Starting phenix.real_space_refine (version: dev) on Thu Apr 7 17:29:23 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d04_7784/04_2022/6d04_7784_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d04_7784/04_2022/6d04_7784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d04_7784/04_2022/6d04_7784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d04_7784/04_2022/6d04_7784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d04_7784/04_2022/6d04_7784_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d04_7784/04_2022/6d04_7784_updated.pdb" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.015 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 324": "NH1" <-> "NH2" Residue "C ARG 475": "NH1" <-> "NH2" Residue "C ARG 522": "NH1" <-> "NH2" Residue "C ARG 568": "NH1" <-> "NH2" Residue "C TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 632": "NH1" <-> "NH2" Residue "C ARG 678": "NH1" <-> "NH2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 50": "NH1" <-> "NH2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 324": "NH1" <-> "NH2" Residue "D ARG 475": "NH1" <-> "NH2" Residue "D ARG 522": "NH1" <-> "NH2" Residue "D ARG 568": "NH1" <-> "NH2" Residue "D TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 632": "NH1" <-> "NH2" Residue "D ARG 678": "NH1" <-> "NH2" Residue "E ARG 193": "NH1" <-> "NH2" Residue "E ARG 207": "NH1" <-> "NH2" Residue "E ARG 217": "NH1" <-> "NH2" Residue "E ARG 235": "NH1" <-> "NH2" Residue "E ARG 242": "NH1" <-> "NH2" Residue "E ARG 272": "NH1" <-> "NH2" Residue "E ARG 418": "NH1" <-> "NH2" Residue "E ARG 468": "NH1" <-> "NH2" Residue "F ARG 193": "NH1" <-> "NH2" Residue "F ARG 207": "NH1" <-> "NH2" Residue "F ARG 217": "NH1" <-> "NH2" Residue "F ARG 235": "NH1" <-> "NH2" Residue "F ARG 242": "NH1" <-> "NH2" Residue "F ARG 272": "NH1" <-> "NH2" Residue "F ARG 418": "NH1" <-> "NH2" Residue "F ARG 468": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 28748 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5081 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 615} Chain: "B" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5081 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 615} Chain: "C" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5266 Classifications: {'peptide': 679} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'CIS': 2, 'TRANS': 644, 'PCIS': 3} Chain: "D" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5266 Classifications: {'peptide': 679} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'CIS': 2, 'TRANS': 644, 'PCIS': 3} Chain: "E" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3904 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 6, 'CIS': 1, 'TRANS': 457, 'PCIS': 1} Chain: "F" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3904 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 6, 'CIS': 1, 'TRANS': 457, 'PCIS': 1} Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' CA': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' CA': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'CO3': 2, ' FE': 2, 'NAG': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'CO3': 2, ' FE': 2, 'NAG': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 15.69, per 1000 atoms: 0.55 Number of scatterers: 28748 At special positions: 0 Unit cell: (168.75, 148.5, 166.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 Ca 2 19.99 S 142 16.00 O 5498 8.00 N 4850 7.00 C 18252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 353 " - pdb=" SG CYS A 363 " distance=2.04 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 353 " - pdb=" SG CYS B 363 " distance=2.04 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 48 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 39 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 137 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 158 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 161 " - pdb=" SG CYS C 179 " distance=2.02 Simple disulfide: pdb=" SG CYS C 171 " - pdb=" SG CYS C 177 " distance=2.03 Simple disulfide: pdb=" SG CYS C 227 " - pdb=" SG CYS C 241 " distance=2.02 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 596 " distance=2.02 Simple disulfide: pdb=" SG CYS C 345 " - pdb=" SG CYS C 377 " distance=2.02 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 368 " distance=2.03 Simple disulfide: pdb=" SG CYS C 402 " - pdb=" SG CYS C 674 " distance=2.03 Simple disulfide: pdb=" SG CYS C 418 " - pdb=" SG CYS C 637 " distance=2.03 Simple disulfide: pdb=" SG CYS C 450 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 665 " distance=2.03 Simple disulfide: pdb=" SG CYS C 484 " - pdb=" SG CYS C 498 " distance=2.03 Simple disulfide: pdb=" SG CYS C 495 " - pdb=" SG CYS C 506 " distance=2.02 Simple disulfide: pdb=" SG CYS C 563 " - pdb=" SG CYS C 577 " distance=2.02 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 620 " distance=2.03 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 48 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 39 " distance=2.03 Simple disulfide: pdb=" SG CYS D 118 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 137 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 158 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 161 " - pdb=" SG CYS D 179 " distance=2.02 Simple disulfide: pdb=" SG CYS D 171 " - pdb=" SG CYS D 177 " distance=2.03 Simple disulfide: pdb=" SG CYS D 227 " - pdb=" SG CYS D 241 " distance=2.02 Simple disulfide: pdb=" SG CYS D 339 " - pdb=" SG CYS D 596 " distance=2.02 Simple disulfide: pdb=" SG CYS D 345 " - pdb=" SG CYS D 377 " distance=2.02 Simple disulfide: pdb=" SG CYS D 355 " - pdb=" SG CYS D 368 " distance=2.03 Simple disulfide: pdb=" SG CYS D 402 " - pdb=" SG CYS D 674 " distance=2.03 Simple disulfide: pdb=" SG CYS D 418 " - pdb=" SG CYS D 637 " distance=2.03 Simple disulfide: pdb=" SG CYS D 450 " - pdb=" SG CYS D 523 " distance=2.03 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 665 " distance=2.03 Simple disulfide: pdb=" SG CYS D 484 " - pdb=" SG CYS D 498 " distance=2.03 Simple disulfide: pdb=" SG CYS D 495 " - pdb=" SG CYS D 506 " distance=2.02 Simple disulfide: pdb=" SG CYS D 563 " - pdb=" SG CYS D 577 " distance=2.02 Simple disulfide: pdb=" SG CYS D 615 " - pdb=" SG CYS D 620 " distance=2.03 Simple disulfide: pdb=" SG CYS E 240 " - pdb=" SG CYS E 284 " distance=2.03 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 316 " distance=2.04 Simple disulfide: pdb=" SG CYS F 240 " - pdb=" SG CYS F 284 " distance=2.03 Simple disulfide: pdb=" SG CYS F 312 " - pdb=" SG CYS F 316 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 803 " - " NAG A 804 " " NAG A 805 " - " NAG A 806 " " NAG B 803 " - " NAG B 804 " " NAG B 805 " - " NAG B 806 " " NAG C 705 " - " NAG C 706 " " NAG D 705 " - " NAG D 706 " NAG-ASN " NAG A 802 " - " ASN A 251 " " NAG A 803 " - " ASN A 317 " " NAG A 805 " - " ASN A 727 " " NAG B 802 " - " ASN B 251 " " NAG B 803 " - " ASN B 317 " " NAG B 805 " - " ASN B 727 " " NAG C 705 " - " ASN C 413 " " NAG C 707 " - " ASN C 611 " " NAG D 705 " - " ASN D 413 " " NAG D 707 " - " ASN D 611 " Time building additional restraints: 11.42 Conformation dependent library (CDL) restraints added in 4.1 seconds 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6740 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 110 helices and 20 sheets defined 44.6% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.31 Creating SS restraints... Processing helix chain 'A' and resid 124 through 135 removed outlier: 4.034A pdb=" N ARG A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.522A pdb=" N ASN A 148 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'A' and resid 339 through 346 removed outlier: 3.655A pdb=" N LYS A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 438 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 471 through 474 No H-bonds generated for 'chain 'A' and resid 471 through 474' Processing helix chain 'A' and resid 500 through 511 removed outlier: 5.156A pdb=" N THR A 504 " --> pdb=" O LEU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 530 No H-bonds generated for 'chain 'A' and resid 528 through 530' Processing helix chain 'A' and resid 542 through 545 No H-bonds generated for 'chain 'A' and resid 542 through 545' Processing helix chain 'A' and resid 573 through 579 Processing helix chain 'A' and resid 584 through 602 Processing helix chain 'A' and resid 611 through 634 removed outlier: 3.799A pdb=" N TYR A 614 " --> pdb=" O TYR A 611 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 618 " --> pdb=" O ASN A 615 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 622 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 623 " --> pdb=" O SER A 620 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN A 627 " --> pdb=" O ASP A 624 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG A 629 " --> pdb=" O ASN A 626 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ALA A 630 " --> pdb=" O GLN A 627 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 632 " --> pdb=" O ARG A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 661 Processing helix chain 'A' and resid 669 through 680 removed outlier: 3.537A pdb=" N LYS A 673 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 674 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG A 677 " --> pdb=" O LYS A 673 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 678 " --> pdb=" O LEU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 685 No H-bonds generated for 'chain 'A' and resid 683 through 685' Processing helix chain 'A' and resid 709 through 720 removed outlier: 4.125A pdb=" N LEU A 718 " --> pdb=" O GLU A 714 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG A 719 " --> pdb=" O ASN A 715 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 749 Processing helix chain 'B' and resid 124 through 135 removed outlier: 4.034A pdb=" N ARG B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 148 removed outlier: 3.521A pdb=" N ASN B 148 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 339 through 346 removed outlier: 3.654A pdb=" N LYS B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 438 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 471 through 474 No H-bonds generated for 'chain 'B' and resid 471 through 474' Processing helix chain 'B' and resid 500 through 511 removed outlier: 5.155A pdb=" N THR B 504 " --> pdb=" O LEU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 530 No H-bonds generated for 'chain 'B' and resid 528 through 530' Processing helix chain 'B' and resid 542 through 545 No H-bonds generated for 'chain 'B' and resid 542 through 545' Processing helix chain 'B' and resid 573 through 579 Processing helix chain 'B' and resid 584 through 602 Processing helix chain 'B' and resid 611 through 634 removed outlier: 3.799A pdb=" N TYR B 614 " --> pdb=" O TYR B 611 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 618 " --> pdb=" O ASN B 615 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 622 " --> pdb=" O LEU B 619 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 623 " --> pdb=" O SER B 620 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN B 627 " --> pdb=" O ASP B 624 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG B 629 " --> pdb=" O ASN B 626 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ALA B 630 " --> pdb=" O GLN B 627 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 632 " --> pdb=" O ARG B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 661 Processing helix chain 'B' and resid 669 through 680 removed outlier: 3.538A pdb=" N LYS B 673 " --> pdb=" O PHE B 669 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 674 " --> pdb=" O VAL B 670 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG B 677 " --> pdb=" O LYS B 673 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL B 678 " --> pdb=" O LEU B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 685 No H-bonds generated for 'chain 'B' and resid 683 through 685' Processing helix chain 'B' and resid 709 through 720 removed outlier: 4.125A pdb=" N LEU B 718 " --> pdb=" O GLU B 714 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG B 719 " --> pdb=" O ASN B 715 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS B 720 " --> pdb=" O LEU B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 749 Processing helix chain 'C' and resid 13 through 26 Processing helix chain 'C' and resid 45 through 53 Processing helix chain 'C' and resid 64 through 67 No H-bonds generated for 'chain 'C' and resid 64 through 67' Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 146 through 153 Processing helix chain 'C' and resid 188 through 196 Processing helix chain 'C' and resid 209 through 213 Processing helix chain 'C' and resid 217 through 222 Processing helix chain 'C' and resid 260 through 274 removed outlier: 3.833A pdb=" N HIS C 273 " --> pdb=" O GLN C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 314 No H-bonds generated for 'chain 'C' and resid 311 through 314' Processing helix chain 'C' and resid 317 through 328 Processing helix chain 'C' and resid 352 through 361 Processing helix chain 'C' and resid 374 through 383 removed outlier: 3.519A pdb=" N ALA C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 402 removed outlier: 3.808A pdb=" N ILE C 398 " --> pdb=" O GLY C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 471 removed outlier: 3.711A pdb=" N LEU C 466 " --> pdb=" O ILE C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 495 No H-bonds generated for 'chain 'C' and resid 493 through 495' Processing helix chain 'C' and resid 516 through 526 removed outlier: 3.602A pdb=" N ALA C 520 " --> pdb=" O GLY C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 541 Processing helix chain 'C' and resid 594 through 608 removed outlier: 4.026A pdb=" N LEU C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 651 Processing helix chain 'C' and resid 653 through 662 removed outlier: 3.748A pdb=" N LEU C 662 " --> pdb=" O ALA C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 675 Processing helix chain 'D' and resid 13 through 26 Processing helix chain 'D' and resid 45 through 53 Processing helix chain 'D' and resid 64 through 67 No H-bonds generated for 'chain 'D' and resid 64 through 67' Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 188 through 196 Processing helix chain 'D' and resid 209 through 213 Processing helix chain 'D' and resid 217 through 222 Processing helix chain 'D' and resid 260 through 274 removed outlier: 3.832A pdb=" N HIS D 273 " --> pdb=" O GLN D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 314 No H-bonds generated for 'chain 'D' and resid 311 through 314' Processing helix chain 'D' and resid 317 through 328 Processing helix chain 'D' and resid 352 through 361 Processing helix chain 'D' and resid 374 through 383 removed outlier: 3.519A pdb=" N ALA D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 402 removed outlier: 3.807A pdb=" N ILE D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 471 removed outlier: 3.711A pdb=" N LEU D 466 " --> pdb=" O ILE D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 495 No H-bonds generated for 'chain 'D' and resid 493 through 495' Processing helix chain 'D' and resid 516 through 526 removed outlier: 3.604A pdb=" N ALA D 520 " --> pdb=" O GLY D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 541 Processing helix chain 'D' and resid 594 through 608 removed outlier: 4.025A pdb=" N LEU D 607 " --> pdb=" O GLN D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 651 Processing helix chain 'D' and resid 653 through 662 removed outlier: 3.748A pdb=" N LEU D 662 " --> pdb=" O ALA D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 675 Processing helix chain 'E' and resid 197 through 211 Processing helix chain 'E' and resid 217 through 239 Processing helix chain 'E' and resid 241 through 254 Processing helix chain 'E' and resid 258 through 261 No H-bonds generated for 'chain 'E' and resid 258 through 261' Processing helix chain 'E' and resid 267 through 307 removed outlier: 3.564A pdb=" N LYS E 288 " --> pdb=" O CYS E 284 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LYS E 291 " --> pdb=" O ASN E 287 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASN E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 334 removed outlier: 4.569A pdb=" N LYS E 326 " --> pdb=" O PHE E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 361 removed outlier: 3.594A pdb=" N LYS E 360 " --> pdb=" O ASP E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 407 Processing helix chain 'E' and resid 416 through 476 removed outlier: 3.620A pdb=" N GLU E 460 " --> pdb=" O ASN E 456 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY E 463 " --> pdb=" O GLY E 459 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS E 464 " --> pdb=" O GLU E 460 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU E 467 " --> pdb=" O GLY E 463 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG E 468 " --> pdb=" O HIS E 464 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP E 474 " --> pdb=" O SER E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 511 removed outlier: 5.466A pdb=" N LYS E 505 " --> pdb=" O ASP E 501 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 520 through 565 removed outlier: 4.035A pdb=" N ASP E 524 " --> pdb=" O GLU E 520 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL E 560 " --> pdb=" O GLU E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 632 removed outlier: 4.170A pdb=" N ASN E 591 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N PHE E 592 " --> pdb=" O SER E 588 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N SER E 593 " --> pdb=" O TYR E 589 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 211 Processing helix chain 'F' and resid 217 through 239 Processing helix chain 'F' and resid 241 through 254 Processing helix chain 'F' and resid 258 through 261 No H-bonds generated for 'chain 'F' and resid 258 through 261' Processing helix chain 'F' and resid 267 through 307 removed outlier: 3.564A pdb=" N LYS F 288 " --> pdb=" O CYS F 284 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LYS F 291 " --> pdb=" O ASN F 287 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASN F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 334 removed outlier: 4.569A pdb=" N LYS F 326 " --> pdb=" O PHE F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 361 removed outlier: 3.594A pdb=" N LYS F 360 " --> pdb=" O ASP F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 407 Processing helix chain 'F' and resid 416 through 476 removed outlier: 3.620A pdb=" N GLU F 460 " --> pdb=" O ASN F 456 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLY F 463 " --> pdb=" O GLY F 459 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS F 464 " --> pdb=" O GLU F 460 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU F 467 " --> pdb=" O GLY F 463 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG F 468 " --> pdb=" O HIS F 464 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP F 474 " --> pdb=" O SER F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 511 removed outlier: 5.466A pdb=" N LYS F 505 " --> pdb=" O ASP F 501 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 565 removed outlier: 4.034A pdb=" N ASP F 524 " --> pdb=" O GLU F 520 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL F 560 " --> pdb=" O GLU F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 575 through 632 removed outlier: 4.170A pdb=" N ASN F 591 " --> pdb=" O ILE F 587 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N PHE F 592 " --> pdb=" O SER F 588 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N SER F 593 " --> pdb=" O TYR F 589 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 180 through 193 removed outlier: 9.057A pdb=" N GLU A 398 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N ILE A 449 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 12.830A pdb=" N ASP A 400 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 14.748A pdb=" N ALA A 451 " --> pdb=" O ASP A 400 " (cutoff:3.500A) removed outlier: 15.233A pdb=" N TYR A 402 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 16.415A pdb=" N TRP A 453 " --> pdb=" O TYR A 402 " (cutoff:3.500A) removed outlier: 14.836A pdb=" N VAL A 404 " --> pdb=" O TRP A 453 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY A 406 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE A 555 " --> pdb=" O ASN A 483 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 226 through 230 removed outlier: 5.871A pdb=" N ILE A 202 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LEU A 212 " --> pdb=" O ILE A 202 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 232 through 234 removed outlier: 6.183A pdb=" N ILE A 254 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLY A 278 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL A 257 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU A 280 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N ILE A 281 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLN A 335 " --> pdb=" O ILE A 281 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 180 through 193 removed outlier: 9.058A pdb=" N GLU B 398 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N ILE B 449 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 12.830A pdb=" N ASP B 400 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 14.748A pdb=" N ALA B 451 " --> pdb=" O ASP B 400 " (cutoff:3.500A) removed outlier: 15.232A pdb=" N TYR B 402 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 16.415A pdb=" N TRP B 453 " --> pdb=" O TYR B 402 " (cutoff:3.500A) removed outlier: 14.835A pdb=" N VAL B 404 " --> pdb=" O TRP B 453 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY B 406 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE B 555 " --> pdb=" O ASN B 483 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 226 through 230 removed outlier: 3.501A pdb=" N GLU B 214 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ILE B 202 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LEU B 212 " --> pdb=" O ILE B 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 232 through 234 removed outlier: 6.182A pdb=" N ILE B 254 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLY B 278 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL B 257 " --> pdb=" O GLY B 278 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU B 280 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N ILE B 281 " --> pdb=" O PRO B 333 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLN B 335 " --> pdb=" O ILE B 281 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 5 through 10 removed outlier: 6.272A pdb=" N SER C 36 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N TRP C 8 " --> pdb=" O SER C 36 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA C 38 " --> pdb=" O TRP C 8 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ALA C 10 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL C 40 " --> pdb=" O ALA C 10 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 60 through 62 removed outlier: 3.932A pdb=" N VAL C 60 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 81 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA C 253 " --> pdb=" O PRO C 79 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 244 through 246 removed outlier: 3.894A pdb=" N ALA C 244 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 224 through 226 Processing sheet with id= K, first strand: chain 'C' and resid 342 through 347 Processing sheet with id= L, first strand: chain 'C' and resid 388 through 391 removed outlier: 3.680A pdb=" N LEU C 408 " --> pdb=" O VAL C 587 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR C 589 " --> pdb=" O PRO C 406 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 531 through 534 removed outlier: 5.128A pdb=" N ALA C 430 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 562 " --> pdb=" O ALA C 430 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS C 569 " --> pdb=" O LEU C 561 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 5 through 10 removed outlier: 6.272A pdb=" N SER D 36 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N TRP D 8 " --> pdb=" O SER D 36 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA D 38 " --> pdb=" O TRP D 8 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ALA D 10 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL D 40 " --> pdb=" O ALA D 10 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 60 through 62 removed outlier: 3.933A pdb=" N VAL D 60 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 81 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA D 253 " --> pdb=" O PRO D 79 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 244 through 246 removed outlier: 3.894A pdb=" N ALA D 244 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 224 through 226 Processing sheet with id= R, first strand: chain 'D' and resid 342 through 347 Processing sheet with id= S, first strand: chain 'D' and resid 388 through 391 removed outlier: 3.680A pdb=" N LEU D 408 " --> pdb=" O VAL D 587 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR D 589 " --> pdb=" O PRO D 406 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 531 through 534 removed outlier: 5.129A pdb=" N ALA D 430 " --> pdb=" O LEU D 562 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 562 " --> pdb=" O ALA D 430 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS D 569 " --> pdb=" O LEU D 561 " (cutoff:3.500A) 1229 hydrogen bonds defined for protein. 3501 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.62 Time building geometry restraints manager: 12.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8531 1.34 - 1.46: 6384 1.46 - 1.58: 14253 1.58 - 1.70: 0 1.70 - 1.83: 192 Bond restraints: 29360 Sorted by residual: bond pdb=" CA ARG B 155 " pdb=" CB ARG B 155 " ideal model delta sigma weight residual 1.524 1.564 -0.040 1.46e-02 4.69e+03 7.32e+00 bond pdb=" CA ARG A 155 " pdb=" CB ARG A 155 " ideal model delta sigma weight residual 1.524 1.563 -0.039 1.46e-02 4.69e+03 7.13e+00 bond pdb=" C4 NAG B 805 " pdb=" C5 NAG B 805 " ideal model delta sigma weight residual 1.526 1.557 -0.031 1.30e-02 5.92e+03 5.66e+00 bond pdb=" N ASN B 236 " pdb=" CA ASN B 236 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.29e-02 6.01e+03 4.79e+00 bond pdb=" N ASN A 236 " pdb=" CA ASN A 236 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.71e+00 ... (remaining 29355 not shown) Histogram of bond angle deviations from ideal: 97.33 - 104.71: 402 104.71 - 112.09: 14137 112.09 - 119.47: 10211 119.47 - 126.85: 14557 126.85 - 134.23: 357 Bond angle restraints: 39664 Sorted by residual: angle pdb=" CA TYR E 422 " pdb=" CB TYR E 422 " pdb=" CG TYR E 422 " ideal model delta sigma weight residual 113.90 127.79 -13.89 1.80e+00 3.09e-01 5.96e+01 angle pdb=" CA TYR F 422 " pdb=" CB TYR F 422 " pdb=" CG TYR F 422 " ideal model delta sigma weight residual 113.90 127.76 -13.86 1.80e+00 3.09e-01 5.93e+01 angle pdb=" C GLY C 502 " pdb=" N LEU C 503 " pdb=" CA LEU C 503 " ideal model delta sigma weight residual 121.54 130.89 -9.35 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C GLY D 502 " pdb=" N LEU D 503 " pdb=" CA LEU D 503 " ideal model delta sigma weight residual 121.54 130.87 -9.33 1.91e+00 2.74e-01 2.38e+01 angle pdb=" C3 NAG B 805 " pdb=" C4 NAG B 805 " pdb=" C5 NAG B 805 " ideal model delta sigma weight residual 110.18 117.06 -6.88 1.42e+00 4.96e-01 2.35e+01 ... (remaining 39659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.26: 17053 21.26 - 42.51: 617 42.51 - 63.77: 90 63.77 - 85.02: 30 85.02 - 106.28: 12 Dihedral angle restraints: 17802 sinusoidal: 7330 harmonic: 10472 Sorted by residual: dihedral pdb=" CA GLN F 317 " pdb=" C GLN F 317 " pdb=" N THR F 318 " pdb=" CA THR F 318 " ideal model delta harmonic sigma weight residual 180.00 92.36 87.64 0 5.00e+00 4.00e-02 3.07e+02 dihedral pdb=" CA GLN E 317 " pdb=" C GLN E 317 " pdb=" N THR E 318 " pdb=" CA THR E 318 " ideal model delta harmonic sigma weight residual 180.00 92.41 87.59 0 5.00e+00 4.00e-02 3.07e+02 dihedral pdb=" CA ASP F 407 " pdb=" C ASP F 407 " pdb=" N GLY F 408 " pdb=" CA GLY F 408 " ideal model delta harmonic sigma weight residual -180.00 -93.39 -86.61 0 5.00e+00 4.00e-02 3.00e+02 ... (remaining 17799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.187: 4325 0.187 - 0.374: 21 0.374 - 0.561: 4 0.561 - 0.748: 2 0.748 - 0.934: 2 Chirality restraints: 4354 Sorted by residual: chirality pdb=" C1 NAG B 805 " pdb=" ND2 ASN B 727 " pdb=" C2 NAG B 805 " pdb=" O5 NAG B 805 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.18e+01 chirality pdb=" C1 NAG A 805 " pdb=" ND2 ASN A 727 " pdb=" C2 NAG A 805 " pdb=" O5 NAG A 805 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.18e+01 chirality pdb=" C1 NAG B 802 " pdb=" ND2 ASN B 251 " pdb=" C2 NAG B 802 " pdb=" O5 NAG B 802 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 4351 not shown) Planarity restraints: 5116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 422 " 0.049 2.00e-02 2.50e+03 3.04e-02 1.85e+01 pdb=" CG TYR F 422 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR F 422 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR F 422 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR F 422 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR F 422 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR F 422 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR F 422 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 422 " -0.049 2.00e-02 2.50e+03 3.03e-02 1.83e+01 pdb=" CG TYR E 422 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR E 422 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR E 422 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 422 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR E 422 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR E 422 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR E 422 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 251 " -0.035 2.00e-02 2.50e+03 3.27e-02 1.34e+01 pdb=" CG ASN B 251 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN B 251 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B 251 " 0.037 2.00e-02 2.50e+03 pdb=" C1 NAG B 802 " -0.035 2.00e-02 2.50e+03 ... (remaining 5113 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 201 2.58 - 3.16: 22985 3.16 - 3.74: 43570 3.74 - 4.32: 60002 4.32 - 4.90: 97829 Nonbonded interactions: 224587 Sorted by model distance: nonbonded pdb="FE FE D 703 " pdb=" O3 CO3 D 704 " model vdw 2.001 2.260 nonbonded pdb="FE FE C 703 " pdb=" O3 CO3 C 704 " model vdw 2.012 2.260 nonbonded pdb=" OD1 ASP D 63 " pdb="FE FE D 703 " model vdw 2.035 2.260 nonbonded pdb=" OH TYR C 95 " pdb="FE FE C 703 " model vdw 2.039 2.260 nonbonded pdb=" OD1 ASP C 63 " pdb="FE FE C 703 " model vdw 2.043 2.260 ... (remaining 224582 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' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 4 7.16 5 S 142 5.16 5 C 18252 2.51 5 N 4850 2.21 5 O 5498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.070 Check model and map are aligned: 0.430 Convert atoms to be neutral: 0.250 Process input model: 69.280 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.074 29360 Z= 0.524 Angle : 1.067 13.894 39664 Z= 0.609 Chirality : 0.062 0.934 4354 Planarity : 0.007 0.071 5106 Dihedral : 11.616 106.278 10924 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -3.02 (0.11), residues: 3560 helix: -2.00 (0.10), residues: 1672 sheet: -1.14 (0.26), residues: 336 loop : -2.07 (0.13), residues: 1552 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 394 time to evaluate : 3.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 4 residues processed: 428 average time/residue: 0.4315 time to fit residues: 281.6241 Evaluate side-chains 139 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 135 time to evaluate : 3.470 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3305 time to fit residues: 6.8792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 5.9990 chunk 268 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 180 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 277 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 206 optimal weight: 10.0000 chunk 321 optimal weight: 9.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 197 GLN A 236 ASN A 275 ASN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN A 640 GLN A 715 ASN B 148 ASN B 197 GLN B 236 ASN B 275 ASN B 401 HIS B 483 ASN B 608 ASN B 626 ASN B 640 GLN B 715 ASN B 721 GLN C 55 ASN C 300 HIS ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 ASN D 55 ASN D 300 HIS ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 ASN ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 618 ASN E 252 ASN E 292 ASN E 346 GLN E 364 GLN E 397 HIS E 444 ASN E 456 ASN E 527 ASN F 252 ASN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 GLN F 397 HIS F 444 ASN F 456 ASN F 483 ASN F 527 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.087 29360 Z= 0.439 Angle : 0.735 11.783 39664 Z= 0.396 Chirality : 0.051 0.917 4354 Planarity : 0.005 0.067 5106 Dihedral : 7.002 107.622 3968 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.71 % Favored : 96.18 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -1.33 (0.13), residues: 3560 helix: -0.10 (0.12), residues: 1668 sheet: -1.05 (0.27), residues: 342 loop : -1.67 (0.14), residues: 1550 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 138 time to evaluate : 3.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 45 residues processed: 215 average time/residue: 0.3890 time to fit residues: 137.7241 Evaluate side-chains 147 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 102 time to evaluate : 3.232 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.2751 time to fit residues: 27.0388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 178 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 267 optimal weight: 6.9990 chunk 218 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 322 optimal weight: 5.9990 chunk 347 optimal weight: 2.9990 chunk 286 optimal weight: 6.9990 chunk 319 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 258 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 ASN C 245 GLN ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 604 GLN E 292 ASN E 346 GLN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.100 29360 Z= 0.294 Angle : 0.625 14.941 39664 Z= 0.333 Chirality : 0.046 0.776 4354 Planarity : 0.004 0.080 5106 Dihedral : 6.708 108.231 3968 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.85 % Favored : 96.10 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.13), residues: 3560 helix: 0.61 (0.12), residues: 1656 sheet: -0.94 (0.27), residues: 358 loop : -1.45 (0.14), residues: 1546 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 115 time to evaluate : 3.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 23 residues processed: 172 average time/residue: 0.3651 time to fit residues: 107.9665 Evaluate side-chains 121 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 3.707 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2826 time to fit residues: 16.8620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 318 optimal weight: 8.9990 chunk 242 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 216 optimal weight: 0.0070 chunk 323 optimal weight: 7.9990 chunk 342 optimal weight: 0.0040 chunk 168 optimal weight: 8.9990 chunk 306 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 overall best weight: 2.0016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 HIS ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 HIS F 252 ASN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 29360 Z= 0.211 Angle : 0.562 12.489 39664 Z= 0.298 Chirality : 0.045 0.796 4354 Planarity : 0.004 0.077 5106 Dihedral : 6.396 108.154 3968 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.79 % Favored : 96.15 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 3560 helix: 1.08 (0.12), residues: 1654 sheet: -0.82 (0.28), residues: 334 loop : -1.29 (0.14), residues: 1572 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 120 time to evaluate : 3.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 21 residues processed: 167 average time/residue: 0.3776 time to fit residues: 107.0347 Evaluate side-chains 117 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 3.420 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2540 time to fit residues: 14.7820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 284 optimal weight: 10.0000 chunk 194 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 254 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 291 optimal weight: 4.9990 chunk 236 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 307 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 ASN ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 GLN B 723 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 483 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 29360 Z= 0.241 Angle : 0.577 13.560 39664 Z= 0.304 Chirality : 0.045 0.831 4354 Planarity : 0.003 0.064 5106 Dihedral : 6.345 108.249 3968 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.65 % Favored : 96.32 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3560 helix: 1.31 (0.13), residues: 1664 sheet: -0.78 (0.28), residues: 334 loop : -1.20 (0.15), residues: 1562 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 104 time to evaluate : 3.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 19 residues processed: 147 average time/residue: 0.3788 time to fit residues: 95.0921 Evaluate side-chains 115 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 3.678 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 19 outliers final: 1 residues processed: 19 average time/residue: 0.2521 time to fit residues: 14.0840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 115 optimal weight: 3.9990 chunk 308 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 342 optimal weight: 0.0170 chunk 284 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 179 optimal weight: 8.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 475 HIS B 640 GLN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 29360 Z= 0.233 Angle : 0.565 12.157 39664 Z= 0.297 Chirality : 0.045 0.842 4354 Planarity : 0.004 0.090 5106 Dihedral : 6.235 108.255 3968 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3560 helix: 1.52 (0.13), residues: 1652 sheet: -0.73 (0.28), residues: 334 loop : -1.16 (0.15), residues: 1574 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 111 time to evaluate : 3.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 18 residues processed: 145 average time/residue: 0.3884 time to fit residues: 96.6107 Evaluate side-chains 110 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 3.423 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2569 time to fit residues: 13.2272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 330 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 195 optimal weight: 0.9990 chunk 250 optimal weight: 8.9990 chunk 193 optimal weight: 0.8980 chunk 288 optimal weight: 3.9990 chunk 191 optimal weight: 9.9990 chunk 341 optimal weight: 4.9990 chunk 213 optimal weight: 0.5980 chunk 208 optimal weight: 3.9990 chunk 157 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.092 29360 Z= 0.176 Angle : 0.540 12.035 39664 Z= 0.283 Chirality : 0.043 0.697 4354 Planarity : 0.004 0.101 5106 Dihedral : 6.105 108.237 3968 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3560 helix: 1.72 (0.13), residues: 1652 sheet: -0.60 (0.28), residues: 334 loop : -1.07 (0.15), residues: 1574 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 117 time to evaluate : 3.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 141 average time/residue: 0.3575 time to fit residues: 86.6507 Evaluate side-chains 109 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 3.283 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2473 time to fit residues: 9.0607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 211 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 203 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 216 optimal weight: 10.0000 chunk 232 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 268 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.156 29360 Z= 0.261 Angle : 0.583 19.013 39664 Z= 0.307 Chirality : 0.044 0.649 4354 Planarity : 0.004 0.143 5106 Dihedral : 6.121 108.335 3968 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.14), residues: 3560 helix: 1.73 (0.13), residues: 1656 sheet: -0.66 (0.27), residues: 354 loop : -1.04 (0.15), residues: 1550 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 3.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 6 residues processed: 118 average time/residue: 0.3886 time to fit residues: 79.3544 Evaluate side-chains 99 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 3.592 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2893 time to fit residues: 8.0643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 310 optimal weight: 1.9990 chunk 326 optimal weight: 4.9990 chunk 298 optimal weight: 10.0000 chunk 317 optimal weight: 0.7980 chunk 191 optimal weight: 0.0050 chunk 138 optimal weight: 0.9990 chunk 249 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 287 optimal weight: 3.9990 chunk 300 optimal weight: 0.9990 chunk 316 optimal weight: 10.0000 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.159 29360 Z= 0.175 Angle : 0.554 18.376 39664 Z= 0.291 Chirality : 0.042 0.590 4354 Planarity : 0.004 0.116 5106 Dihedral : 5.996 108.066 3968 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.14), residues: 3560 helix: 1.87 (0.13), residues: 1652 sheet: -0.59 (0.27), residues: 354 loop : -0.96 (0.15), residues: 1554 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 3.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 115 average time/residue: 0.3805 time to fit residues: 76.6788 Evaluate side-chains 100 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 4.112 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3405 time to fit residues: 8.2822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 208 optimal weight: 3.9990 chunk 336 optimal weight: 3.9990 chunk 205 optimal weight: 8.9990 chunk 159 optimal weight: 4.9990 chunk 233 optimal weight: 5.9990 chunk 352 optimal weight: 5.9990 chunk 324 optimal weight: 2.9990 chunk 280 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 216 optimal weight: 9.9990 chunk 172 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 640 GLN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.146 29360 Z= 0.218 Angle : 0.563 16.437 39664 Z= 0.295 Chirality : 0.043 0.563 4354 Planarity : 0.004 0.116 5106 Dihedral : 5.958 108.018 3968 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.14), residues: 3560 helix: 1.89 (0.13), residues: 1656 sheet: -0.62 (0.27), residues: 354 loop : -0.94 (0.16), residues: 1550 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 3.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 107 average time/residue: 0.3886 time to fit residues: 71.7618 Evaluate side-chains 94 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 3.494 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2879 time to fit residues: 6.2545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 223 optimal weight: 9.9990 chunk 299 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 258 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 78 optimal weight: 0.2980 chunk 281 optimal weight: 0.1980 chunk 117 optimal weight: 0.9980 chunk 288 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 528 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.115001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.088182 restraints weight = 54939.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.087238 restraints weight = 69387.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.088285 restraints weight = 73539.022| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.123 29360 Z= 0.245 Angle : 0.573 15.783 39664 Z= 0.299 Chirality : 0.044 0.550 4354 Planarity : 0.004 0.108 5106 Dihedral : 5.967 107.960 3968 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.14), residues: 3560 helix: 1.86 (0.13), residues: 1656 sheet: -0.66 (0.28), residues: 354 loop : -0.97 (0.16), residues: 1550 =============================================================================== Job complete usr+sys time: 3696.52 seconds wall clock time: 70 minutes 36.24 seconds (4236.24 seconds total)