Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 6 07:14:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfd_12300/10_2023/7nfd_12300_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfd_12300/10_2023/7nfd_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_12300/10_2023/7nfd_12300.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfd_12300/10_2023/7nfd_12300.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfd_12300/10_2023/7nfd_12300_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfd_12300/10_2023/7nfd_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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 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 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: 6.78, per 1000 atoms: 0.55 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: 5.49 Conformation dependent library (CDL) restraints added in 1.7 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: 2.03 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: 2.99 Time building geometry restraints manager: 5.89 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 - 17.96: 6614 17.96 - 35.92: 662 35.92 - 53.88: 109 53.88 - 71.84: 18 71.84 - 89.80: 12 Dihedral angle restraints: 7415 sinusoidal: 2879 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 7412 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: 7.120 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: 0.000 Extract box with map and model: 14.280 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 34.370 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.790 ------------------------------------------------------------------------------- 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 : 14.732 89.803 4498 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 *********************** 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 : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 283 average time/residue: 0.2688 time to fit residues: 106.7759 Evaluate side-chains 212 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 208 time to evaluate : 1.379 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1178 time to fit residues: 2.7529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12670 Z= 0.205 Angle : 0.684 9.468 17166 Z= 0.342 Chirality : 0.046 0.320 1964 Planarity : 0.004 0.046 2133 Dihedral : 6.168 56.300 1710 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.37 % Allowed : 10.15 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -4.19 (0.18), residues: 1558 helix: -1.38 (0.19), residues: 616 sheet: -3.31 (0.33), residues: 196 loop : -3.96 (0.18), residues: 746 *********************** 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 259 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 227 time to evaluate : 1.442 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 26 residues processed: 241 average time/residue: 0.2400 time to fit residues: 83.9408 Evaluate side-chains 226 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 200 time to evaluate : 1.436 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1114 time to fit residues: 7.3760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 0.3980 chunk 43 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 47 optimal weight: 0.0370 chunk 112 optimal weight: 20.0000 overall best weight: 1.8864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 109 ASN ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 GLN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 GLN B 425 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12670 Z= 0.241 Angle : 0.645 9.202 17166 Z= 0.324 Chirality : 0.045 0.248 1964 Planarity : 0.004 0.040 2133 Dihedral : 5.846 58.384 1710 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 1.41 % Allowed : 15.56 % Favored : 83.04 % 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: -3.67 (0.19), residues: 1558 helix: -0.93 (0.20), residues: 616 sheet: -3.33 (0.33), residues: 192 loop : -3.59 (0.19), residues: 750 *********************** 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 238 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 219 time to evaluate : 1.565 Fit side-chains outliers start: 19 outliers final: 13 residues processed: 230 average time/residue: 0.2394 time to fit residues: 79.8580 Evaluate side-chains 213 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 200 time to evaluate : 1.326 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1106 time to fit residues: 4.5371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 590 ASN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2798 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= 0.239 Angle : 0.627 8.308 17166 Z= 0.316 Chirality : 0.044 0.236 1964 Planarity : 0.004 0.041 2133 Dihedral : 5.739 59.999 1710 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 2.22 % Allowed : 18.07 % Favored : 79.70 % 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: -3.29 (0.20), residues: 1558 helix: -0.65 (0.20), residues: 626 sheet: -3.19 (0.33), residues: 194 loop : -3.34 (0.20), residues: 738 *********************** 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 234 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 204 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 218 average time/residue: 0.2243 time to fit residues: 73.1258 Evaluate side-chains 209 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 191 time to evaluate : 1.519 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1139 time to fit residues: 5.9275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 110 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- 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 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN B 155 HIS B 457 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 12670 Z= 0.480 Angle : 0.778 11.063 17166 Z= 0.395 Chirality : 0.049 0.222 1964 Planarity : 0.005 0.040 2133 Dihedral : 6.249 59.895 1710 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.64 % Favored : 87.36 % Rotamer: Outliers : 3.11 % Allowed : 20.59 % Favored : 76.30 % 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: -3.36 (0.20), residues: 1558 helix: -0.68 (0.21), residues: 598 sheet: -3.27 (0.35), residues: 172 loop : -3.34 (0.20), residues: 788 *********************** 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 245 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 203 time to evaluate : 1.427 Fit side-chains outliers start: 42 outliers final: 31 residues processed: 225 average time/residue: 0.2172 time to fit residues: 73.7449 Evaluate side-chains 222 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 191 time to evaluate : 1.388 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1278 time to fit residues: 8.9448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 123 optimal weight: 0.0870 chunk 68 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- 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: 0.7979 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12670 Z= 0.283 Angle : 0.667 9.314 17166 Z= 0.334 Chirality : 0.045 0.275 1964 Planarity : 0.004 0.042 2133 Dihedral : 5.889 58.362 1710 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 1.63 % Allowed : 22.30 % 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: -3.13 (0.20), residues: 1558 helix: -0.43 (0.21), residues: 594 sheet: -3.34 (0.36), residues: 162 loop : -3.21 (0.20), residues: 802 *********************** 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 228 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 206 time to evaluate : 1.475 Fit side-chains outliers start: 22 outliers final: 13 residues processed: 217 average time/residue: 0.2282 time to fit residues: 73.6067 Evaluate side-chains 204 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 1.350 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1139 time to fit residues: 4.7571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 125 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12670 Z= 0.183 Angle : 0.613 9.613 17166 Z= 0.302 Chirality : 0.043 0.217 1964 Planarity : 0.003 0.038 2133 Dihedral : 5.552 55.285 1710 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 0.74 % Allowed : 23.56 % Favored : 75.70 % 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: -2.71 (0.21), residues: 1558 helix: 0.01 (0.22), residues: 578 sheet: -3.00 (0.36), residues: 172 loop : -3.01 (0.20), residues: 808 *********************** 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 214 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 204 time to evaluate : 1.459 Fit side-chains TARDY: cannot create tardy model for: "THR F 93 " (corrupted residue). Skipping it. outliers start: 10 outliers final: 7 residues processed: 209 average time/residue: 0.2374 time to fit residues: 74.0988 Evaluate side-chains 193 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 186 time to evaluate : 1.461 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1183 time to fit residues: 3.5913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 4.9990 chunk 88 optimal weight: 0.0170 chunk 44 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 HIS B 582 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12670 Z= 0.199 Angle : 0.619 9.180 17166 Z= 0.303 Chirality : 0.044 0.327 1964 Planarity : 0.004 0.062 2133 Dihedral : 5.404 52.097 1710 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 0.74 % Allowed : 24.15 % Favored : 75.11 % 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: -2.59 (0.21), residues: 1558 helix: 0.13 (0.22), residues: 578 sheet: -3.01 (0.34), residues: 184 loop : -2.92 (0.21), residues: 796 *********************** 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 214 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 204 time to evaluate : 1.300 Fit side-chains TARDY: cannot create tardy model for: "THR F 93 " (corrupted residue). Skipping it. outliers start: 10 outliers final: 5 residues processed: 208 average time/residue: 0.2255 time to fit residues: 70.6659 Evaluate side-chains 202 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 197 time to evaluate : 1.343 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1138 time to fit residues: 2.9003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 0.4980 chunk 129 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 83 optimal weight: 0.0970 chunk 60 optimal weight: 0.7980 chunk 108 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12670 Z= 0.185 Angle : 0.627 13.166 17166 Z= 0.302 Chirality : 0.043 0.216 1964 Planarity : 0.004 0.064 2133 Dihedral : 5.212 46.860 1710 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.30 % Allowed : 24.96 % Favored : 74.74 % 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: -2.44 (0.21), residues: 1558 helix: 0.25 (0.22), residues: 578 sheet: -2.85 (0.35), residues: 184 loop : -2.85 (0.21), residues: 796 *********************** 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 209 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 205 time to evaluate : 1.471 Fit side-chains TARDY: cannot create tardy model for: "THR F 93 " (corrupted residue). Skipping it. outliers start: 4 outliers final: 3 residues processed: 205 average time/residue: 0.2248 time to fit residues: 69.4556 Evaluate side-chains 196 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 193 time to evaluate : 1.348 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1176 time to fit residues: 2.5120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 5.9990 chunk 89 optimal weight: 0.0170 chunk 69 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 153 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 122 optimal weight: 0.4980 chunk 12 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 overall best weight: 0.6822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12670 Z= 0.151 Angle : 0.627 14.217 17166 Z= 0.297 Chirality : 0.042 0.217 1964 Planarity : 0.004 0.059 2133 Dihedral : 5.007 42.898 1710 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.30 % Allowed : 25.11 % Favored : 74.59 % 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: -2.28 (0.21), residues: 1558 helix: 0.27 (0.22), residues: 590 sheet: -2.62 (0.37), residues: 162 loop : -2.76 (0.21), residues: 806 ********************** REFINEMENT MACRO_CYCLE 10 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 210 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 206 time to evaluate : 1.488 Fit side-chains TARDY: cannot create tardy model for: "THR F 93 " (corrupted residue). Skipping it. outliers start: 4 outliers final: 4 residues processed: 207 average time/residue: 0.2207 time to fit residues: 69.9089 Evaluate side-chains 203 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 199 time to evaluate : 1.393 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1295 time to fit residues: 2.8876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 112 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 125 optimal weight: 0.0470 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.167297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.136860 restraints weight = 17484.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.140210 restraints weight = 8722.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.142329 restraints weight = 5498.054| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12670 Z= 0.210 Angle : 0.666 17.048 17166 Z= 0.313 Chirality : 0.043 0.216 1964 Planarity : 0.004 0.056 2133 Dihedral : 5.018 44.363 1710 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 0.30 % Allowed : 25.56 % Favored : 74.15 % 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: -2.19 (0.21), residues: 1558 helix: 0.39 (0.22), residues: 570 sheet: -2.59 (0.38), residues: 162 loop : -2.66 (0.20), residues: 826 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2840.38 seconds wall clock time: 52 minutes 53.34 seconds (3173.34 seconds total)