Starting phenix.real_space_refine on Sat Jun 29 19:18:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rh0_19164/06_2024/8rh0_19164.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rh0_19164/06_2024/8rh0_19164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rh0_19164/06_2024/8rh0_19164.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rh0_19164/06_2024/8rh0_19164.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rh0_19164/06_2024/8rh0_19164.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rh0_19164/06_2024/8rh0_19164.pdb" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 93 5.16 5 C 12021 2.51 5 N 3387 2.21 5 O 3636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 219": "OE1" <-> "OE2" Residue "A GLU 652": "OE1" <-> "OE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 651": "OE1" <-> "OE2" Residue "C PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 502": "OE1" <-> "OE2" Residue "H GLU 51": "OE1" <-> "OE2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "D GLU 87": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 19137 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4705 Classifications: {'peptide': 583} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 555} Chain breaks: 1 Chain: "B" Number of atoms: 4705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4705 Classifications: {'peptide': 583} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 555} Chain breaks: 1 Chain: "C" Number of atoms: 4705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4705 Classifications: {'peptide': 583} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 555} Chain breaks: 1 Chain: "H" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 773 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "E" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 773 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "G" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 773 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "D" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "F" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Time building chain proxies: 10.48, per 1000 atoms: 0.55 Number of scatterers: 19137 At special positions: 0 Unit cell: (185.231, 173.203, 174.406, 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 93 16.00 O 3636 8.00 N 3387 7.00 C 12021 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 573 " distance=2.06 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 529 " distance=2.06 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.07 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 412 " distance=2.05 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 633 " distance=2.05 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 573 " distance=2.04 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 529 " distance=2.06 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.07 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 412 " distance=2.04 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 633 " distance=2.05 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 573 " distance=2.06 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 529 " distance=2.06 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 271 " distance=2.07 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 412 " distance=2.10 Simple disulfide: pdb=" SG CYS C 596 " - pdb=" SG CYS C 633 " distance=2.05 Simple disulfide: pdb=" SG CYS H 27 " - pdb=" SG CYS H 101 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.06 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 87 " distance=2.04 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS D 101 " distance=2.03 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS F 101 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.06 Conformation dependent library (CDL) restraints added in 3.2 seconds 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4476 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 47 sheets defined 18.1% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.625A pdb=" N ARG A 406 " --> pdb=" O PRO A 403 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 407 " --> pdb=" O LEU A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 407' Processing helix chain 'A' and resid 411 through 428 removed outlier: 4.302A pdb=" N LYS A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 546 removed outlier: 3.586A pdb=" N ARG A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU A 538 " --> pdb=" O HIS A 534 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS A 544 " --> pdb=" O ASN A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 removed outlier: 3.558A pdb=" N ILE A 550 " --> pdb=" O ASN A 546 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'A' and resid 660 through 664 removed outlier: 3.514A pdb=" N ILE A 664 " --> pdb=" O ARG A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 697 Processing helix chain 'A' and resid 701 through 710 Processing helix chain 'A' and resid 711 through 716 Processing helix chain 'B' and resid 193 through 198 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 410 through 428 removed outlier: 4.625A pdb=" N GLY B 414 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS B 415 " --> pdb=" O ASP B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 543 removed outlier: 3.725A pdb=" N GLY B 522 " --> pdb=" O ASN B 518 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU B 538 " --> pdb=" O HIS B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 removed outlier: 3.698A pdb=" N ILE B 550 " --> pdb=" O ASN B 546 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 556 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 660 through 664 Processing helix chain 'B' and resid 690 through 697 Processing helix chain 'B' and resid 701 through 710 Processing helix chain 'B' and resid 711 through 716 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 306 through 310 removed outlier: 3.877A pdb=" N THR C 309 " --> pdb=" O GLY C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 411 through 428 removed outlier: 4.320A pdb=" N LYS C 415 " --> pdb=" O ASP C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 546 removed outlier: 3.711A pdb=" N LEU C 536 " --> pdb=" O GLN C 532 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR C 537 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU C 538 " --> pdb=" O HIS C 534 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU C 541 " --> pdb=" O THR C 537 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS C 544 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 removed outlier: 3.600A pdb=" N ILE C 550 " --> pdb=" O ASN C 546 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY C 556 " --> pdb=" O SER C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 660 through 664 removed outlier: 3.606A pdb=" N ILE C 664 " --> pdb=" O ARG C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 697 Processing helix chain 'C' and resid 701 through 710 Processing helix chain 'C' and resid 711 through 717 removed outlier: 3.516A pdb=" N ALA C 717 " --> pdb=" O ASP C 713 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 70 removed outlier: 3.725A pdb=" N GLN H 70 " --> pdb=" O ARG H 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 67 through 70' Processing helix chain 'H' and resid 92 through 96 removed outlier: 3.777A pdb=" N THR H 96 " --> pdb=" O PHE H 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 30 removed outlier: 3.536A pdb=" N SER L 29 " --> pdb=" O ASN L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.841A pdb=" N GLU L 82 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 30 removed outlier: 3.579A pdb=" N SER E 29 " --> pdb=" O ASN E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 82 removed outlier: 3.867A pdb=" N GLU E 82 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 30 Processing helix chain 'G' and resid 78 through 82 removed outlier: 3.951A pdb=" N GLU G 82 " --> pdb=" O ALA G 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 70 removed outlier: 3.662A pdb=" N GLN D 70 " --> pdb=" O ARG D 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 67 through 70' Processing helix chain 'D' and resid 92 through 96 removed outlier: 3.749A pdb=" N THR D 96 " --> pdb=" O PHE D 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 70 removed outlier: 3.682A pdb=" N GLN F 70 " --> pdb=" O ARG F 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 67 through 70' Processing helix chain 'F' and resid 92 through 96 removed outlier: 3.769A pdb=" N THR F 96 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 574 through 576 removed outlier: 7.018A pdb=" N TYR A 114 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 559 through 563 removed outlier: 3.506A pdb=" N MET A 568 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 124 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL C 667 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLN A 126 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 366 through 372 removed outlier: 5.400A pdb=" N LYS A 368 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LYS A 151 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 366 through 372 removed outlier: 5.400A pdb=" N LYS A 368 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LYS A 151 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 191 removed outlier: 5.532A pdb=" N PHE A 182 " --> pdb=" O TRP A 174 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP A 174 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 184 " --> pdb=" O GLN A 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 235 through 236 removed outlier: 7.016A pdb=" N LYS A 160 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP A 355 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N THR A 340 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY A 324 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 206 through 208 Processing sheet with id=AA8, first strand: chain 'A' and resid 210 through 214 Processing sheet with id=AA9, first strand: chain 'A' and resid 375 through 380 Processing sheet with id=AB1, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AB2, first strand: chain 'A' and resid 638 through 643 removed outlier: 5.414A pdb=" N GLU A 651 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N TYR A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 665 through 667 removed outlier: 4.205A pdb=" N THR A 665 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET B 568 " --> pdb=" O VAL B 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 574 through 576 removed outlier: 6.757A pdb=" N TYR B 114 " --> pdb=" O LEU B 623 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 366 through 372 removed outlier: 6.601A pdb=" N VAL B 149 " --> pdb=" O TRP B 369 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU B 371 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA B 147 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 366 through 372 removed outlier: 6.601A pdb=" N VAL B 149 " --> pdb=" O TRP B 369 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU B 371 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA B 147 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 180 through 191 removed outlier: 5.610A pdb=" N PHE B 182 " --> pdb=" O TRP B 174 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TRP B 174 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 184 " --> pdb=" O GLN B 172 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 235 through 236 removed outlier: 7.106A pdb=" N LYS B 160 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP B 355 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N THR B 340 " --> pdb=" O GLY B 324 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY B 324 " --> pdb=" O THR B 340 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 206 through 208 Processing sheet with id=AC1, first strand: chain 'B' and resid 210 through 214 Processing sheet with id=AC2, first strand: chain 'B' and resid 375 through 380 Processing sheet with id=AC3, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AC4, first strand: chain 'B' and resid 638 through 643 removed outlier: 5.927A pdb=" N GLU B 651 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TYR B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 666 through 667 removed outlier: 3.616A pdb=" N MET C 568 " --> pdb=" O VAL C 125 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 574 through 576 removed outlier: 6.797A pdb=" N TYR C 114 " --> pdb=" O LEU C 623 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 366 through 372 removed outlier: 5.473A pdb=" N LYS C 368 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LYS C 151 " --> pdb=" O LYS C 368 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 366 through 372 removed outlier: 5.473A pdb=" N LYS C 368 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LYS C 151 " --> pdb=" O LYS C 368 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 180 through 191 removed outlier: 5.594A pdb=" N PHE C 182 " --> pdb=" O TRP C 174 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TRP C 174 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY C 184 " --> pdb=" O GLN C 172 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 235 through 236 removed outlier: 7.304A pdb=" N LYS C 160 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASP C 355 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N THR C 340 " --> pdb=" O GLY C 324 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY C 324 " --> pdb=" O THR C 340 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AD3, first strand: chain 'C' and resid 210 through 214 Processing sheet with id=AD4, first strand: chain 'C' and resid 375 through 380 Processing sheet with id=AD5, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AD6, first strand: chain 'C' and resid 638 through 643 removed outlier: 5.675A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 8 through 11 Processing sheet with id=AD8, first strand: chain 'H' and resid 15 through 16 removed outlier: 6.605A pdb=" N ILE H 39 " --> pdb=" O TRP H 55 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TRP H 55 " --> pdb=" O ILE H 39 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP H 41 " --> pdb=" O MET H 53 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.735A pdb=" N VAL L 10 " --> pdb=" O THR L 104 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.735A pdb=" N VAL L 10 " --> pdb=" O THR L 104 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AE3, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.685A pdb=" N TRP E 34 " --> pdb=" O VAL E 46 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 9 through 12 Processing sheet with id=AE5, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AE6, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.810A pdb=" N VAL G 10 " --> pdb=" O THR G 104 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TRP G 34 " --> pdb=" O VAL G 46 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AE8, first strand: chain 'D' and resid 8 through 11 Processing sheet with id=AE9, first strand: chain 'D' and resid 15 through 16 removed outlier: 5.798A pdb=" N ARG D 43 " --> pdb=" O TRP D 52 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N TRP D 52 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 8 through 11 Processing sheet with id=AF2, first strand: chain 'F' and resid 15 through 16 removed outlier: 6.653A pdb=" N ILE F 39 " --> pdb=" O TRP F 55 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TRP F 55 " --> pdb=" O ILE F 39 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TRP F 41 " --> pdb=" O MET F 53 " (cutoff:3.500A) 825 hydrogen bonds defined for protein. 2190 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: 6.78 Time building geometry restraints manager: 6.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6333 1.34 - 1.47: 5044 1.47 - 1.59: 8081 1.59 - 1.71: 0 1.71 - 1.84: 144 Bond restraints: 19602 Sorted by residual: bond pdb=" CE1 HIS A 308 " pdb=" NE2 HIS A 308 " ideal model delta sigma weight residual 1.321 1.363 -0.042 1.00e-02 1.00e+04 1.77e+01 bond pdb=" CE1 HIS A 512 " pdb=" NE2 HIS A 512 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.71e+01 bond pdb=" CE1 HIS F 32 " pdb=" NE2 HIS F 32 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.69e+01 bond pdb=" NE ARG C 132 " pdb=" CZ ARG C 132 " ideal model delta sigma weight residual 1.326 1.371 -0.045 1.10e-02 8.26e+03 1.69e+01 bond pdb=" CE1 HIS B 692 " pdb=" NE2 HIS B 692 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.68e+01 ... (remaining 19597 not shown) Histogram of bond angle deviations from ideal: 99.23 - 106.23: 504 106.23 - 113.23: 10361 113.23 - 120.23: 6788 120.23 - 127.23: 8760 127.23 - 134.23: 224 Bond angle restraints: 26637 Sorted by residual: angle pdb=" CA THR B 690 " pdb=" C THR B 690 " pdb=" O THR B 690 " ideal model delta sigma weight residual 121.99 118.12 3.87 1.14e+00 7.69e-01 1.15e+01 angle pdb=" CA ARG B 242 " pdb=" C ARG B 242 " pdb=" O ARG B 242 " ideal model delta sigma weight residual 121.84 118.13 3.71 1.16e+00 7.43e-01 1.02e+01 angle pdb=" CA THR B 241 " pdb=" C THR B 241 " pdb=" O THR B 241 " ideal model delta sigma weight residual 121.56 118.09 3.47 1.09e+00 8.42e-01 1.01e+01 angle pdb=" CA LEU A 601 " pdb=" C LEU A 601 " pdb=" O LEU A 601 " ideal model delta sigma weight residual 121.47 117.94 3.53 1.15e+00 7.56e-01 9.41e+00 angle pdb=" CA LEU A 564 " pdb=" CB LEU A 564 " pdb=" CG LEU A 564 " ideal model delta sigma weight residual 116.30 126.64 -10.34 3.50e+00 8.16e-02 8.73e+00 ... (remaining 26632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 10572 17.68 - 35.36: 813 35.36 - 53.03: 156 53.03 - 70.71: 61 70.71 - 88.39: 20 Dihedral angle restraints: 11622 sinusoidal: 4614 harmonic: 7008 Sorted by residual: dihedral pdb=" CB CYS A 116 " pdb=" SG CYS A 116 " pdb=" SG CYS A 573 " pdb=" CB CYS A 573 " ideal model delta sinusoidal sigma weight residual 93.00 10.67 82.33 1 1.00e+01 1.00e-02 8.32e+01 dihedral pdb=" CA TYR E 49 " pdb=" C TYR E 49 " pdb=" N ASP E 50 " pdb=" CA ASP E 50 " ideal model delta harmonic sigma weight residual 180.00 157.67 22.33 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA CYS A 573 " pdb=" C CYS A 573 " pdb=" N VAL A 574 " pdb=" CA VAL A 574 " ideal model delta harmonic sigma weight residual -180.00 -158.13 -21.87 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 11619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1398 0.030 - 0.061: 954 0.061 - 0.091: 305 0.091 - 0.121: 186 0.121 - 0.152: 43 Chirality restraints: 2886 Sorted by residual: chirality pdb=" CA LEU A 601 " pdb=" N LEU A 601 " pdb=" C LEU A 601 " pdb=" CB LEU A 601 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA ILE A 675 " pdb=" N ILE A 675 " pdb=" C ILE A 675 " pdb=" CB ILE A 675 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA VAL B 570 " pdb=" N VAL B 570 " pdb=" C VAL B 570 " pdb=" CB VAL B 570 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 2883 not shown) Planarity restraints: 3483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 512 " 0.032 2.00e-02 2.50e+03 2.98e-02 1.33e+01 pdb=" CG HIS A 512 " -0.063 2.00e-02 2.50e+03 pdb=" ND1 HIS A 512 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS A 512 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 HIS A 512 " 0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS A 512 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 264 " 0.231 9.50e-02 1.11e+02 1.03e-01 6.73e+00 pdb=" NE ARG C 264 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG C 264 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG C 264 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG C 264 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 512 " 0.027 2.00e-02 2.50e+03 2.01e-02 6.09e+00 pdb=" CG HIS B 512 " -0.026 2.00e-02 2.50e+03 pdb=" ND1 HIS B 512 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 HIS B 512 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 HIS B 512 " 0.018 2.00e-02 2.50e+03 pdb=" NE2 HIS B 512 " 0.013 2.00e-02 2.50e+03 ... (remaining 3480 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1271 2.74 - 3.28: 17817 3.28 - 3.82: 30668 3.82 - 4.36: 37314 4.36 - 4.90: 66349 Nonbonded interactions: 153419 Sorted by model distance: nonbonded pdb=" OE2 GLU A 687 " pdb=" OG1 THR B 498 " model vdw 2.202 2.440 nonbonded pdb=" OG SER H 60 " pdb=" OD1 ASN H 62 " model vdw 2.207 2.440 nonbonded pdb=" OH TYR A 380 " pdb=" OD2 ASP C 680 " model vdw 2.216 2.440 nonbonded pdb=" OG1 THR A 642 " pdb=" OD2 ASP B 566 " model vdw 2.229 2.440 nonbonded pdb=" O ASN C 202 " pdb=" NH2 ARG C 335 " model vdw 2.244 2.520 ... (remaining 153414 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.290 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: 5.910 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 48.690 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.005 0.045 19602 Z= 0.323 Angle : 0.616 10.341 26637 Z= 0.359 Chirality : 0.048 0.152 2886 Planarity : 0.008 0.103 3483 Dihedral : 14.040 88.388 7083 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.19 (0.16), residues: 2397 helix: 0.59 (0.29), residues: 309 sheet: 0.73 (0.18), residues: 840 loop : -0.37 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.005 TRP A 539 HIS 0.027 0.003 HIS A 512 PHE 0.025 0.003 PHE A 294 TYR 0.031 0.004 TYR B 303 ARG 0.026 0.002 ARG C 691 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 2.232 Fit side-chains REVERT: B 568 MET cc_start: 0.7809 (ptp) cc_final: 0.7434 (ptp) REVERT: B 677 MET cc_start: 0.8459 (mmp) cc_final: 0.8123 (mmm) REVERT: C 653 TYR cc_start: 0.6305 (m-80) cc_final: 0.5791 (m-80) REVERT: C 677 MET cc_start: 0.8451 (mmm) cc_final: 0.7948 (mmm) REVERT: E 68 ASN cc_start: 0.8422 (m-40) cc_final: 0.8210 (m-40) REVERT: D 8 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7618 (mt0) REVERT: D 75 MET cc_start: 0.8804 (mtt) cc_final: 0.8529 (mtt) REVERT: D 92 ARG cc_start: 0.8077 (mtt180) cc_final: 0.7740 (mtt-85) REVERT: D 115 ASP cc_start: 0.8423 (p0) cc_final: 0.7945 (t70) REVERT: F 75 MET cc_start: 0.9247 (mtt) cc_final: 0.8977 (mtt) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.3313 time to fit residues: 145.4857 Evaluate side-chains 224 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 185 optimal weight: 0.4980 chunk 71 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN A 507 GLN A 511 ASN A 532 GLN ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 HIS C 534 HIS ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN D 32 HIS ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 HIS ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19602 Z= 0.296 Angle : 0.561 13.006 26637 Z= 0.299 Chirality : 0.044 0.179 2886 Planarity : 0.004 0.038 3483 Dihedral : 4.324 22.059 2712 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.22 % Allowed : 7.37 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.22 (0.16), residues: 2397 helix: 0.69 (0.29), residues: 315 sheet: 0.72 (0.17), residues: 849 loop : -0.35 (0.16), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 52 HIS 0.008 0.001 HIS A 534 PHE 0.017 0.002 PHE F 34 TYR 0.033 0.002 TYR G 48 ARG 0.005 0.001 ARG B 691 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 236 time to evaluate : 2.096 Fit side-chains REVERT: A 366 MET cc_start: 0.8085 (mmt) cc_final: 0.7772 (mmt) REVERT: B 366 MET cc_start: 0.8587 (mmt) cc_final: 0.8296 (mmt) REVERT: B 562 ARG cc_start: 0.7842 (ptm-80) cc_final: 0.7612 (ptm160) REVERT: B 568 MET cc_start: 0.7886 (ptp) cc_final: 0.7345 (ptp) REVERT: C 568 MET cc_start: 0.7010 (mtp) cc_final: 0.6673 (ttm) REVERT: C 677 MET cc_start: 0.8524 (mmm) cc_final: 0.8034 (mmm) REVERT: E 68 ASN cc_start: 0.8534 (m-40) cc_final: 0.8329 (m-40) REVERT: D 8 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7677 (mt0) REVERT: D 92 ARG cc_start: 0.8029 (mtt180) cc_final: 0.7745 (mtt-85) outliers start: 25 outliers final: 18 residues processed: 250 average time/residue: 0.3259 time to fit residues: 120.9410 Evaluate side-chains 231 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 213 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 56 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 119 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 213 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 HIS B 238 ASN ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 ASN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 19602 Z= 0.405 Angle : 0.595 13.390 26637 Z= 0.321 Chirality : 0.046 0.203 2886 Planarity : 0.005 0.049 3483 Dihedral : 4.563 22.149 2712 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.34 % Allowed : 10.00 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.05 (0.16), residues: 2397 helix: 0.39 (0.29), residues: 315 sheet: 0.45 (0.17), residues: 882 loop : -0.45 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 52 HIS 0.008 0.002 HIS A 534 PHE 0.019 0.002 PHE B 641 TYR 0.032 0.002 TYR G 48 ARG 0.005 0.001 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 220 time to evaluate : 2.239 Fit side-chains revert: symmetry clash REVERT: B 568 MET cc_start: 0.8068 (ptp) cc_final: 0.7593 (ptp) REVERT: C 568 MET cc_start: 0.7049 (mtp) cc_final: 0.6649 (ttm) REVERT: C 677 MET cc_start: 0.8497 (mmm) cc_final: 0.7977 (mmm) REVERT: H 67 ARG cc_start: 0.7255 (mtm110) cc_final: 0.7034 (mtm110) REVERT: E 68 ASN cc_start: 0.8666 (m-40) cc_final: 0.8438 (m-40) REVERT: D 92 ARG cc_start: 0.8089 (mtt180) cc_final: 0.7719 (mtt-85) outliers start: 48 outliers final: 35 residues processed: 254 average time/residue: 0.3491 time to fit residues: 131.6923 Evaluate side-chains 244 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 209 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 512 HIS Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain F residue 42 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 213 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 102 optimal weight: 0.0980 chunk 144 optimal weight: 1.9990 chunk 216 optimal weight: 4.9990 chunk 229 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19602 Z= 0.178 Angle : 0.485 13.374 26637 Z= 0.259 Chirality : 0.042 0.143 2886 Planarity : 0.004 0.042 3483 Dihedral : 4.141 22.271 2712 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.56 % Allowed : 12.40 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.24 (0.17), residues: 2397 helix: 0.86 (0.29), residues: 315 sheet: 0.67 (0.17), residues: 864 loop : -0.34 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 52 HIS 0.006 0.001 HIS B 534 PHE 0.014 0.001 PHE F 34 TYR 0.021 0.001 TYR C 655 ARG 0.006 0.000 ARG A 624 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 232 time to evaluate : 2.142 Fit side-chains revert: symmetry clash REVERT: A 604 PHE cc_start: 0.7927 (p90) cc_final: 0.7484 (p90) REVERT: B 366 MET cc_start: 0.8661 (mmt) cc_final: 0.8378 (mmt) REVERT: B 562 ARG cc_start: 0.7953 (ptm-80) cc_final: 0.7653 (ptm160) REVERT: B 568 MET cc_start: 0.7999 (ptp) cc_final: 0.7547 (ptp) REVERT: C 677 MET cc_start: 0.8508 (mmm) cc_final: 0.8058 (mmm) REVERT: H 67 ARG cc_start: 0.7349 (mtm110) cc_final: 0.7118 (mtm110) REVERT: E 68 ASN cc_start: 0.8587 (m-40) cc_final: 0.8328 (m-40) outliers start: 32 outliers final: 23 residues processed: 256 average time/residue: 0.3345 time to fit residues: 127.4643 Evaluate side-chains 243 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 220 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain F residue 42 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 190 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 195 optimal weight: 0.0470 chunk 158 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 205 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 19602 Z= 0.308 Angle : 0.528 14.185 26637 Z= 0.284 Chirality : 0.044 0.171 2886 Planarity : 0.004 0.043 3483 Dihedral : 4.300 22.293 2712 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.49 % Allowed : 12.45 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.15 (0.17), residues: 2397 helix: 0.64 (0.29), residues: 315 sheet: 0.61 (0.17), residues: 873 loop : -0.36 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 52 HIS 0.006 0.001 HIS B 534 PHE 0.018 0.001 PHE F 34 TYR 0.025 0.002 TYR E 48 ARG 0.005 0.000 ARG A 624 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 218 time to evaluate : 2.155 Fit side-chains revert: symmetry clash REVERT: A 534 HIS cc_start: 0.8355 (OUTLIER) cc_final: 0.8137 (t-90) REVERT: A 673 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8683 (tt) REVERT: B 562 ARG cc_start: 0.7980 (ptm-80) cc_final: 0.7693 (ptm160) REVERT: B 568 MET cc_start: 0.8024 (ptp) cc_final: 0.7648 (ptp) REVERT: C 677 MET cc_start: 0.8524 (mmm) cc_final: 0.8093 (mmm) REVERT: H 67 ARG cc_start: 0.7261 (mtm110) cc_final: 0.7013 (mtm110) REVERT: E 68 ASN cc_start: 0.8649 (m-40) cc_final: 0.8421 (m-40) outliers start: 51 outliers final: 41 residues processed: 258 average time/residue: 0.3540 time to fit residues: 135.2996 Evaluate side-chains 258 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 215 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 512 HIS Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 640 TYR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain F residue 42 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 77 optimal weight: 0.8980 chunk 206 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 229 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19602 Z= 0.189 Angle : 0.474 13.224 26637 Z= 0.255 Chirality : 0.042 0.143 2886 Planarity : 0.004 0.040 3483 Dihedral : 4.098 22.218 2712 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.15 % Allowed : 13.47 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.29 (0.17), residues: 2397 helix: 0.86 (0.29), residues: 315 sheet: 0.73 (0.17), residues: 864 loop : -0.33 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 52 HIS 0.006 0.001 HIS B 534 PHE 0.014 0.001 PHE F 34 TYR 0.018 0.001 TYR E 48 ARG 0.006 0.000 ARG F 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 224 time to evaluate : 2.126 Fit side-chains revert: symmetry clash REVERT: A 534 HIS cc_start: 0.8246 (OUTLIER) cc_final: 0.8031 (t-90) REVERT: B 562 ARG cc_start: 0.7951 (ptm-80) cc_final: 0.7658 (ptm160) REVERT: B 568 MET cc_start: 0.7946 (ptp) cc_final: 0.7432 (ptp) REVERT: C 677 MET cc_start: 0.8437 (mmm) cc_final: 0.8095 (mmm) outliers start: 44 outliers final: 37 residues processed: 255 average time/residue: 0.3383 time to fit residues: 128.6570 Evaluate side-chains 259 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 221 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 512 HIS Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 42 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 221 optimal weight: 0.0670 chunk 25 optimal weight: 0.1980 chunk 130 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 193 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 228 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19602 Z= 0.220 Angle : 0.488 14.919 26637 Z= 0.261 Chirality : 0.042 0.147 2886 Planarity : 0.004 0.040 3483 Dihedral : 4.110 22.150 2712 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.68 % Allowed : 13.27 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.28 (0.17), residues: 2397 helix: 0.84 (0.29), residues: 315 sheet: 0.67 (0.17), residues: 882 loop : -0.29 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 52 HIS 0.005 0.001 HIS B 534 PHE 0.015 0.001 PHE F 34 TYR 0.022 0.001 TYR C 429 ARG 0.006 0.000 ARG F 89 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 229 time to evaluate : 2.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 534 HIS cc_start: 0.8297 (OUTLIER) cc_final: 0.8075 (t-90) REVERT: A 604 PHE cc_start: 0.7743 (p90) cc_final: 0.7496 (p90) REVERT: A 673 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8600 (tt) REVERT: B 562 ARG cc_start: 0.7922 (ptm-80) cc_final: 0.7641 (ptm160) REVERT: B 568 MET cc_start: 0.7990 (ptp) cc_final: 0.7417 (ptp) REVERT: C 677 MET cc_start: 0.8450 (mmm) cc_final: 0.8119 (mmm) outliers start: 55 outliers final: 46 residues processed: 269 average time/residue: 0.3280 time to fit residues: 131.8912 Evaluate side-chains 269 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 221 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 512 HIS Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 115 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 141 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 145 optimal weight: 0.0770 chunk 155 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 207 optimal weight: 0.0970 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 GLN ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 ASN D 32 HIS ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19602 Z= 0.153 Angle : 0.461 14.434 26637 Z= 0.247 Chirality : 0.041 0.140 2886 Planarity : 0.004 0.040 3483 Dihedral : 3.930 21.702 2712 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.24 % Allowed : 13.62 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.47 (0.17), residues: 2397 helix: 1.09 (0.30), residues: 315 sheet: 0.86 (0.17), residues: 864 loop : -0.24 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 52 HIS 0.005 0.001 HIS B 534 PHE 0.013 0.001 PHE B 262 TYR 0.018 0.001 TYR C 429 ARG 0.008 0.000 ARG F 89 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 237 time to evaluate : 2.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 MET cc_start: 0.8049 (tpp) cc_final: 0.7590 (mtp) REVERT: A 534 HIS cc_start: 0.8142 (OUTLIER) cc_final: 0.7926 (t-90) REVERT: A 604 PHE cc_start: 0.7733 (p90) cc_final: 0.7475 (p90) REVERT: A 616 GLN cc_start: 0.7915 (tp-100) cc_final: 0.7689 (tp-100) REVERT: B 562 ARG cc_start: 0.7932 (ptm-80) cc_final: 0.7640 (ptm160) REVERT: B 568 MET cc_start: 0.7951 (ptp) cc_final: 0.7380 (ptp) REVERT: C 677 MET cc_start: 0.8510 (mmm) cc_final: 0.8224 (mmm) outliers start: 46 outliers final: 37 residues processed: 270 average time/residue: 0.3466 time to fit residues: 137.2890 Evaluate side-chains 258 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 220 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 42 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 218 optimal weight: 0.8980 chunk 199 optimal weight: 0.6980 chunk 212 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 192 optimal weight: 0.9990 chunk 201 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 GLN D 32 HIS ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19602 Z= 0.198 Angle : 0.481 14.888 26637 Z= 0.257 Chirality : 0.042 0.145 2886 Planarity : 0.004 0.041 3483 Dihedral : 3.982 21.735 2712 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.29 % Allowed : 14.20 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.46 (0.17), residues: 2397 helix: 1.00 (0.29), residues: 315 sheet: 0.85 (0.17), residues: 867 loop : -0.22 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 52 HIS 0.005 0.001 HIS B 534 PHE 0.020 0.001 PHE B 650 TYR 0.019 0.001 TYR L 48 ARG 0.008 0.000 ARG D 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 223 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 MET cc_start: 0.8035 (tpp) cc_final: 0.7620 (mtp) REVERT: A 534 HIS cc_start: 0.8155 (OUTLIER) cc_final: 0.7946 (t-90) REVERT: A 604 PHE cc_start: 0.7783 (p90) cc_final: 0.7505 (p90) REVERT: A 616 GLN cc_start: 0.7974 (tp-100) cc_final: 0.7646 (tp-100) REVERT: B 562 ARG cc_start: 0.7948 (ptm-80) cc_final: 0.7650 (ptm160) REVERT: B 568 MET cc_start: 0.7965 (ptp) cc_final: 0.7391 (ptp) REVERT: C 653 TYR cc_start: 0.6189 (m-80) cc_final: 0.5448 (m-80) REVERT: C 677 MET cc_start: 0.8512 (mmm) cc_final: 0.8243 (mmm) REVERT: G 48 TYR cc_start: 0.9119 (OUTLIER) cc_final: 0.8726 (p90) outliers start: 47 outliers final: 42 residues processed: 256 average time/residue: 0.3282 time to fit residues: 125.2055 Evaluate side-chains 262 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 218 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 512 HIS Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain G residue 48 TYR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 115 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 236 optimal weight: 6.9990 chunk 217 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 GLN ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 657 HIS D 32 HIS ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19602 Z= 0.273 Angle : 0.516 14.295 26637 Z= 0.276 Chirality : 0.043 0.157 2886 Planarity : 0.004 0.051 3483 Dihedral : 4.151 21.873 2712 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.59 % Allowed : 14.10 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.32 (0.17), residues: 2397 helix: 0.82 (0.29), residues: 315 sheet: 0.71 (0.17), residues: 882 loop : -0.26 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 52 HIS 0.005 0.001 HIS B 534 PHE 0.022 0.001 PHE B 650 TYR 0.024 0.002 TYR L 48 ARG 0.010 0.000 ARG C 599 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 222 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 534 HIS cc_start: 0.8273 (OUTLIER) cc_final: 0.8050 (t-90) REVERT: B 562 ARG cc_start: 0.7952 (ptm-80) cc_final: 0.7680 (ptm160) REVERT: B 568 MET cc_start: 0.7953 (ptp) cc_final: 0.7575 (ptp) REVERT: C 677 MET cc_start: 0.8522 (mmm) cc_final: 0.8233 (mmm) outliers start: 53 outliers final: 46 residues processed: 262 average time/residue: 0.3428 time to fit residues: 134.4546 Evaluate side-chains 269 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 222 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 512 HIS Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain G residue 48 TYR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 115 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 57 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS ** D 40 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 = 0.3566 r_free = 0.3566 target = 0.123845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.097756 restraints weight = 29447.346| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.82 r_work: 0.3062 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 19602 Z= 0.317 Angle : 0.543 14.568 26637 Z= 0.291 Chirality : 0.044 0.176 2886 Planarity : 0.004 0.052 3483 Dihedral : 4.297 22.301 2712 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.44 % Allowed : 14.25 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.18 (0.17), residues: 2397 helix: 0.69 (0.29), residues: 315 sheet: 0.61 (0.17), residues: 882 loop : -0.35 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 539 HIS 0.005 0.001 HIS B 534 PHE 0.024 0.002 PHE B 650 TYR 0.026 0.002 TYR L 48 ARG 0.010 0.000 ARG C 599 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3960.47 seconds wall clock time: 71 minutes 19.76 seconds (4279.76 seconds total)