Starting phenix.real_space_refine on Fri Mar 15 18:08:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfd_12300/03_2024/7nfd_12300_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfd_12300/03_2024/7nfd_12300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfd_12300/03_2024/7nfd_12300.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfd_12300/03_2024/7nfd_12300.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfd_12300/03_2024/7nfd_12300_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfd_12300/03_2024/7nfd_12300_updated.pdb" } resolution = 3.51 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= 0.001 sd= 0.081 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 68 5.16 5 C 7998 2.51 5 N 2040 2.21 5 O 2288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 62": "OE1" <-> "OE2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "F ARG 65": "NH1" <-> "NH2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B GLU 330": "OE1" <-> "OE2" Residue "B GLU 344": "OE1" <-> "OE2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B ARG 426": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12394 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 926 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 926 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "B" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'MIX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.57, per 1000 atoms: 0.53 Number of scatterers: 12394 At special positions: 0 Unit cell: (100.32, 98.34, 147.18, 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 68 16.00 O 2288 8.00 N 2040 7.00 C 7998 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.05 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.02 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.02 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG G 1 " - " ASN A 596 " " NAG H 1 " - " ASN B 596 " Time building additional restraints: 4.63 Conformation dependent library (CDL) restraints added in 2.1 seconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 10 sheets defined 37.5% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 86 through 94 Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 136 through 147 removed outlier: 3.717A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 167 Processing helix chain 'A' and resid 188 through 199 removed outlier: 3.807A pdb=" N ARG A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 232 Processing helix chain 'A' and resid 270 through 280 removed outlier: 4.860A pdb=" N LEU A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLY A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 300 removed outlier: 4.559A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLY A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 332 No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 334 through 337 No H-bonds generated for 'chain 'A' and resid 334 through 337' Processing helix chain 'A' and resid 340 through 352 removed outlier: 4.260A pdb=" N GLU A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 390 removed outlier: 4.101A pdb=" N VAL A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 382 " --> pdb=" O ARG A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 412 Processing helix chain 'A' and resid 420 through 441 removed outlier: 4.591A pdb=" N GLN A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 460 Processing helix chain 'A' and resid 466 through 476 Processing helix chain 'A' and resid 479 through 482 No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 488 through 497 removed outlier: 3.848A pdb=" N TYR A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 527 removed outlier: 4.502A pdb=" N MET A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 550 Processing helix chain 'A' and resid 566 through 570 removed outlier: 3.528A pdb=" N GLN A 569 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR A 570 " --> pdb=" O TRP A 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 566 through 570' Processing helix chain 'A' and resid 573 through 585 removed outlier: 3.727A pdb=" N ALA A 580 " --> pdb=" O TYR A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 616 Processing helix chain 'A' and resid 623 through 649 removed outlier: 4.672A pdb=" N LYS A 628 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 631 " --> pdb=" O LYS A 628 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 632 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA A 634 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N CYS A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET A 636 " --> pdb=" O LEU A 633 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE A 637 " --> pdb=" O ALA A 634 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE A 639 " --> pdb=" O MET A 636 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE A 643 " --> pdb=" O PHE A 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 82 No H-bonds generated for 'chain 'C' and resid 80 through 82' Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'B' and resid 86 through 94 Processing helix chain 'B' and resid 118 through 120 No H-bonds generated for 'chain 'B' and resid 118 through 120' Processing helix chain 'B' and resid 136 through 147 removed outlier: 3.717A pdb=" N LEU B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 167 Processing helix chain 'B' and resid 188 through 199 removed outlier: 3.807A pdb=" N ARG B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 232 Processing helix chain 'B' and resid 270 through 280 removed outlier: 4.860A pdb=" N LEU B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLY B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 300 removed outlier: 4.558A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 332 No H-bonds generated for 'chain 'B' and resid 329 through 332' Processing helix chain 'B' and resid 334 through 337 No H-bonds generated for 'chain 'B' and resid 334 through 337' Processing helix chain 'B' and resid 340 through 352 removed outlier: 4.260A pdb=" N GLU B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 390 removed outlier: 4.100A pdb=" N VAL B 380 " --> pdb=" O GLN B 376 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS B 382 " --> pdb=" O ARG B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 412 Processing helix chain 'B' and resid 420 through 439 removed outlier: 4.591A pdb=" N GLN B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE B 431 " --> pdb=" O ALA B 427 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN B 436 " --> pdb=" O PHE B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 444 No H-bonds generated for 'chain 'B' and resid 442 through 444' Processing helix chain 'B' and resid 452 through 460 Processing helix chain 'B' and resid 466 through 476 Processing helix chain 'B' and resid 479 through 482 No H-bonds generated for 'chain 'B' and resid 479 through 482' Processing helix chain 'B' and resid 488 through 497 removed outlier: 3.848A pdb=" N TYR B 494 " --> pdb=" O THR B 490 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 527 removed outlier: 4.502A pdb=" N MET B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 550 Processing helix chain 'B' and resid 566 through 570 removed outlier: 3.528A pdb=" N GLN B 569 " --> pdb=" O SER B 566 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR B 570 " --> pdb=" O TRP B 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 566 through 570' Processing helix chain 'B' and resid 573 through 585 removed outlier: 3.728A pdb=" N ALA B 580 " --> pdb=" O TYR B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 616 Processing helix chain 'B' and resid 623 through 649 removed outlier: 4.672A pdb=" N LYS B 628 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 631 " --> pdb=" O LYS B 628 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 632 " --> pdb=" O ASN B 629 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA B 634 " --> pdb=" O VAL B 631 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N CYS B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET B 636 " --> pdb=" O LEU B 633 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE B 637 " --> pdb=" O ALA B 634 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE B 639 " --> pdb=" O MET B 636 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE B 643 " --> pdb=" O PHE B 640 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 75 through 77 removed outlier: 6.206A pdb=" N ILE A 238 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 239 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 241 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 122 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP A 210 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 258 through 260 removed outlier: 6.143A pdb=" N ALA A 260 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 20 through 24 removed outlier: 3.761A pdb=" N TYR C 71 " --> pdb=" O CYS C 23 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 86 through 90 removed outlier: 5.696A pdb=" N GLN C 37 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU C 46 " --> pdb=" O GLN C 37 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 68 through 71 Processing sheet with id= F, first strand: chain 'E' and resid 20 through 24 removed outlier: 3.761A pdb=" N TYR E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 86 through 90 removed outlier: 5.695A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 68 through 71 Processing sheet with id= I, first strand: chain 'B' and resid 75 through 77 removed outlier: 6.206A pdb=" N ILE B 238 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE B 239 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER B 241 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY B 122 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP B 210 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 258 through 260 removed outlier: 6.143A pdb=" N ALA B 260 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 996 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: 2.97 Time building geometry restraints manager: 5.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1934 1.28 - 1.42: 3372 1.42 - 1.55: 7248 1.55 - 1.68: 10 1.68 - 1.81: 106 Bond restraints: 12670 Sorted by residual: bond pdb=" C PHE B 432 " pdb=" O PHE B 432 " ideal model delta sigma weight residual 1.236 1.150 0.085 1.29e-02 6.01e+03 4.38e+01 bond pdb=" C VAL B 546 " pdb=" O VAL B 546 " ideal model delta sigma weight residual 1.237 1.163 0.074 1.19e-02 7.06e+03 3.82e+01 bond pdb=" CA ASN A 436 " pdb=" CB ASN A 436 " ideal model delta sigma weight residual 1.531 1.446 0.085 1.56e-02 4.11e+03 3.00e+01 bond pdb=" C MET B 549 " pdb=" O MET B 549 " ideal model delta sigma weight residual 1.237 1.178 0.058 1.19e-02 7.06e+03 2.41e+01 bond pdb=" C PHE B 432 " pdb=" N LEU B 433 " ideal model delta sigma weight residual 1.334 1.269 0.065 1.41e-02 5.03e+03 2.12e+01 ... (remaining 12665 not shown) Histogram of bond angle deviations from ideal: 97.03 - 104.44: 188 104.44 - 111.84: 5987 111.84 - 119.24: 4319 119.24 - 126.65: 6502 126.65 - 134.05: 170 Bond angle restraints: 17166 Sorted by residual: angle pdb=" CA THR A 435 " pdb=" CB THR A 435 " pdb=" OG1 THR A 435 " ideal model delta sigma weight residual 109.60 97.03 12.57 1.50e+00 4.44e-01 7.02e+01 angle pdb=" CA THR A 542 " pdb=" CB THR A 542 " pdb=" OG1 THR A 542 " ideal model delta sigma weight residual 109.60 98.27 11.33 1.50e+00 4.44e-01 5.71e+01 angle pdb=" C ASN B 436 " pdb=" CA ASN B 436 " pdb=" CB ASN B 436 " ideal model delta sigma weight residual 110.79 100.32 10.47 1.68e+00 3.54e-01 3.89e+01 angle pdb=" CA MET B 549 " pdb=" C MET B 549 " pdb=" O MET B 549 " ideal model delta sigma weight residual 120.42 114.19 6.23 1.06e+00 8.90e-01 3.46e+01 angle pdb=" CA THR B 542 " pdb=" CB THR B 542 " pdb=" OG1 THR B 542 " ideal model delta sigma weight residual 109.60 101.46 8.14 1.50e+00 4.44e-01 2.94e+01 ... (remaining 17161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.68: 6896 21.68 - 43.35: 513 43.35 - 65.03: 50 65.03 - 86.71: 29 86.71 - 108.38: 11 Dihedral angle restraints: 7499 sinusoidal: 2963 harmonic: 4536 Sorted by residual: dihedral pdb=" CA LYS A 233 " pdb=" C LYS A 233 " pdb=" N GLN A 234 " pdb=" CA GLN A 234 " ideal model delta harmonic sigma weight residual 180.00 137.29 42.71 0 5.00e+00 4.00e-02 7.29e+01 dihedral pdb=" CA LYS B 233 " pdb=" C LYS B 233 " pdb=" N GLN B 234 " pdb=" CA GLN B 234 " ideal model delta harmonic sigma weight residual 180.00 137.32 42.68 0 5.00e+00 4.00e-02 7.29e+01 dihedral pdb=" CA ASP A 217 " pdb=" C ASP A 217 " pdb=" N SER A 218 " pdb=" CA SER A 218 " ideal model delta harmonic sigma weight residual -180.00 -144.44 -35.56 0 5.00e+00 4.00e-02 5.06e+01 ... (remaining 7496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1617 0.069 - 0.138: 314 0.138 - 0.206: 27 0.206 - 0.275: 1 0.275 - 0.344: 5 Chirality restraints: 1964 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.49e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.33e+01 chirality pdb=" CA PHE B 432 " pdb=" N PHE B 432 " pdb=" C PHE B 432 " pdb=" CB PHE B 432 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 1961 not shown) Planarity restraints: 2135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 442 " -0.014 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C VAL A 442 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL A 442 " -0.019 2.00e-02 2.50e+03 pdb=" N SER A 443 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 439 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.97e+00 pdb=" C PHE B 439 " -0.046 2.00e-02 2.50e+03 pdb=" O PHE B 439 " 0.017 2.00e-02 2.50e+03 pdb=" N SER B 440 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 436 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.91e+00 pdb=" CG ASN A 436 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A 436 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 436 " 0.015 2.00e-02 2.50e+03 ... (remaining 2132 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 266 2.64 - 3.20: 12562 3.20 - 3.77: 18152 3.77 - 4.33: 25678 4.33 - 4.90: 42534 Nonbonded interactions: 99192 Sorted by model distance: nonbonded pdb=" CD1 TYR A 287 " pdb=" CD1 TYR B 287 " model vdw 2.071 3.640 nonbonded pdb=" NH1 ARG C 61 " pdb=" OD2 ASP C 82 " model vdw 2.082 2.520 nonbonded pdb=" ND2 ASN A 68 " pdb=" NZ LYS A 346 " model vdw 2.186 3.200 nonbonded pdb=" NAV MIX B1201 " pdb=" OAB MIX B1201 " model vdw 2.197 2.520 nonbonded pdb=" NE2 GLN C 89 " pdb=" O GLN C 90 " model vdw 2.199 2.520 ... (remaining 99187 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' and resid 35 through 654) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.580 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 33.170 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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 : 0.009 0.085 12670 Z= 0.597 Angle : 1.016 12.569 17166 Z= 0.567 Chirality : 0.055 0.344 1964 Planarity : 0.005 0.044 2133 Dihedral : 16.114 108.383 4582 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 25.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.92 % Favored : 83.95 % Rotamer: Outliers : 0.37 % Allowed : 0.00 % Favored : 99.63 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.50 (0.16), residues: 1558 helix: -2.76 (0.16), residues: 642 sheet: -3.65 (0.33), residues: 198 loop : -4.56 (0.17), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 92 HIS 0.006 0.002 HIS A 267 PHE 0.035 0.003 PHE B 432 TYR 0.019 0.002 TYR E 91 ARG 0.014 0.001 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 280 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ASN cc_start: 0.7514 (m-40) cc_final: 0.7071 (p0) REVERT: A 96 ARG cc_start: 0.8339 (mmt-90) cc_final: 0.8073 (tpp80) REVERT: A 127 ASP cc_start: 0.7706 (p0) cc_final: 0.7207 (p0) REVERT: A 465 ARG cc_start: 0.6257 (ptp-110) cc_final: 0.5865 (mmt-90) REVERT: A 481 MET cc_start: 0.7616 (tpt) cc_final: 0.6682 (ttp) REVERT: A 515 MET cc_start: 0.8892 (mmm) cc_final: 0.8611 (mmp) REVERT: C 24 LYS cc_start: 0.8326 (ptpp) cc_final: 0.7835 (mmtt) REVERT: C 69 LYS cc_start: 0.8362 (mttt) cc_final: 0.8116 (mttm) REVERT: C 82 ASP cc_start: 0.8123 (m-30) cc_final: 0.7653 (m-30) REVERT: D 16 GLN cc_start: 0.8324 (mm-40) cc_final: 0.8050 (mt0) REVERT: D 73 ASP cc_start: 0.8158 (t0) cc_final: 0.7858 (t70) REVERT: D 100 TYR cc_start: 0.7881 (t80) cc_final: 0.7400 (t80) REVERT: F 100 TYR cc_start: 0.7442 (t80) cc_final: 0.7101 (t80) REVERT: B 288 ASN cc_start: 0.6996 (t0) cc_final: 0.6474 (p0) REVERT: B 341 PHE cc_start: 0.7027 (m-80) cc_final: 0.6787 (m-80) REVERT: B 407 LEU cc_start: 0.9039 (mt) cc_final: 0.8766 (mt) REVERT: B 451 GLU cc_start: 0.7787 (pt0) cc_final: 0.7455 (pt0) REVERT: B 523 MET cc_start: 0.8741 (ttp) cc_final: 0.8492 (ttt) REVERT: B 585 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7732 (tm-30) outliers start: 5 outliers final: 4 residues processed: 283 average time/residue: 0.2688 time to fit residues: 108.1049 Evaluate side-chains 215 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 211 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain B residue 542 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 68 ASN A 139 ASN A 166 GLN A 222 ASN A 338 ASN A 424 GLN A 425 ASN A 436 ASN A 437 GLN A 583 HIS D 5 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN B 155 HIS B 234 GLN ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 GLN B 583 HIS B 617 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12670 Z= 0.194 Angle : 0.677 8.250 17166 Z= 0.337 Chirality : 0.045 0.202 1964 Planarity : 0.004 0.046 2133 Dihedral : 10.175 79.441 1800 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 2.44 % Allowed : 10.44 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.11 (0.19), residues: 1558 helix: -1.29 (0.19), residues: 610 sheet: -3.45 (0.32), residues: 190 loop : -3.87 (0.18), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.014 0.002 HIS B 243 PHE 0.020 0.002 PHE A 432 TYR 0.020 0.002 TYR A 287 ARG 0.006 0.000 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 229 time to evaluate : 1.461 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.6219 (mtt) cc_final: 0.5980 (mtp) REVERT: A 96 ARG cc_start: 0.8273 (mmt-90) cc_final: 0.7911 (tpp80) REVERT: A 127 ASP cc_start: 0.7657 (p0) cc_final: 0.7124 (p0) REVERT: A 177 LYS cc_start: 0.7679 (ttmm) cc_final: 0.7331 (tttt) REVERT: A 206 ILE cc_start: 0.8651 (mm) cc_final: 0.8285 (mt) REVERT: A 225 LEU cc_start: 0.7825 (mm) cc_final: 0.7577 (mm) REVERT: A 292 ASP cc_start: 0.8318 (t0) cc_final: 0.7966 (m-30) REVERT: A 458 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7872 (mt-10) REVERT: A 465 ARG cc_start: 0.6133 (ptp-110) cc_final: 0.5560 (mmt-90) REVERT: A 481 MET cc_start: 0.7498 (tpt) cc_final: 0.6745 (ttp) REVERT: A 515 MET cc_start: 0.8862 (mmm) cc_final: 0.8590 (mmp) REVERT: C 24 LYS cc_start: 0.8208 (ptpp) cc_final: 0.7680 (mmtt) REVERT: C 82 ASP cc_start: 0.7972 (m-30) cc_final: 0.7745 (m-30) REVERT: D 16 GLN cc_start: 0.8309 (mm-40) cc_final: 0.7530 (tt0) REVERT: D 73 ASP cc_start: 0.8164 (t0) cc_final: 0.7836 (t70) REVERT: B 71 MET cc_start: 0.7800 (mmt) cc_final: 0.7266 (mmm) REVERT: B 211 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7398 (mt-10) REVERT: B 265 MET cc_start: 0.6511 (mtm) cc_final: 0.6069 (ptt) REVERT: B 267 HIS cc_start: 0.5617 (t70) cc_final: 0.5312 (t70) REVERT: B 407 LEU cc_start: 0.9016 (mt) cc_final: 0.8773 (mt) REVERT: B 451 GLU cc_start: 0.7649 (pt0) cc_final: 0.7270 (pt0) REVERT: B 523 MET cc_start: 0.8669 (ttp) cc_final: 0.8411 (ttt) REVERT: B 585 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7750 (tm-30) outliers start: 33 outliers final: 27 residues processed: 246 average time/residue: 0.2372 time to fit residues: 84.1547 Evaluate side-chains 228 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 201 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 631 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 151 optimal weight: 0.2980 chunk 124 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 GLN A 590 ASN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 GLN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12670 Z= 0.291 Angle : 0.663 8.105 17166 Z= 0.337 Chirality : 0.045 0.185 1964 Planarity : 0.004 0.041 2133 Dihedral : 7.070 54.571 1795 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer: Outliers : 3.04 % Allowed : 15.26 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.19), residues: 1558 helix: -0.90 (0.20), residues: 614 sheet: -3.49 (0.32), residues: 204 loop : -3.57 (0.19), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 379 HIS 0.009 0.002 HIS B 243 PHE 0.024 0.002 PHE F 79 TYR 0.018 0.002 TYR D 94 ARG 0.005 0.000 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 210 time to evaluate : 1.454 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.6417 (mtt) cc_final: 0.6113 (mtp) REVERT: A 127 ASP cc_start: 0.7650 (p0) cc_final: 0.7091 (p0) REVERT: A 156 GLU cc_start: 0.6107 (pm20) cc_final: 0.5878 (pm20) REVERT: A 225 LEU cc_start: 0.8012 (mm) cc_final: 0.7786 (mm) REVERT: A 292 ASP cc_start: 0.8366 (t0) cc_final: 0.8055 (m-30) REVERT: A 385 PHE cc_start: 0.7911 (t80) cc_final: 0.7586 (t80) REVERT: A 465 ARG cc_start: 0.6160 (ptp-110) cc_final: 0.5637 (mmt-90) REVERT: A 481 MET cc_start: 0.7714 (tpt) cc_final: 0.6791 (ttp) REVERT: C 24 LYS cc_start: 0.8190 (ptpp) cc_final: 0.7579 (mmtm) REVERT: C 82 ASP cc_start: 0.8104 (m-30) cc_final: 0.7781 (m-30) REVERT: D 16 GLN cc_start: 0.8312 (mm-40) cc_final: 0.7860 (mt0) REVERT: D 73 ASP cc_start: 0.8197 (t0) cc_final: 0.7830 (t70) REVERT: B 265 MET cc_start: 0.6440 (mtm) cc_final: 0.6061 (ptt) REVERT: B 288 ASN cc_start: 0.7242 (t0) cc_final: 0.6794 (p0) REVERT: B 451 GLU cc_start: 0.7749 (pt0) cc_final: 0.7434 (pt0) REVERT: B 523 MET cc_start: 0.8660 (ttp) cc_final: 0.8380 (ttt) REVERT: B 585 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7812 (tm-30) outliers start: 41 outliers final: 35 residues processed: 230 average time/residue: 0.2278 time to fit residues: 77.1260 Evaluate side-chains 234 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 199 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 550 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 72 optimal weight: 0.0570 chunk 15 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 40 optimal weight: 0.0980 overall best weight: 2.2304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12670 Z= 0.261 Angle : 0.617 7.768 17166 Z= 0.316 Chirality : 0.044 0.182 1964 Planarity : 0.004 0.053 2133 Dihedral : 6.403 57.094 1794 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 3.33 % Allowed : 18.44 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.20), residues: 1558 helix: -0.67 (0.20), residues: 624 sheet: -3.20 (0.36), residues: 172 loop : -3.36 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.008 0.001 HIS B 267 PHE 0.018 0.001 PHE F 79 TYR 0.016 0.001 TYR D 94 ARG 0.003 0.000 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 200 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.7693 (p0) cc_final: 0.7107 (p0) REVERT: A 177 LYS cc_start: 0.7554 (ttmm) cc_final: 0.7148 (tttt) REVERT: A 225 LEU cc_start: 0.8020 (mm) cc_final: 0.7753 (mm) REVERT: A 233 LYS cc_start: 0.8578 (pttt) cc_final: 0.8243 (mmtm) REVERT: A 292 ASP cc_start: 0.8350 (t0) cc_final: 0.8033 (m-30) REVERT: A 522 SER cc_start: 0.8573 (p) cc_final: 0.8357 (p) REVERT: C 24 LYS cc_start: 0.8203 (ptpp) cc_final: 0.7569 (mttp) REVERT: C 82 ASP cc_start: 0.8144 (m-30) cc_final: 0.7817 (m-30) REVERT: D 16 GLN cc_start: 0.8310 (mm-40) cc_final: 0.7490 (tt0) REVERT: D 73 ASP cc_start: 0.8133 (t0) cc_final: 0.7758 (t70) REVERT: F 29 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7870 (pt) REVERT: B 211 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7311 (mt-10) REVERT: B 288 ASN cc_start: 0.7149 (t0) cc_final: 0.6811 (p0) REVERT: B 451 GLU cc_start: 0.7775 (pt0) cc_final: 0.7519 (pt0) REVERT: B 523 MET cc_start: 0.8675 (ttp) cc_final: 0.8440 (ttt) REVERT: B 585 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7827 (tm-30) outliers start: 45 outliers final: 34 residues processed: 222 average time/residue: 0.2190 time to fit residues: 72.2009 Evaluate side-chains 222 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 187 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 2 optimal weight: 0.0040 chunk 110 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 127 optimal weight: 0.3980 chunk 102 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12670 Z= 0.322 Angle : 0.660 11.946 17166 Z= 0.335 Chirality : 0.045 0.248 1964 Planarity : 0.004 0.039 2133 Dihedral : 6.320 54.070 1794 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 5.19 % Allowed : 18.74 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.20), residues: 1558 helix: -0.43 (0.21), residues: 600 sheet: -3.25 (0.35), residues: 172 loop : -3.25 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 564 HIS 0.009 0.001 HIS A 267 PHE 0.031 0.002 PHE A 266 TYR 0.017 0.002 TYR D 94 ARG 0.004 0.000 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 207 time to evaluate : 1.521 Fit side-chains REVERT: A 127 ASP cc_start: 0.7690 (p0) cc_final: 0.7057 (p0) REVERT: A 155 HIS cc_start: 0.7352 (t70) cc_final: 0.6969 (m-70) REVERT: A 156 GLU cc_start: 0.6186 (pm20) cc_final: 0.5671 (pm20) REVERT: A 159 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6963 (mt-10) REVERT: A 177 LYS cc_start: 0.7540 (ttmm) cc_final: 0.7054 (tttt) REVERT: A 225 LEU cc_start: 0.8104 (mm) cc_final: 0.7809 (mm) REVERT: A 244 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8155 (pm20) REVERT: A 292 ASP cc_start: 0.8362 (t0) cc_final: 0.8076 (m-30) REVERT: A 522 SER cc_start: 0.8615 (p) cc_final: 0.8402 (p) REVERT: C 24 LYS cc_start: 0.8240 (ptpp) cc_final: 0.7541 (mttp) REVERT: C 82 ASP cc_start: 0.8239 (m-30) cc_final: 0.7909 (m-30) REVERT: D 16 GLN cc_start: 0.8289 (mm-40) cc_final: 0.7545 (tt0) REVERT: D 73 ASP cc_start: 0.8169 (t0) cc_final: 0.7765 (t70) REVERT: F 29 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7853 (pt) REVERT: B 211 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7444 (mt-10) REVERT: B 256 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7533 (pt) REVERT: B 288 ASN cc_start: 0.7213 (t0) cc_final: 0.6954 (p0) REVERT: B 451 GLU cc_start: 0.7814 (pt0) cc_final: 0.7558 (pt0) REVERT: B 523 MET cc_start: 0.8672 (ttp) cc_final: 0.8397 (ttt) REVERT: B 585 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7745 (tm-30) outliers start: 70 outliers final: 56 residues processed: 244 average time/residue: 0.2229 time to fit residues: 81.2422 Evaluate side-chains 254 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 195 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 123 optimal weight: 20.0000 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 12670 Z= 0.422 Angle : 0.719 9.388 17166 Z= 0.367 Chirality : 0.047 0.214 1964 Planarity : 0.004 0.041 2133 Dihedral : 6.514 55.582 1794 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 5.11 % Allowed : 20.67 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.20), residues: 1558 helix: -0.52 (0.21), residues: 600 sheet: -3.44 (0.35), residues: 162 loop : -3.24 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 564 HIS 0.006 0.002 HIS A 267 PHE 0.028 0.002 PHE D 79 TYR 0.018 0.002 TYR D 94 ARG 0.006 0.001 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 203 time to evaluate : 1.365 Fit side-chains REVERT: A 127 ASP cc_start: 0.7685 (p0) cc_final: 0.7093 (p0) REVERT: A 155 HIS cc_start: 0.7327 (t70) cc_final: 0.6905 (m-70) REVERT: A 156 GLU cc_start: 0.6205 (pm20) cc_final: 0.5679 (pm20) REVERT: A 159 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6701 (mt-10) REVERT: A 177 LYS cc_start: 0.7450 (ttmm) cc_final: 0.6970 (tttt) REVERT: A 225 LEU cc_start: 0.8278 (mm) cc_final: 0.7949 (mm) REVERT: A 244 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8346 (pm20) REVERT: A 292 ASP cc_start: 0.8388 (t0) cc_final: 0.8114 (m-30) REVERT: A 652 LYS cc_start: 0.8398 (mptt) cc_final: 0.8117 (mmtm) REVERT: C 24 LYS cc_start: 0.8265 (ptpp) cc_final: 0.7530 (mttp) REVERT: C 82 ASP cc_start: 0.8274 (m-30) cc_final: 0.7941 (m-30) REVERT: D 16 GLN cc_start: 0.8296 (mm-40) cc_final: 0.7563 (tt0) REVERT: D 73 ASP cc_start: 0.8210 (t0) cc_final: 0.7783 (t70) REVERT: F 29 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7892 (pt) REVERT: B 71 MET cc_start: 0.7548 (mmt) cc_final: 0.7199 (mmm) REVERT: B 267 HIS cc_start: 0.6245 (t-90) cc_final: 0.5923 (t-90) REVERT: B 288 ASN cc_start: 0.7352 (t0) cc_final: 0.7023 (p0) REVERT: B 416 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8312 (mp) REVERT: B 451 GLU cc_start: 0.7891 (pt0) cc_final: 0.7690 (pt0) REVERT: B 523 MET cc_start: 0.8697 (ttp) cc_final: 0.8463 (ttt) REVERT: B 585 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7909 (tm-30) outliers start: 69 outliers final: 57 residues processed: 241 average time/residue: 0.2042 time to fit residues: 74.2185 Evaluate side-chains 259 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 199 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12670 Z= 0.258 Angle : 0.631 9.198 17166 Z= 0.318 Chirality : 0.043 0.182 1964 Planarity : 0.004 0.040 2133 Dihedral : 6.114 53.692 1794 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 4.74 % Allowed : 21.70 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.20), residues: 1558 helix: -0.30 (0.21), residues: 600 sheet: -3.12 (0.35), residues: 172 loop : -3.10 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 35 HIS 0.004 0.001 HIS A 267 PHE 0.017 0.001 PHE D 79 TYR 0.014 0.001 TYR A 413 ARG 0.003 0.000 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 206 time to evaluate : 1.400 Fit side-chains REVERT: A 127 ASP cc_start: 0.7673 (p0) cc_final: 0.7193 (p0) REVERT: A 155 HIS cc_start: 0.7303 (t70) cc_final: 0.6981 (m-70) REVERT: A 156 GLU cc_start: 0.6171 (pm20) cc_final: 0.5664 (pm20) REVERT: A 159 GLU cc_start: 0.7434 (mt-10) cc_final: 0.6995 (mt-10) REVERT: A 225 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7925 (mm) REVERT: A 244 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8327 (pm20) REVERT: A 292 ASP cc_start: 0.8391 (t0) cc_final: 0.8120 (m-30) REVERT: A 339 SER cc_start: 0.7800 (t) cc_final: 0.7598 (m) REVERT: A 522 SER cc_start: 0.8579 (p) cc_final: 0.8377 (p) REVERT: A 652 LYS cc_start: 0.8371 (mptt) cc_final: 0.8077 (mmtm) REVERT: C 24 LYS cc_start: 0.8253 (ptpp) cc_final: 0.7502 (mttp) REVERT: C 82 ASP cc_start: 0.8224 (m-30) cc_final: 0.7910 (m-30) REVERT: D 16 GLN cc_start: 0.8311 (mm-40) cc_final: 0.7535 (tt0) REVERT: D 73 ASP cc_start: 0.8130 (t0) cc_final: 0.7745 (t70) REVERT: F 29 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7842 (pt) REVERT: B 70 ILE cc_start: 0.8186 (pt) cc_final: 0.7954 (pt) REVERT: B 71 MET cc_start: 0.7487 (mmt) cc_final: 0.7267 (mmm) REVERT: B 288 ASN cc_start: 0.7346 (t0) cc_final: 0.7011 (p0) REVERT: B 523 MET cc_start: 0.8673 (ttp) cc_final: 0.8410 (ttt) REVERT: B 585 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7871 (tm-30) outliers start: 64 outliers final: 52 residues processed: 242 average time/residue: 0.2137 time to fit residues: 77.8433 Evaluate side-chains 255 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 200 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 116 optimal weight: 0.5980 chunk 135 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS A 244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12670 Z= 0.173 Angle : 0.577 9.903 17166 Z= 0.288 Chirality : 0.041 0.172 1964 Planarity : 0.003 0.039 2133 Dihedral : 5.656 50.256 1794 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.26 % Allowed : 23.70 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.21), residues: 1558 helix: 0.07 (0.22), residues: 584 sheet: -3.05 (0.34), residues: 184 loop : -2.91 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 35 HIS 0.003 0.001 HIS A 155 PHE 0.023 0.001 PHE B 578 TYR 0.014 0.001 TYR D 51 ARG 0.004 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 218 time to evaluate : 1.338 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR F 93 " (corrupted residue). Skipping it. REVERT: A 127 ASP cc_start: 0.7621 (p0) cc_final: 0.7176 (p0) REVERT: A 156 GLU cc_start: 0.6165 (pm20) cc_final: 0.5909 (pm20) REVERT: A 177 LYS cc_start: 0.7296 (ttmm) cc_final: 0.6831 (tttt) REVERT: A 225 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7771 (mm) REVERT: A 292 ASP cc_start: 0.8350 (t0) cc_final: 0.8092 (m-30) REVERT: A 339 SER cc_start: 0.7819 (t) cc_final: 0.7521 (m) REVERT: A 652 LYS cc_start: 0.8355 (mptt) cc_final: 0.8059 (mmtm) REVERT: C 24 LYS cc_start: 0.8227 (ptpp) cc_final: 0.7461 (mttp) REVERT: C 82 ASP cc_start: 0.8127 (m-30) cc_final: 0.7808 (m-30) REVERT: D 16 GLN cc_start: 0.8295 (mm-40) cc_final: 0.7718 (tt0) REVERT: D 73 ASP cc_start: 0.8077 (t0) cc_final: 0.7682 (t70) REVERT: E 105 GLU cc_start: 0.7331 (mm-30) cc_final: 0.6968 (mp0) REVERT: F 29 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7749 (pt) REVERT: B 70 ILE cc_start: 0.8196 (pt) cc_final: 0.7979 (pt) REVERT: B 288 ASN cc_start: 0.7267 (t0) cc_final: 0.7047 (p0) REVERT: B 523 MET cc_start: 0.8638 (ttp) cc_final: 0.8352 (ttt) REVERT: B 585 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7890 (tm-30) outliers start: 44 outliers final: 35 residues processed: 237 average time/residue: 0.2211 time to fit residues: 77.7429 Evaluate side-chains 237 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 200 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 60 optimal weight: 0.1980 chunk 108 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 130 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12670 Z= 0.245 Angle : 0.636 13.231 17166 Z= 0.312 Chirality : 0.043 0.158 1964 Planarity : 0.004 0.071 2133 Dihedral : 5.685 50.734 1794 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 3.63 % Allowed : 23.56 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.21), residues: 1558 helix: 0.08 (0.22), residues: 578 sheet: -3.25 (0.32), residues: 204 loop : -2.71 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 35 HIS 0.007 0.001 HIS A 243 PHE 0.020 0.001 PHE B 578 TYR 0.016 0.001 TYR D 94 ARG 0.004 0.000 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 202 time to evaluate : 1.420 Fit side-chains REVERT: A 127 ASP cc_start: 0.7651 (p0) cc_final: 0.7191 (p0) REVERT: A 156 GLU cc_start: 0.6180 (pm20) cc_final: 0.5653 (pm20) REVERT: A 177 LYS cc_start: 0.7351 (ttmm) cc_final: 0.6872 (tttt) REVERT: A 225 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7821 (mm) REVERT: A 247 TYR cc_start: 0.7121 (t80) cc_final: 0.6920 (t80) REVERT: A 292 ASP cc_start: 0.8311 (t0) cc_final: 0.8043 (m-30) REVERT: A 652 LYS cc_start: 0.8383 (mptt) cc_final: 0.8098 (mmtm) REVERT: C 24 LYS cc_start: 0.8231 (ptpp) cc_final: 0.7467 (mttp) REVERT: C 82 ASP cc_start: 0.8144 (m-30) cc_final: 0.7830 (m-30) REVERT: D 16 GLN cc_start: 0.8342 (mm-40) cc_final: 0.7633 (tt0) REVERT: D 73 ASP cc_start: 0.8071 (t0) cc_final: 0.7652 (t70) REVERT: E 45 ARG cc_start: 0.7760 (ptm160) cc_final: 0.7305 (ttp80) REVERT: F 29 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7807 (pt) REVERT: B 71 MET cc_start: 0.7078 (mmm) cc_final: 0.6766 (mmm) REVERT: B 106 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8425 (p) REVERT: B 288 ASN cc_start: 0.7250 (t0) cc_final: 0.6993 (p0) REVERT: B 523 MET cc_start: 0.8648 (ttp) cc_final: 0.8382 (ttt) REVERT: B 585 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7869 (tm-30) outliers start: 49 outliers final: 42 residues processed: 226 average time/residue: 0.2147 time to fit residues: 72.7433 Evaluate side-chains 243 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 198 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.6625 > 50: distance: 46 - 52: 24.657 distance: 52 - 53: 18.162 distance: 53 - 54: 18.588 distance: 53 - 56: 17.401 distance: 54 - 55: 13.496 distance: 54 - 60: 33.705 distance: 56 - 57: 26.776 distance: 57 - 58: 26.522 distance: 57 - 59: 14.926 distance: 60 - 61: 21.559 distance: 61 - 62: 10.238 distance: 62 - 63: 11.605 distance: 62 - 64: 6.736 distance: 64 - 65: 21.376 distance: 65 - 66: 18.770 distance: 65 - 68: 19.383 distance: 66 - 67: 18.353 distance: 66 - 72: 23.349 distance: 68 - 69: 14.608 distance: 69 - 70: 10.600 distance: 69 - 71: 5.245 distance: 72 - 73: 9.690 distance: 73 - 74: 14.627 distance: 73 - 76: 4.375 distance: 74 - 75: 9.915 distance: 74 - 80: 11.273 distance: 76 - 77: 15.068 distance: 77 - 78: 11.021 distance: 77 - 79: 9.159 distance: 80 - 81: 11.042 distance: 81 - 82: 16.508 distance: 81 - 84: 7.013 distance: 82 - 83: 4.754 distance: 82 - 89: 18.005 distance: 84 - 85: 4.178 distance: 85 - 86: 12.928 distance: 86 - 87: 9.639 distance: 87 - 88: 3.067 distance: 89 - 90: 11.415 distance: 90 - 91: 26.086 distance: 90 - 93: 8.410 distance: 91 - 92: 10.799 distance: 91 - 96: 16.950 distance: 93 - 94: 17.975 distance: 93 - 95: 11.402 distance: 96 - 97: 26.484 distance: 97 - 98: 48.118 distance: 97 - 100: 40.792 distance: 98 - 99: 18.776 distance: 98 - 101: 38.641 distance: 101 - 102: 41.135 distance: 102 - 103: 45.525 distance: 102 - 105: 45.606 distance: 103 - 104: 28.885 distance: 103 - 109: 29.086 distance: 105 - 106: 43.733 distance: 106 - 107: 47.390 distance: 106 - 108: 22.307 distance: 109 - 110: 13.270 distance: 110 - 111: 22.855 distance: 110 - 113: 15.327 distance: 111 - 112: 27.851 distance: 111 - 115: 7.754 distance: 113 - 114: 16.132 distance: 115 - 116: 39.129 distance: 116 - 117: 55.076 distance: 116 - 119: 37.903 distance: 117 - 118: 19.087 distance: 117 - 124: 33.624 distance: 119 - 120: 6.419 distance: 120 - 121: 23.061 distance: 121 - 122: 18.395 distance: 122 - 123: 4.262