=2.03 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 536 " distance=2.03 Simple disulfide: pdb=" SG CYS L 367 " - pdb=" SG CYS L 426 " distance=2.03 Simple disulfide: pdb=" SG CYS L 414 " - pdb=" SG CYS I 414 " distance=2.04 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.04 Simple disulfide: pdb=" SG CYS I 367 " - pdb=" SG CYS I 426 " distance=2.04 Simple disulfide: pdb=" SG CYS I 474 " - pdb=" SG CYS I 536 " distance=2.04 Simple disulfide: pdb=" SG CYS J 367 " - pdb=" SG CYS J 426 " distance=2.03 Simple disulfide: pdb=" SG CYS J 414 " - pdb=" SG CYS E 414 " distance=2.03 Simple disulfide: pdb=" SG CYS J 474 " - pdb=" SG CYS J 536 " distance=2.04 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 426 " distance=2.03 Simple disulfide: pdb=" SG CYS E 474 " - pdb=" SG CYS E 536 " distance=2.04 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 426 " distance=2.03 Simple disulfide: pdb=" SG CYS H 414 " - pdb=" SG CYS G 414 " distance=2.03 Simple disulfide: pdb=" SG CYS H 474 " - pdb=" SG CYS H 536 " distance=2.02 Simple disulfide: pdb=" SG CYS H 575 " - pdb=" SG CYS G 575 " distance=2.03 Simple disulfide: pdb=" SG CYS D 13 " - pdb=" SG CYS D 101 " distance=2.02 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS F 575 " distance=2.01 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS D 134 " distance=2.03 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 426 " distance=2.03 Simple disulfide: pdb=" SG CYS G 474 " - pdb=" SG CYS G 536 " distance=2.06 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 426 " distance=2.03 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 536 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG M 1 " - " ASN D 49 " Time building additional restraints: 9.26 Conformation dependent library (CDL) restraints added in 3.9 seconds 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5510 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 69 sheets defined 11.4% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 57 through 61 removed outlier: 3.834A pdb=" N ALA C 61 " --> pdb=" O SER C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.716A pdb=" N SER C 87 " --> pdb=" O GLN C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 removed outlier: 3.772A pdb=" N ALA C 197 " --> pdb=" O LEU C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 246 removed outlier: 3.610A pdb=" N VAL C 245 " --> pdb=" O GLY C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 276 Processing helix chain 'C' and resid 298 through 302 removed outlier: 4.082A pdb=" N ALA C 302 " --> pdb=" O LYS C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 360 removed outlier: 3.889A pdb=" N SER C 360 " --> pdb=" O ARG C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 392 removed outlier: 4.199A pdb=" N GLU C 392 " --> pdb=" O ALA C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 418 removed outlier: 3.841A pdb=" N ALA C 418 " --> pdb=" O SER C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 471 Processing helix chain 'C' and resid 517 through 521 Processing helix chain 'A' and resid 353 through 361 Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'B' and resid 353 through 361 Processing helix chain 'B' and resid 415 through 421 removed outlier: 3.598A pdb=" N ASN B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 467 Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 524 through 529 Processing helix chain 'K' and resid 353 through 361 Processing helix chain 'K' and resid 414 through 420 removed outlier: 4.123A pdb=" N TRP K 418 " --> pdb=" O CYS K 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 462 through 466 Processing helix chain 'K' and resid 524 through 529 Processing helix chain 'L' and resid 353 through 361 Processing helix chain 'L' and resid 415 through 421 removed outlier: 3.873A pdb=" N ASN L 419 " --> pdb=" O GLU L 415 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY L 421 " --> pdb=" O ASP L 417 " (cutoff:3.500A) Processing helix chain 'L' and resid 460 through 465 removed outlier: 3.503A pdb=" N LEU L 464 " --> pdb=" O ALA L 460 " (cutoff:3.500A) Processing helix chain 'L' and resid 524 through 531 Processing helix chain 'I' and resid 353 through 361 Processing helix chain 'I' and resid 417 through 421 removed outlier: 3.891A pdb=" N GLY I 421 " --> pdb=" O TRP I 418 " (cutoff:3.500A) Processing helix chain 'I' and resid 462 through 467 removed outlier: 3.607A pdb=" N ARG I 467 " --> pdb=" O GLN I 463 " (cutoff:3.500A) Processing helix chain 'I' and resid 525 through 530 Processing helix chain 'J' and resid 353 through 360 Processing helix chain 'J' and resid 525 through 529 Processing helix chain 'E' and resid 353 through 361 removed outlier: 4.256A pdb=" N THR E 360 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 removed outlier: 3.773A pdb=" N TRP E 418 " --> pdb=" O CYS E 414 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER E 420 " --> pdb=" O ASP E 416 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY E 421 " --> pdb=" O ASP E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 465 Processing helix chain 'E' and resid 525 through 529 Processing helix chain 'H' and resid 353 through 361 Processing helix chain 'H' and resid 414 through 420 removed outlier: 3.994A pdb=" N TRP H 418 " --> pdb=" O CYS H 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 462 through 466 Processing helix chain 'H' and resid 525 through 529 Processing helix chain 'H' and resid 553 through 557 removed outlier: 3.927A pdb=" N THR H 556 " --> pdb=" O ASP H 553 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY H 557 " --> pdb=" O LYS H 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 553 through 557' Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'G' and resid 353 through 360 removed outlier: 3.542A pdb=" N LEU G 359 " --> pdb=" O ALA G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 421 removed outlier: 3.796A pdb=" N TRP G 418 " --> pdb=" O CYS G 414 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY G 421 " --> pdb=" O ASP G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 466 removed outlier: 4.088A pdb=" N LEU G 464 " --> pdb=" O ALA G 460 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU G 466 " --> pdb=" O GLU G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 498 No H-bonds generated for 'chain 'G' and resid 496 through 498' Processing helix chain 'G' and resid 525 through 529 Processing helix chain 'F' and resid 353 through 361 Processing helix chain 'F' and resid 415 through 419 Processing helix chain 'F' and resid 462 through 466 Processing sheet with id=AA1, first strand: chain 'C' and resid 9 through 13 removed outlier: 3.645A pdb=" N GLU C 108 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER C 12 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LYS C 35 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N SER C 51 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N TRP C 37 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 17 through 23 Processing sheet with id=AA3, first strand: chain 'C' and resid 123 through 125 removed outlier: 6.436A pdb=" N VAL C 124 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 130 through 135 removed outlier: 3.548A pdb=" N VAL C 130 " --> pdb=" O ILE C 189 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 147 through 151 removed outlier: 6.966A pdb=" N LEU C 147 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 226 through 229 removed outlier: 7.265A pdb=" N LEU C 252 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 234 through 239 Processing sheet with id=AA8, first strand: chain 'C' and resid 340 through 344 removed outlier: 3.616A pdb=" N GLY C 419 " --> pdb=" O ILE C 437 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS C 367 " --> pdb=" O TRP C 422 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 424 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TRP C 366 " --> pdb=" O LEU C 380 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 349 through 354 Processing sheet with id=AB1, first strand: chain 'C' and resid 460 through 462 Processing sheet with id=AB2, first strand: chain 'C' and resid 474 through 479 removed outlier: 4.043A pdb=" N GLU C 474 " --> pdb=" O LYS C 529 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N GLY C 522 " --> pdb=" O TYR C 541 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N TYR C 541 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TYR C 524 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA C 539 " --> pdb=" O TYR C 524 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N CYS C 526 " --> pdb=" O THR C 537 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR C 537 " --> pdb=" O CYS C 526 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N VAL C 528 " --> pdb=" O GLY C 535 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 346 through 350 removed outlier: 5.025A pdb=" N PHE A 405 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 379 through 383 removed outlier: 3.610A pdb=" N THR A 379 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 428 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 437 " --> pdb=" O VAL A 428 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 456 through 457 removed outlier: 3.527A pdb=" N VAL A 476 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 517 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 493 through 494 Processing sheet with id=AB7, first strand: chain 'A' and resid 561 through 562 Processing sheet with id=AB8, first strand: chain 'A' and resid 567 through 569 removed outlier: 7.248A pdb=" N VAL A 567 " --> pdb=" O TYR D 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.727A pdb=" N THR B 366 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU B 365 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 381 through 382 Processing sheet with id=AC2, first strand: chain 'B' and resid 455 through 457 removed outlier: 3.661A pdb=" N ALA B 517 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N HIS B 518 " --> pdb=" O ALA B 504 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA B 504 " --> pdb=" O HIS B 518 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE B 520 " --> pdb=" O THR B 502 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR B 502 " --> pdb=" O ILE B 520 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N THR B 522 " --> pdb=" O TYR B 500 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR B 500 " --> pdb=" O THR B 522 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 493 through 494 removed outlier: 3.507A pdb=" N GLN B 490 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG B 550 " --> pdb=" O CYS B 536 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 565 through 566 removed outlier: 3.518A pdb=" N VAL L 567 " --> pdb=" O LEU K 566 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU L 566 " --> pdb=" O VAL I 567 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 346 through 350 removed outlier: 6.079A pdb=" N THR K 366 " --> pdb=" O ALA K 411 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ALA K 411 " --> pdb=" O THR K 366 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU K 368 " --> pdb=" O GLY K 409 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N GLY K 409 " --> pdb=" O LEU K 368 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N THR K 370 " --> pdb=" O ALA K 407 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ALA K 407 " --> pdb=" O THR K 370 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 379 through 383 removed outlier: 3.683A pdb=" N THR K 379 " --> pdb=" O THR K 429 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS K 426 " --> pdb=" O GLN K 439 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN K 439 " --> pdb=" O CYS K 426 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 455 through 457 removed outlier: 3.902A pdb=" N LEU K 475 " --> pdb=" O TYR K 455 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR K 473 " --> pdb=" O LEU K 457 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER K 519 " --> pdb=" O CYS K 474 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 455 through 457 removed outlier: 3.902A pdb=" N LEU K 475 " --> pdb=" O TYR K 455 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR K 473 " --> pdb=" O LEU K 457 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR K 515 " --> pdb=" O GLY K 478 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 493 through 494 removed outlier: 3.736A pdb=" N THR K 535 " --> pdb=" O MET K 489 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 346 through 348 Processing sheet with id=AD2, first strand: chain 'L' and resid 379 through 382 removed outlier: 3.552A pdb=" N ILE L 441 " --> pdb=" O PHE L 424 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 455 through 457 removed outlier: 3.522A pdb=" N LEU L 457 " --> pdb=" O THR L 473 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR L 473 " --> pdb=" O LEU L 457 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL L 501 " --> pdb=" O ILE L 520 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 493 through 494 removed outlier: 3.808A pdb=" N ARG L 550 " --> pdb=" O CYS L 536 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR L 548 " --> pdb=" O VAL L 538 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 506 through 507 Processing sheet with id=AD6, first strand: chain 'I' and resid 347 through 348 Processing sheet with id=AD7, first strand: chain 'I' and resid 364 through 365 removed outlier: 3.546A pdb=" N LEU I 365 " --> pdb=" O ALA I 411 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA I 411 " --> pdb=" O LEU I 365 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'I' and resid 381 through 383 removed outlier: 4.275A pdb=" N SER I 381 " --> pdb=" O THR I 427 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR I 427 " --> pdb=" O SER I 381 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE I 424 " --> pdb=" O ILE I 441 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE I 441 " --> pdb=" O PHE I 424 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 455 through 457 removed outlier: 3.851A pdb=" N THR I 473 " --> pdb=" O LEU I 457 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE I 472 " --> pdb=" O LEU I 521 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 493 through 494 Processing sheet with id=AE2, first strand: chain 'I' and resid 506 through 507 Processing sheet with id=AE3, first strand: chain 'J' and resid 348 through 350 removed outlier: 3.619A pdb=" N PHE J 348 " --> pdb=" O LEU J 368 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR J 366 " --> pdb=" O ILE J 350 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 424 through 427 removed outlier: 3.657A pdb=" N PHE J 424 " --> pdb=" O ILE J 441 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN J 439 " --> pdb=" O CYS J 426 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 455 through 457 removed outlier: 3.845A pdb=" N THR J 473 " --> pdb=" O LEU J 457 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N THR J 477 " --> pdb=" O ALA J 517 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA J 517 " --> pdb=" O THR J 477 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE J 479 " --> pdb=" O TYR J 515 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 455 through 457 removed outlier: 3.845A pdb=" N THR J 473 " --> pdb=" O LEU J 457 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 493 through 494 removed outlier: 3.538A pdb=" N GLN J 487 " --> pdb=" O VAL J 537 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 566 through 567 Processing sheet with id=AE9, first strand: chain 'E' and resid 347 through 350 removed outlier: 3.854A pdb=" N THR E 366 " --> pdb=" O ILE E 350 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 379 through 383 Processing sheet with id=AF2, first strand: chain 'E' and resid 455 through 457 removed outlier: 3.559A pdb=" N LEU E 457 " --> pdb=" O THR E 473 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR E 473 " --> pdb=" O LEU E 457 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL E 501 " --> pdb=" O ILE E 520 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 469 through 471 removed outlier: 3.815A pdb=" N VAL E 523 " --> pdb=" O ALA E 470 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 493 through 494 Processing sheet with id=AF5, first strand: chain 'H' and resid 364 through 369 removed outlier: 3.714A pdb=" N LEU H 365 " --> pdb=" O ALA H 411 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA H 411 " --> pdb=" O LEU H 365 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA H 407 " --> pdb=" O VAL H 369 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR H 404 " --> pdb=" O HIS H 400 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU H 398 " --> pdb=" O SER H 406 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL H 408 " --> pdb=" O ILE H 396 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ILE H 396 " --> pdb=" O VAL H 408 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 379 through 383 removed outlier: 4.455A pdb=" N THR H 379 " --> pdb=" O THR H 429 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR H 429 " --> pdb=" O THR H 379 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 469 through 473 Processing sheet with id=AF8, first strand: chain 'H' and resid 476 through 479 removed outlier: 5.146A pdb=" N THR H 477 " --> pdb=" O ALA H 517 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALA H 517 " --> pdb=" O THR H 477 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE H 479 " --> pdb=" O TYR H 515 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 493 through 494 Processing sheet with id=AG1, first strand: chain 'D' and resid 9 through 11 Processing sheet with id=AG2, first strand: chain 'D' and resid 21 through 22 removed outlier: 8.226A pdb=" N ASN F 563 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ARG D 36 " --> pdb=" O ASN F 563 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 41 through 42 removed outlier: 3.720A pdb=" N VAL D 42 " --> pdb=" O VAL F 567 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AG5, first strand: chain 'G' and resid 364 through 370 removed outlier: 3.611A pdb=" N CYS G 367 " --> pdb=" O GLY G 409 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY G 409 " --> pdb=" O CYS G 367 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 379 through 380 removed outlier: 4.036A pdb=" N THR G 379 " --> pdb=" O THR G 429 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 383 through 384 Processing sheet with id=AG8, first strand: chain 'G' and resid 455 through 457 removed outlier: 4.004A pdb=" N CYS G 474 " --> pdb=" O SER G 519 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER G 519 " --> pdb=" O CYS G 474 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 493 through 494 Processing sheet with id=AH1, first strand: chain 'G' and resid 506 through 507 Processing sheet with id=AH2, first strand: chain 'F' and resid 349 through 350 removed outlier: 3.605A pdb=" N ALA F 411 " --> pdb=" O LEU F 365 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 381 through 383 removed outlier: 3.584A pdb=" N VAL F 428 " --> pdb=" O LEU F 437 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU F 437 " --> pdb=" O VAL F 428 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N HIS F 430 " --> pdb=" O SER F 435 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N SER F 435 " --> pdb=" O HIS F 430 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 456 through 457 removed outlier: 3.611A pdb=" N SER F 519 " --> pdb=" O CYS F 474 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 485 through 488 Processing sheet with id=AH6, first strand: chain 'F' and resid 506 through 507 562 hydrogen bonds defined for protein. 1341 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: 8.11 Time building geometry restraints manager: 10.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3774 1.32 - 1.45: 6372 1.45 - 1.58: 12802 1.58 - 1.71: 1 1.71 - 1.85: 141 Bond restraints: 23090 Sorted by residual: bond pdb=" C MET A 506 " pdb=" N PRO A 507 " ideal model delta sigma weight residual 1.332 1.482 -0.150 1.33e-02 5.65e+03 1.27e+02 bond pdb=" C PRO B 505 " pdb=" O PRO B 505 " ideal model delta sigma weight residual 1.235 1.183 0.052 1.30e-02 5.92e+03 1.63e+01 bond pdb=" CB VAL B 567 " pdb=" CG1 VAL B 567 " ideal model delta sigma weight residual 1.521 1.426 0.095 3.30e-02 9.18e+02 8.25e+00 bond pdb=" CB VAL G 567 " pdb=" CG1 VAL G 567 " ideal model delta sigma weight residual 1.521 1.427 0.094 3.30e-02 9.18e+02 8.11e+00 bond pdb=" CA ALA B 517 " pdb=" CB ALA B 517 " ideal model delta sigma weight residual 1.532 1.488 0.043 1.56e-02 4.11e+03 7.68e+00 ... (remaining 23085 not shown) Histogram of bond angle deviations from ideal: 97.62 - 104.91: 625 104.91 - 112.20: 11920 112.20 - 119.49: 7294 119.49 - 126.78: 11326 126.78 - 134.07: 406 Bond angle restraints: 31571 Sorted by residual: angle pdb=" C MET A 506 " pdb=" N PRO A 507 " pdb=" CA PRO A 507 " ideal model delta sigma weight residual 119.89 131.39 -11.50 1.02e+00 9.61e-01 1.27e+02 angle pdb=" C VAL B 501 " pdb=" N THR B 502 " pdb=" CA THR B 502 " ideal model delta sigma weight residual 122.99 114.16 8.83 1.41e+00 5.03e-01 3.92e+01 angle pdb=" CA CYS G 536 " pdb=" CB CYS G 536 " pdb=" SG CYS G 536 " ideal model delta sigma weight residual 114.40 128.62 -14.22 2.30e+00 1.89e-01 3.82e+01 angle pdb=" CA CYS G 474 " pdb=" CB CYS G 474 " pdb=" SG CYS G 474 " ideal model delta sigma weight residual 114.40 128.09 -13.69 2.30e+00 1.89e-01 3.54e+01 angle pdb=" N MET A 506 " pdb=" CA MET A 506 " pdb=" CB MET A 506 " ideal model delta sigma weight residual 110.37 119.96 -9.59 1.78e+00 3.16e-01 2.90e+01 ... (remaining 31566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 12624 18.01 - 36.03: 1185 36.03 - 54.04: 151 54.04 - 72.05: 26 72.05 - 90.06: 14 Dihedral angle restraints: 14000 sinusoidal: 5519 harmonic: 8481 Sorted by residual: dihedral pdb=" CB CYS C 253 " pdb=" SG CYS C 253 " pdb=" SG CYS C 261 " pdb=" CB CYS C 261 " ideal model delta sinusoidal sigma weight residual 93.00 14.36 78.64 1 1.00e+01 1.00e-02 7.71e+01 dihedral pdb=" CB CYS F 367 " pdb=" SG CYS F 367 " pdb=" SG CYS F 426 " pdb=" CB CYS F 426 " ideal model delta sinusoidal sigma weight residual 93.00 166.72 -73.72 1 1.00e+01 1.00e-02 6.91e+01 dihedral pdb=" CB CYS L 414 " pdb=" SG CYS L 414 " pdb=" SG CYS I 414 " pdb=" CB CYS I 414 " ideal model delta sinusoidal sigma weight residual -86.00 -159.15 73.15 1 1.00e+01 1.00e-02 6.82e+01 ... (remaining 13997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3075 0.076 - 0.152: 566 0.152 - 0.229: 34 0.229 - 0.305: 6 0.305 - 0.381: 2 Chirality restraints: 3683 Sorted by residual: chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 5.49e+00 chirality pdb=" CA VAL B 501 " pdb=" N VAL B 501 " pdb=" C VAL B 501 " pdb=" CB VAL B 501 " both_signs ideal model delta sigma weight residual False 2.44 2.82 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CA ARG K 514 " pdb=" N ARG K 514 " pdb=" C ARG K 514 " pdb=" CB ARG K 514 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 3680 not shown) Planarity restraints: 4057 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG I 443 " 0.082 5.00e-02 4.00e+02 1.25e-01 2.52e+01 pdb=" N PRO I 444 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO I 444 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO I 444 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 488 " 0.028 2.00e-02 2.50e+03 2.71e-02 1.83e+01 pdb=" CG TRP G 488 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP G 488 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP G 488 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP G 488 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP G 488 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP G 488 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 488 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 488 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP G 488 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 42 " -0.064 5.00e-02 4.00e+02 9.85e-02 1.55e+01 pdb=" N PRO D 43 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO D 43 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO D 43 " -0.053 5.00e-02 4.00e+02 ... (remaining 4054 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 431 2.53 - 3.12: 19850 3.12 - 3.72: 36888 3.72 - 4.31: 49179 4.31 - 4.90: 77083 Nonbonded interactions: 183431 Sorted by model distance: nonbonded pdb=" OD1 ASP B 453 " pdb=" OG1 THR B 477 " model vdw 1.940 2.440 nonbonded pdb=" O THR I 533 " pdb=" OG1 THR I 551 " model vdw 2.021 2.440 nonbonded pdb=" OG SER K 524 " pdb=" OE1 GLU K 527 " model vdw 2.044 2.440 nonbonded pdb=" OG SER B 381 " pdb=" OG1 THR B 427 " model vdw 2.045 2.440 nonbonded pdb=" O GLU G 526 " pdb=" OG1 THR G 530 " model vdw 2.052 2.440 ... (remaining 183426 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 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 442 or (resid 443 and (name N \ or name CA or name C or name O or name CB )) or resid 444 or resid 449 through 5 \ 12 or (resid 513 and (name N or name CA or name C )) or resid 514 through 568)) selection = (chain 'B' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 442 or (resid 443 and (name N \ or name CA or name C or name O or name CB )) or resid 444 or resid 449 through 5 \ 12 or (resid 513 and (name N or name CA or name C )) or resid 514 through 568)) selection = (chain 'E' and (resid 345 through 442 or (resid 443 and (name N or name CA or na \ me C or name O or name CB )) or resid 444 or resid 449 through 512 or (resid 513 \ and (name N or name CA or name C )) or resid 514 through 568)) selection = (chain 'F' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 442 or (resid 443 and (name N \ or name CA or name C or name O or name CB )) or resid 444 through 512 or (resid \ 513 and (name N or name CA or name C )) or resid 514 through 568)) selection = (chain 'G' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 442 or (resid 443 and (name N \ or name CA or name C or name O or name CB )) or resid 444 or resid 449 through 5 \ 12 or (resid 513 and (name N or name CA or name C )) or resid 514 through 568)) selection = (chain 'H' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 442 or (resid 443 and (name N \ or name CA or name C or name O or name CB )) or resid 444 or resid 449 through 5 \ 12 or (resid 513 and (name N or name CA or name C )) or resid 514 through 568)) selection = (chain 'I' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 442 or (resid 443 and (name N \ or name CA or name C or name O or name CB )) or resid 444 or resid 449 through 5 \ 12 or (resid 513 and (name N or name CA or name C )) or resid 514 through 568)) selection = (chain 'J' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 442 or (resid 443 and (name N \ or name CA or name C or name O or name CB )) or resid 444 or resid 449 through 5 \ 12 or (resid 513 and (name N or name CA or name C )) or resid 514 through 568)) selection = (chain 'K' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 442 or (resid 443 and (name N \ or name CA or name C or name O or name CB )) or resid 444 or resid 449 through 5 \ 68)) selection = (chain 'L' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568)) } 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: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 14198 2.51 5 N 3833 2.21 5 O 4399 1.98 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 individual isotropic 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: 5.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 15.950 Check model and map are aligned: 0.410 Process input model: 59.400 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 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 : 0.008 0.150 23090 Z= 0.497 Angle : 1.013 14.781 31571 Z= 0.543 Chirality : 0.056 0.381 3683 Planarity : 0.007 0.125 4056 Dihedral : 13.527 90.064 8382 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 33.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.07 % Favored : 84.93 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.35 (0.15), residues: 2860 helix: -3.09 (0.29), residues: 183 sheet: -1.86 (0.15), residues: 1084 loop : -2.40 (0.15), residues: 1593 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 426 time to evaluate : 2.578 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: 3 outliers final: 0 residues processed: 428 average time/residue: 0.3898 time to fit residues: 248.0524 Evaluate side-chains 298 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 2.761 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 7.9990 chunk 216 optimal weight: 7.9990 chunk 119 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 223 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 135 optimal weight: 0.0050 chunk 166 optimal weight: 0.2980 chunk 258 optimal weight: 0.9990 overall best weight: 1.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 ASN C 97 ASN C 426 ASN ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 GLN ** K 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 450 HIS ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 493 GLN ** L 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 ASN ** J 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 23090 Z= 0.261 Angle : 0.817 17.809 31571 Z= 0.417 Chirality : 0.050 0.301 3683 Planarity : 0.006 0.089 4056 Dihedral : 6.800 29.635 3126 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.15), residues: 2860 helix: -2.87 (0.26), residues: 214 sheet: -1.64 (0.15), residues: 1095 loop : -2.25 (0.15), residues: 1551 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 390 time to evaluate : 2.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 31 residues processed: 414 average time/residue: 0.3530 time to fit residues: 225.4079 Evaluate side-chains 352 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 321 time to evaluate : 2.681 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1997 time to fit residues: 15.3672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 215 optimal weight: 30.0000 chunk 176 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 259 optimal weight: 5.9990 chunk 280 optimal weight: 7.9990 chunk 230 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 23090 Z= 0.293 Angle : 0.771 17.232 31571 Z= 0.393 Chirality : 0.048 0.297 3683 Planarity : 0.006 0.070 4056 Dihedral : 6.529 28.173 3126 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 24.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.22 % Favored : 88.78 % Rotamer Outliers : 2.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.15), residues: 2860 helix: -2.52 (0.29), residues: 205 sheet: -1.48 (0.15), residues: 1060 loop : -2.11 (0.15), residues: 1595 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 364 time to evaluate : 2.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 34 residues processed: 403 average time/residue: 0.3460 time to fit residues: 216.6442 Evaluate side-chains 356 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 322 time to evaluate : 2.921 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2234 time to fit residues: 17.6716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 7.9990 chunk 194 optimal weight: 9.9990 chunk 134 optimal weight: 0.0870 chunk 28 optimal weight: 8.9990 chunk 123 optimal weight: 0.0670 chunk 174 optimal weight: 1.9990 chunk 260 optimal weight: 0.9990 chunk 275 optimal weight: 9.9990 chunk 135 optimal weight: 0.7980 chunk 246 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 ASN B 400 HIS ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN K 439 GLN ** L 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 400 HIS I 540 HIS ** J 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 ASN ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 23090 Z= 0.199 Angle : 0.734 18.541 31571 Z= 0.366 Chirality : 0.047 0.303 3683 Planarity : 0.005 0.062 4056 Dihedral : 6.026 27.360 3126 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer Outliers : 2.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.15), residues: 2860 helix: -2.30 (0.30), residues: 211 sheet: -1.29 (0.15), residues: 1056 loop : -2.00 (0.15), residues: 1593 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 387 time to evaluate : 2.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 32 residues processed: 430 average time/residue: 0.3413 time to fit residues: 227.1817 Evaluate side-chains 362 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 330 time to evaluate : 2.496 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2133 time to fit residues: 15.7640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 4.9990 chunk 156 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 205 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 235 optimal weight: 0.5980 chunk 190 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 247 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 GLN ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 439 GLN K 487 GLN ** L 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 439 GLN ** I 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 23090 Z= 0.202 Angle : 0.705 16.938 31571 Z= 0.354 Chirality : 0.047 0.304 3683 Planarity : 0.005 0.057 4056 Dihedral : 5.806 26.757 3126 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.15), residues: 2860 helix: -2.16 (0.30), residues: 223 sheet: -1.21 (0.16), residues: 1041 loop : -1.80 (0.16), residues: 1596 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 367 time to evaluate : 2.690 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: 58 outliers final: 25 residues processed: 409 average time/residue: 0.3411 time to fit residues: 217.6103 Evaluate side-chains 355 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 330 time to evaluate : 2.813 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1952 time to fit residues: 12.8720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 3.9990 chunk 248 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 68 optimal weight: 0.0010 chunk 275 optimal weight: 7.9990 chunk 228 optimal weight: 0.7980 chunk 127 optimal weight: 30.0000 chunk 22 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 ASN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 HIS ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN K 395 ASN ** L 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 463 GLN ** J 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 23090 Z= 0.218 Angle : 0.712 17.051 31571 Z= 0.357 Chirality : 0.047 0.295 3683 Planarity : 0.005 0.066 4056 Dihedral : 5.706 28.177 3126 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer Outliers : 2.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.15), residues: 2860 helix: -2.10 (0.30), residues: 219 sheet: -1.17 (0.16), residues: 1036 loop : -1.75 (0.16), residues: 1605 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 368 time to evaluate : 2.777 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: 66 outliers final: 36 residues processed: 401 average time/residue: 0.3190 time to fit residues: 202.8254 Evaluate side-chains 365 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 329 time to evaluate : 2.613 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.2000 time to fit residues: 17.3148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 20.0000 chunk 31 optimal weight: 0.0670 chunk 157 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 156 optimal weight: 9.9990 chunk 232 optimal weight: 6.9990 chunk 153 optimal weight: 0.6980 chunk 274 optimal weight: 0.9990 chunk 171 optimal weight: 6.9990 chunk 167 optimal weight: 0.6980 chunk 126 optimal weight: 10.0000 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 487 GLN ** L 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 402 ASN ** L 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 ASN ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 518 HIS ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 23090 Z= 0.193 Angle : 0.716 16.472 31571 Z= 0.354 Chirality : 0.047 0.294 3683 Planarity : 0.005 0.061 4056 Dihedral : 5.564 26.438 3126 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.15), residues: 2860 helix: -2.06 (0.30), residues: 225 sheet: -1.08 (0.16), residues: 1035 loop : -1.66 (0.16), residues: 1600 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 371 time to evaluate : 2.833 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: 37 outliers final: 19 residues processed: 395 average time/residue: 0.3384 time to fit residues: 210.1193 Evaluate side-chains 353 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 334 time to evaluate : 2.482 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1984 time to fit residues: 10.5914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 20.0000 chunk 109 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 174 optimal weight: 0.1980 chunk 187 optimal weight: 20.0000 chunk 135 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 215 optimal weight: 30.0000 chunk 249 optimal weight: 9.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 ASN B 400 HIS ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN ** L 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 23090 Z= 0.327 Angle : 0.760 14.162 31571 Z= 0.384 Chirality : 0.049 0.285 3683 Planarity : 0.006 0.068 4056 Dihedral : 5.859 28.964 3126 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 23.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.19 % Favored : 88.78 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.15), residues: 2860 helix: -2.17 (0.30), residues: 213 sheet: -1.21 (0.15), residues: 1046 loop : -1.66 (0.16), residues: 1601 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 328 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 26 residues processed: 350 average time/residue: 0.3335 time to fit residues: 184.3553 Evaluate side-chains 339 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 313 time to evaluate : 2.565 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2047 time to fit residues: 13.4909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 7.9990 chunk 240 optimal weight: 4.9990 chunk 255 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 201 optimal weight: 6.9990 chunk 78 optimal weight: 20.0000 chunk 231 optimal weight: 2.9990 chunk 242 optimal weight: 30.0000 chunk 168 optimal weight: 2.9990 chunk 270 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 23090 Z= 0.321 Angle : 0.772 14.103 31571 Z= 0.388 Chirality : 0.049 0.292 3683 Planarity : 0.006 0.084 4056 Dihedral : 5.974 27.566 3126 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 23.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.15), residues: 2860 helix: -2.25 (0.29), residues: 225 sheet: -1.24 (0.16), residues: 1024 loop : -1.70 (0.16), residues: 1611 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 335 time to evaluate : 2.653 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: 30 outliers final: 20 residues processed: 350 average time/residue: 0.3412 time to fit residues: 187.2063 Evaluate side-chains 332 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 312 time to evaluate : 2.500 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2002 time to fit residues: 11.0901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 188 optimal weight: 10.0000 chunk 283 optimal weight: 1.9990 chunk 261 optimal weight: 0.0370 chunk 226 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 174 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 240 optimal weight: 4.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN ** L 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 GLN ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 518 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 23090 Z= 0.214 Angle : 0.752 15.212 31571 Z= 0.374 Chirality : 0.048 0.294 3683 Planarity : 0.005 0.062 4056 Dihedral : 5.731 29.689 3126 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.16), residues: 2860 helix: -2.04 (0.30), residues: 225 sheet: -1.14 (0.16), residues: 1035 loop : -1.59 (0.16), residues: 1600 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 347 time to evaluate : 2.571 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: 19 outliers final: 15 residues processed: 357 average time/residue: 0.3354 time to fit residues: 188.9878 Evaluate side-chains 336 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 321 time to evaluate : 2.652 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2210 time to fit residues: 9.7085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 0.2980 chunk 208 optimal weight: 8.9990 chunk 33 optimal weight: 0.1980 chunk 62 optimal weight: 7.9990 chunk 226 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 232 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 198 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 400 HIS ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.141524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.105414 restraints weight = 61423.379| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 4.49 r_work: 0.3751 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 23090 Z= 0.236 Angle : 0.756 13.195 31571 Z= 0.376 Chirality : 0.048 0.288 3683 Planarity : 0.006 0.082 4056 Dihedral : 5.710 29.830 3126 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.16), residues: 2860 helix: -2.04 (0.30), residues: 225 sheet: -1.14 (0.16), residues: 1036 loop : -1.59 (0.16), residues: 1599 =============================================================================== Job complete usr+sys time: 5853.64 seconds wall clock time: 106 minutes 23.93 seconds (6383.93 seconds total)