Starting phenix.real_space_refine on Sun Sep 29 22:25:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uda_20735/09_2024/6uda_20735_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uda_20735/09_2024/6uda_20735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uda_20735/09_2024/6uda_20735.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uda_20735/09_2024/6uda_20735.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uda_20735/09_2024/6uda_20735_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uda_20735/09_2024/6uda_20735_neut.cif" } resolution = 4.2 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= 0.004 sd= 0.075 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 141 5.16 5 C 14913 2.51 5 N 4056 2.21 5 O 4623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23733 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3567 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 21, 'TRANS': 428} Chain breaks: 1 Chain: "C" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1645 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1620 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 199} Chain: "F" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1001 Classifications: {'peptide': 126} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: J, Z, M, N, E, I, H, L, G, K Time building chain proxies: 12.29, per 1000 atoms: 0.52 Number of scatterers: 23733 At special positions: 0 Unit cell: (184.68, 182.52, 118.8, 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 141 16.00 O 4623 8.00 N 4056 7.00 C 14913 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.12 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.07 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.05 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 137 " - pdb=" SG CYS C 193 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 ALPHA1-3 " BMA B 3 " - " MAN B 4 " " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A 605 " - " ASN A 448 " " NAG A 606 " - " ASN A 276 " " NAG B 1 " - " ASN A 262 " " NAG E 605 " - " ASN E 448 " " NAG E 606 " - " ASN E 276 " " NAG I 605 " - " ASN I 448 " " NAG I 606 " - " ASN I 276 " " NAG M 1 " - " ASN E 262 " " NAG N 1 " - " ASN I 262 " Time building additional restraints: 5.72 Conformation dependent library (CDL) restraints added in 2.8 seconds 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5640 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 63 sheets defined 19.1% alpha, 43.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.10 Creating SS restraints... Processing helix chain 'A' and resid 100 through 115 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 138 through 143 removed outlier: 4.049A pdb=" N GLU A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 479 through 484 removed outlier: 4.999A pdb=" N TYR A 482 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS A 483 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.708A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 184 through 186 No H-bonds generated for 'chain 'C' and resid 184 through 186' Processing helix chain 'C' and resid 198 through 201 Processing helix chain 'Z' and resid 533 through 535 No H-bonds generated for 'chain 'Z' and resid 533 through 535' Processing helix chain 'Z' and resid 536 through 544 removed outlier: 3.693A pdb=" N LEU Z 544 " --> pdb=" O GLN Z 540 " (cutoff:3.500A) Processing helix chain 'Z' and resid 572 through 596 Processing helix chain 'Z' and resid 621 through 625 Processing helix chain 'Z' and resid 628 through 635 Processing helix chain 'Z' and resid 638 through 663 removed outlier: 4.420A pdb=" N GLY Z 644 " --> pdb=" O GLN Z 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'E' and resid 100 through 115 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 138 through 143 removed outlier: 4.049A pdb=" N GLU E 143 " --> pdb=" O SER E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 334 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 377 through 381 Processing helix chain 'E' and resid 473 through 478 Processing helix chain 'E' and resid 479 through 484 removed outlier: 4.999A pdb=" N TYR E 482 " --> pdb=" O SER E 479 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS E 483 " --> pdb=" O GLU E 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 535 No H-bonds generated for 'chain 'F' and resid 533 through 535' Processing helix chain 'F' and resid 536 through 544 removed outlier: 3.693A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 Processing helix chain 'F' and resid 621 through 625 Processing helix chain 'F' and resid 628 through 635 Processing helix chain 'F' and resid 638 through 663 removed outlier: 4.420A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.709A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'G' and resid 153 through 155 No H-bonds generated for 'chain 'G' and resid 153 through 155' Processing helix chain 'G' and resid 184 through 186 No H-bonds generated for 'chain 'G' and resid 184 through 186' Processing helix chain 'G' and resid 198 through 201 Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'H' and resid 121 through 128 Processing helix chain 'H' and resid 183 through 187 Processing helix chain 'I' and resid 100 through 115 Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 138 through 143 removed outlier: 4.049A pdb=" N GLU I 143 " --> pdb=" O SER I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 179 No H-bonds generated for 'chain 'I' and resid 177 through 179' Processing helix chain 'I' and resid 205 through 209 Processing helix chain 'I' and resid 334 through 350 Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 377 through 381 Processing helix chain 'I' and resid 473 through 478 Processing helix chain 'I' and resid 479 through 484 removed outlier: 4.999A pdb=" N TYR I 482 " --> pdb=" O SER I 479 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS I 483 " --> pdb=" O GLU I 480 " (cutoff:3.500A) Processing helix chain 'J' and resid 533 through 535 No H-bonds generated for 'chain 'J' and resid 533 through 535' Processing helix chain 'J' and resid 536 through 544 removed outlier: 3.692A pdb=" N LEU J 544 " --> pdb=" O GLN J 540 " (cutoff:3.500A) Processing helix chain 'J' and resid 572 through 596 Processing helix chain 'J' and resid 621 through 625 Processing helix chain 'J' and resid 628 through 635 Processing helix chain 'J' and resid 638 through 663 removed outlier: 4.419A pdb=" N GLY J 644 " --> pdb=" O GLN J 640 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.708A pdb=" N TYR K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'K' and resid 153 through 155 No H-bonds generated for 'chain 'K' and resid 153 through 155' Processing helix chain 'K' and resid 184 through 186 No H-bonds generated for 'chain 'K' and resid 184 through 186' Processing helix chain 'K' and resid 198 through 201 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 497 removed outlier: 5.209A pdb=" N VAL Z 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL A 38 " --> pdb=" O THR Z 606 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR Z 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N TYR A 40 " --> pdb=" O CYS Z 604 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N CYS Z 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.903A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 200 through 202 removed outlier: 6.341A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.576A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N ASN A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N CYS A 296 " --> pdb=" O ASN A 442 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N ILE A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.042A pdb=" N VAL A 292 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 9.635A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.754A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.635A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 11.042A pdb=" N VAL A 292 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N ILE A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N CYS A 296 " --> pdb=" O ASN A 442 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N ASN A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR A 465 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR A 359 " --> pdb=" O PHE A 466 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 358 " --> pdb=" O TYR A 395 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 315 through 323 removed outlier: 6.787A pdb=" N ALA A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ILE A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N THR A 320 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N THR A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLN A 321A" --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.635A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 11.042A pdb=" N VAL A 292 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N ILE A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N CYS A 296 " --> pdb=" O ASN A 442 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N ASN A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.810A pdb=" N MET C 34 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 11 through 12 removed outlier: 4.709A pdb=" N TYR C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 120 through 124 removed outlier: 5.385A pdb=" N TYR C 173 " --> pdb=" O ASP C 141 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 120 through 124 removed outlier: 5.385A pdb=" N TYR C 173 " --> pdb=" O ASP C 141 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 148 through 151 Processing sheet with id=AB8, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN D 90 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 114 through 118 Processing sheet with id=AC3, first strand: chain 'D' and resid 153 through 155 removed outlier: 4.779A pdb=" N TRP D 148 " --> pdb=" O GLN D 155 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 492 through 497 removed outlier: 5.208A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.903A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 92 Processing sheet with id=AC8, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AC9, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AD1, first strand: chain 'E' and resid 200 through 202 removed outlier: 6.341A pdb=" N VAL E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.575A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N ASN E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 11.649A pdb=" N CYS E 296 " --> pdb=" O ASN E 442 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N ILE E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N VAL E 292 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 9.635A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.173A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.754A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.173A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.635A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N VAL E 292 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N ILE E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.649A pdb=" N CYS E 296 " --> pdb=" O ASN E 442 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N ASN E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR E 465 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR E 359 " --> pdb=" O PHE E 466 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE E 358 " --> pdb=" O TYR E 395 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 315 through 323 removed outlier: 6.787A pdb=" N ALA E 316 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ILE E 309 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N THR E 320 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N THR E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLN E 321A" --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.173A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.635A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N VAL E 292 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N ILE E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.649A pdb=" N CYS E 296 " --> pdb=" O ASN E 442 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N ASN E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD6, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.811A pdb=" N MET G 34 " --> pdb=" O ILE G 50 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 11 through 12 removed outlier: 4.710A pdb=" N TYR G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 120 through 124 removed outlier: 5.386A pdb=" N TYR G 173 " --> pdb=" O ASP G 141 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 120 through 124 removed outlier: 5.386A pdb=" N TYR G 173 " --> pdb=" O ASP G 141 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 148 through 151 Processing sheet with id=AE2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AE3, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN H 90 " --> pdb=" O THR H 97 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR H 97 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 114 through 118 Processing sheet with id=AE6, first strand: chain 'H' and resid 153 through 155 removed outlier: 4.779A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 492 through 497 removed outlier: 5.209A pdb=" N VAL J 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL I 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR J 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N TYR I 40 " --> pdb=" O CYS J 604 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N CYS J 604 " --> pdb=" O TYR I 40 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.903A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AF1, first strand: chain 'I' and resid 91 through 92 Processing sheet with id=AF2, first strand: chain 'I' and resid 130 through 131 Processing sheet with id=AF3, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AF4, first strand: chain 'I' and resid 200 through 202 removed outlier: 6.341A pdb=" N VAL I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.575A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N ASN I 442 " --> pdb=" O CYS I 296 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N CYS I 296 " --> pdb=" O ASN I 442 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 10.101A pdb=" N ILE I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.042A pdb=" N VAL I 292 " --> pdb=" O ILE I 446 " (cutoff:3.500A) removed outlier: 9.634A pdb=" N ASN I 448 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N GLU I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 271 through 273 removed outlier: 6.754A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N GLU I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.634A pdb=" N ASN I 448 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 11.042A pdb=" N VAL I 292 " --> pdb=" O ILE I 446 " (cutoff:3.500A) removed outlier: 10.101A pdb=" N ILE I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N CYS I 296 " --> pdb=" O ASN I 442 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N ASN I 442 " --> pdb=" O CYS I 296 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR I 465 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR I 359 " --> pdb=" O PHE I 466 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE I 358 " --> pdb=" O TYR I 395 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 315 through 323 removed outlier: 6.788A pdb=" N ALA I 316 " --> pdb=" O ILE I 309 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ILE I 309 " --> pdb=" O ALA I 316 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N TYR I 318 " --> pdb=" O ILE I 307 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE I 307 " --> pdb=" O TYR I 318 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N THR I 320 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N THR I 305 " --> pdb=" O THR I 320 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLN I 321A" --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N GLU I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.634A pdb=" N ASN I 448 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 11.042A pdb=" N VAL I 292 " --> pdb=" O ILE I 446 " (cutoff:3.500A) removed outlier: 10.101A pdb=" N ILE I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N CYS I 296 " --> pdb=" O ASN I 442 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N ASN I 442 " --> pdb=" O CYS I 296 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AF9, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.811A pdb=" N MET K 34 " --> pdb=" O ILE K 50 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 11 through 12 removed outlier: 4.710A pdb=" N TYR K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 120 through 124 removed outlier: 5.386A pdb=" N TYR K 173 " --> pdb=" O ASP K 141 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 120 through 124 removed outlier: 5.386A pdb=" N TYR K 173 " --> pdb=" O ASP K 141 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 148 through 151 Processing sheet with id=AG5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 114 through 118 Processing sheet with id=AG9, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.779A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) 984 hydrogen bonds defined for protein. 2466 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: 9.10 Time building geometry restraints manager: 6.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 4146 1.31 - 1.46: 8860 1.46 - 1.61: 11033 1.61 - 1.76: 18 1.76 - 1.91: 177 Bond restraints: 24234 Sorted by residual: bond pdb=" C4 NAG A 605 " pdb=" C5 NAG A 605 " ideal model delta sigma weight residual 1.532 1.404 0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C4 NAG E 605 " pdb=" C5 NAG E 605 " ideal model delta sigma weight residual 1.532 1.405 0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C4 NAG I 605 " pdb=" C5 NAG I 605 " ideal model delta sigma weight residual 1.532 1.405 0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C ASN A 448 " pdb=" O ASN A 448 " ideal model delta sigma weight residual 1.235 1.161 0.075 1.23e-02 6.61e+03 3.69e+01 bond pdb=" C ASN E 448 " pdb=" O ASN E 448 " ideal model delta sigma weight residual 1.235 1.161 0.074 1.23e-02 6.61e+03 3.61e+01 ... (remaining 24229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.85: 32490 5.85 - 11.71: 396 11.71 - 17.56: 24 17.56 - 23.42: 9 23.42 - 29.27: 3 Bond angle restraints: 32922 Sorted by residual: angle pdb=" N PHE C 100E" pdb=" CA PHE C 100E" pdb=" C PHE C 100E" ideal model delta sigma weight residual 109.52 127.32 -17.80 1.55e+00 4.16e-01 1.32e+02 angle pdb=" N PHE G 100E" pdb=" CA PHE G 100E" pdb=" C PHE G 100E" ideal model delta sigma weight residual 109.52 127.31 -17.79 1.55e+00 4.16e-01 1.32e+02 angle pdb=" N PHE K 100E" pdb=" CA PHE K 100E" pdb=" C PHE K 100E" ideal model delta sigma weight residual 109.52 127.30 -17.78 1.55e+00 4.16e-01 1.32e+02 angle pdb=" C5 NAG I 605 " pdb=" C4 NAG I 605 " pdb=" O4 NAG I 605 " ideal model delta sigma weight residual 111.70 82.43 29.27 3.00e+00 1.11e-01 9.52e+01 angle pdb=" C5 NAG E 605 " pdb=" C4 NAG E 605 " pdb=" O4 NAG E 605 " ideal model delta sigma weight residual 111.70 82.47 29.23 3.00e+00 1.11e-01 9.50e+01 ... (remaining 32917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.74: 14335 23.74 - 47.49: 265 47.49 - 71.23: 76 71.23 - 94.98: 45 94.98 - 118.72: 12 Dihedral angle restraints: 14733 sinusoidal: 5973 harmonic: 8760 Sorted by residual: dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -130.75 44.75 1 1.00e+01 1.00e-02 2.78e+01 dihedral pdb=" CB CYS C 137 " pdb=" SG CYS C 137 " pdb=" SG CYS C 193 " pdb=" CB CYS C 193 " ideal model delta sinusoidal sigma weight residual 93.00 51.08 41.92 1 1.00e+01 1.00e-02 2.46e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 157 " pdb=" CB CYS A 157 " ideal model delta sinusoidal sigma weight residual -86.00 -51.10 -34.90 1 1.00e+01 1.00e-02 1.73e+01 ... (remaining 14730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.045: 3774 1.045 - 2.089: 0 2.089 - 3.134: 0 3.134 - 4.178: 0 4.178 - 5.223: 6 Chirality restraints: 3780 Sorted by residual: chirality pdb=" C1 NAG I 605 " pdb=" ND2 ASN I 448 " pdb=" C2 NAG I 605 " pdb=" O5 NAG I 605 " both_signs ideal model delta sigma weight residual False -2.40 2.82 -5.22 2.00e-01 2.50e+01 6.82e+02 chirality pdb=" C1 NAG E 605 " pdb=" ND2 ASN E 448 " pdb=" C2 NAG E 605 " pdb=" O5 NAG E 605 " both_signs ideal model delta sigma weight residual False -2.40 2.82 -5.22 2.00e-01 2.50e+01 6.82e+02 chirality pdb=" C1 NAG A 605 " pdb=" ND2 ASN A 448 " pdb=" C2 NAG A 605 " pdb=" O5 NAG A 605 " both_signs ideal model delta sigma weight residual False -2.40 2.82 -5.22 2.00e-01 2.50e+01 6.82e+02 ... (remaining 3777 not shown) Planarity restraints: 4179 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " 0.320 2.00e-02 2.50e+03 2.79e-01 9.72e+02 pdb=" C7 NAG M 2 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " 0.063 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " -0.494 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " 0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " -0.320 2.00e-02 2.50e+03 2.79e-01 9.72e+02 pdb=" C7 NAG B 2 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " -0.062 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " 0.494 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " -0.320 2.00e-02 2.50e+03 2.79e-01 9.71e+02 pdb=" C7 NAG N 2 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " -0.062 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " 0.493 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " -0.183 2.00e-02 2.50e+03 ... (remaining 4176 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 196 2.58 - 3.16: 19227 3.16 - 3.74: 34878 3.74 - 4.32: 50353 4.32 - 4.90: 79106 Nonbonded interactions: 183760 Sorted by model distance: nonbonded pdb=" OD1 ASN E 262 " pdb=" C1 NAG M 1 " model vdw 2.004 2.776 nonbonded pdb=" OD1 ASN A 262 " pdb=" C1 NAG B 1 " model vdw 2.005 2.776 nonbonded pdb=" OD1 ASN I 262 " pdb=" C1 NAG N 1 " model vdw 2.005 2.776 nonbonded pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " model vdw 2.020 3.760 nonbonded pdb=" SG CYS D 23 " pdb=" SG CYS D 88 " model vdw 2.020 3.760 ... (remaining 183755 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 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: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 51.390 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 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 : 0.017 0.128 24234 Z= 1.104 Angle : 1.890 29.269 32922 Z= 1.196 Chirality : 0.221 5.223 3780 Planarity : 0.014 0.279 4170 Dihedral : 11.956 118.723 9069 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.50 % Allowed : 2.41 % Favored : 97.08 % Rotamer: Outliers : 0.34 % Allowed : 0.68 % Favored : 98.98 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.15), residues: 2982 helix: -0.58 (0.23), residues: 423 sheet: 1.04 (0.16), residues: 963 loop : 0.82 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.009 TRP D 35 HIS 0.015 0.004 HIS K 100D PHE 0.036 0.007 PHE Z 522 TYR 0.082 0.010 TYR E 191 ARG 0.010 0.001 ARG K 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 367 time to evaluate : 2.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ILE cc_start: 0.7711 (tt) cc_final: 0.7387 (mt) REVERT: Z 523 LEU cc_start: 0.8283 (mt) cc_final: 0.7783 (mp) REVERT: Z 537 LEU cc_start: 0.8530 (mt) cc_final: 0.8304 (mt) REVERT: E 371 ILE cc_start: 0.7610 (tt) cc_final: 0.7345 (mt) REVERT: F 523 LEU cc_start: 0.8270 (mt) cc_final: 0.7805 (mp) REVERT: I 371 ILE cc_start: 0.7528 (tt) cc_final: 0.7230 (mt) REVERT: J 523 LEU cc_start: 0.8380 (mt) cc_final: 0.7906 (mp) REVERT: J 537 LEU cc_start: 0.8638 (mt) cc_final: 0.8436 (mt) outliers start: 9 outliers final: 3 residues processed: 376 average time/residue: 0.4262 time to fit residues: 232.1871 Evaluate side-chains 158 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 155 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 175 optimal weight: 9.9990 chunk 272 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** C 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN E 374 HIS ** G 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 ASN I 374 HIS ** K 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 24234 Z= 0.297 Angle : 0.829 14.325 32922 Z= 0.429 Chirality : 0.055 0.902 3780 Planarity : 0.004 0.041 4170 Dihedral : 9.682 73.748 3603 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.82 % Favored : 97.05 % Rotamer: Outliers : 0.23 % Allowed : 1.36 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.15), residues: 2982 helix: 0.22 (0.25), residues: 429 sheet: 0.71 (0.16), residues: 1032 loop : 0.36 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 35 HIS 0.017 0.002 HIS G 100D PHE 0.024 0.002 PHE L 71 TYR 0.027 0.003 TYR D 36 ARG 0.010 0.001 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 183 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 657 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8336 (tp30) outliers start: 6 outliers final: 0 residues processed: 189 average time/residue: 0.3624 time to fit residues: 106.8182 Evaluate side-chains 123 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 226 optimal weight: 10.0000 chunk 185 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 272 optimal weight: 7.9990 chunk 294 optimal weight: 5.9990 chunk 243 optimal weight: 0.4980 chunk 270 optimal weight: 30.0000 chunk 93 optimal weight: 10.0000 chunk 218 optimal weight: 0.9980 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN F 543 ASN ** G 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 543 ASN ** K 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24234 Z= 0.295 Angle : 0.736 14.057 32922 Z= 0.383 Chirality : 0.048 0.407 3780 Planarity : 0.004 0.043 4170 Dihedral : 7.964 56.693 3603 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.89 % Favored : 96.01 % Rotamer: Outliers : 0.15 % Allowed : 2.23 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 2982 helix: 0.16 (0.25), residues: 429 sheet: 0.58 (0.16), residues: 984 loop : 0.12 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 35 HIS 0.013 0.002 HIS K 100D PHE 0.022 0.002 PHE I 53 TYR 0.056 0.002 TYR L 91 ARG 0.011 0.001 ARG K 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 152 time to evaluate : 2.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 95 MET cc_start: 0.7764 (ppp) cc_final: 0.7127 (ppp) REVERT: I 95 MET cc_start: 0.7863 (ppp) cc_final: 0.7339 (ppp) REVERT: J 657 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8487 (tp30) outliers start: 4 outliers final: 0 residues processed: 156 average time/residue: 0.3559 time to fit residues: 88.7216 Evaluate side-chains 119 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 40.0000 chunk 205 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 273 optimal weight: 10.0000 chunk 289 optimal weight: 9.9990 chunk 143 optimal weight: 0.0770 chunk 259 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 overall best weight: 3.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24234 Z= 0.259 Angle : 0.673 14.113 32922 Z= 0.351 Chirality : 0.046 0.263 3780 Planarity : 0.004 0.042 4170 Dihedral : 7.144 51.358 3603 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.33 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % 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: 0.22 (0.15), residues: 2982 helix: 0.25 (0.25), residues: 429 sheet: 0.46 (0.16), residues: 984 loop : 0.03 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 631 HIS 0.011 0.001 HIS C 100D PHE 0.017 0.002 PHE I 53 TYR 0.046 0.002 TYR L 91 ARG 0.005 0.000 ARG K 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7719 (ppp) cc_final: 0.7383 (ppp) REVERT: E 95 MET cc_start: 0.7785 (ppp) cc_final: 0.7289 (ppp) REVERT: J 530 MET cc_start: 0.7069 (mpp) cc_final: 0.6769 (mpp) REVERT: J 626 MET cc_start: 0.8470 (tpp) cc_final: 0.8246 (tpp) REVERT: J 657 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8462 (tp30) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.3312 time to fit residues: 72.4929 Evaluate side-chains 107 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 8.9990 chunk 164 optimal weight: 3.9990 chunk 4 optimal weight: 0.0980 chunk 215 optimal weight: 8.9990 chunk 119 optimal weight: 9.9990 chunk 247 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 260 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24234 Z= 0.227 Angle : 0.628 13.939 32922 Z= 0.331 Chirality : 0.044 0.236 3780 Planarity : 0.004 0.044 4170 Dihedral : 6.504 53.956 3603 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.33 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % 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: 0.09 (0.15), residues: 2982 helix: 0.13 (0.25), residues: 447 sheet: 0.42 (0.16), residues: 963 loop : -0.09 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 477 HIS 0.009 0.001 HIS K 100D PHE 0.028 0.002 PHE C 63 TYR 0.037 0.002 TYR D 91 ARG 0.004 0.000 ARG G 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 2.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 530 MET cc_start: 0.6950 (mpp) cc_final: 0.6569 (mpp) REVERT: J 530 MET cc_start: 0.7349 (mpp) cc_final: 0.6789 (mpp) REVERT: J 626 MET cc_start: 0.8535 (tpp) cc_final: 0.8304 (tpp) REVERT: J 657 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8425 (tp30) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.3542 time to fit residues: 79.7197 Evaluate side-chains 109 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 0.1980 chunk 261 optimal weight: 4.9990 chunk 57 optimal weight: 30.0000 chunk 170 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 290 optimal weight: 9.9990 chunk 240 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN D 37 GLN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24234 Z= 0.319 Angle : 0.669 14.040 32922 Z= 0.352 Chirality : 0.045 0.221 3780 Planarity : 0.004 0.054 4170 Dihedral : 6.455 56.934 3603 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.93 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 2982 helix: 0.03 (0.25), residues: 447 sheet: 0.24 (0.16), residues: 966 loop : -0.30 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Z 628 HIS 0.011 0.001 HIS G 100D PHE 0.027 0.002 PHE C 63 TYR 0.025 0.002 TYR L 91 ARG 0.005 0.001 ARG C 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 2.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7708 (ppp) cc_final: 0.7363 (ppp) REVERT: F 530 MET cc_start: 0.7192 (mpp) cc_final: 0.6653 (mpp) REVERT: J 530 MET cc_start: 0.7037 (mpp) cc_final: 0.6784 (mpp) REVERT: J 626 MET cc_start: 0.8524 (tpp) cc_final: 0.8287 (tpp) REVERT: J 657 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8488 (tp30) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.3594 time to fit residues: 75.0514 Evaluate side-chains 97 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 10.0000 chunk 32 optimal weight: 0.0010 chunk 165 optimal weight: 10.0000 chunk 211 optimal weight: 20.0000 chunk 164 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 162 optimal weight: 0.5980 chunk 289 optimal weight: 20.0000 chunk 180 optimal weight: 3.9990 chunk 176 optimal weight: 0.6980 chunk 133 optimal weight: 6.9990 overall best weight: 1.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24234 Z= 0.172 Angle : 0.597 14.086 32922 Z= 0.314 Chirality : 0.044 0.197 3780 Planarity : 0.004 0.040 4170 Dihedral : 6.215 59.236 3603 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.39 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.17 (0.15), residues: 2982 helix: 0.18 (0.25), residues: 447 sheet: 0.24 (0.15), residues: 1050 loop : -0.36 (0.17), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 36 HIS 0.008 0.001 HIS C 100D PHE 0.030 0.001 PHE K 63 TYR 0.028 0.002 TYR L 91 ARG 0.006 0.000 ARG C 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 2.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7669 (ppp) cc_final: 0.7424 (ppp) REVERT: Z 654 GLU cc_start: 0.8149 (tp30) cc_final: 0.7646 (tp30) REVERT: F 530 MET cc_start: 0.7120 (mpp) cc_final: 0.6904 (mpp) REVERT: G 50 ILE cc_start: 0.8871 (tp) cc_final: 0.8651 (tp) REVERT: I 145 MET cc_start: 0.6292 (mmp) cc_final: 0.6057 (mmp) REVERT: J 530 MET cc_start: 0.7358 (mpp) cc_final: 0.6926 (mpp) REVERT: J 626 MET cc_start: 0.8541 (tpp) cc_final: 0.8315 (tpp) REVERT: J 657 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8501 (tp30) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.3440 time to fit residues: 75.1994 Evaluate side-chains 100 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 3.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 9.9990 chunk 115 optimal weight: 0.8980 chunk 172 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 196 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 227 optimal weight: 9.9990 chunk 263 optimal weight: 0.6980 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24234 Z= 0.296 Angle : 0.660 14.035 32922 Z= 0.349 Chirality : 0.045 0.196 3780 Planarity : 0.004 0.043 4170 Dihedral : 6.290 59.624 3603 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.57 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % 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: -0.42 (0.15), residues: 2982 helix: -0.14 (0.24), residues: 447 sheet: 0.17 (0.15), residues: 1053 loop : -0.57 (0.17), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 103 HIS 0.012 0.002 HIS G 100D PHE 0.020 0.002 PHE I 53 TYR 0.029 0.002 TYR C 27 ARG 0.006 0.001 ARG C 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 2.973 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: A 95 MET cc_start: 0.7622 (ppp) cc_final: 0.7359 (ppp) REVERT: F 530 MET cc_start: 0.7063 (mpp) cc_final: 0.6691 (mpp) REVERT: I 145 MET cc_start: 0.6479 (mmp) cc_final: 0.6171 (mmp) REVERT: J 530 MET cc_start: 0.6933 (mpp) cc_final: 0.6679 (mpp) REVERT: J 626 MET cc_start: 0.8564 (tpp) cc_final: 0.8305 (tpp) REVERT: J 657 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8512 (tp30) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.3463 time to fit residues: 71.6830 Evaluate side-chains 90 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 2.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 6.9990 chunk 252 optimal weight: 10.0000 chunk 269 optimal weight: 20.0000 chunk 276 optimal weight: 0.1980 chunk 162 optimal weight: 0.5980 chunk 117 optimal weight: 0.0000 chunk 211 optimal weight: 20.0000 chunk 82 optimal weight: 8.9990 chunk 243 optimal weight: 3.9990 chunk 254 optimal weight: 0.6980 chunk 268 optimal weight: 0.7980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 37 GLN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 37 GLN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 229 ASN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24234 Z= 0.141 Angle : 0.592 14.221 32922 Z= 0.311 Chirality : 0.044 0.173 3780 Planarity : 0.004 0.042 4170 Dihedral : 5.871 59.144 3603 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.16 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2982 helix: -0.05 (0.25), residues: 447 sheet: 0.30 (0.16), residues: 987 loop : -0.19 (0.17), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 36 HIS 0.007 0.001 HIS C 100D PHE 0.013 0.001 PHE I 53 TYR 0.028 0.001 TYR L 91 ARG 0.006 0.000 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7671 (ppp) cc_final: 0.7346 (ppp) REVERT: F 530 MET cc_start: 0.7214 (mpp) cc_final: 0.6998 (mpp) REVERT: J 530 MET cc_start: 0.7093 (mpp) cc_final: 0.6715 (mpp) REVERT: J 626 MET cc_start: 0.8611 (tpp) cc_final: 0.8322 (tpp) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.3757 time to fit residues: 90.0084 Evaluate side-chains 99 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 10.0000 chunk 284 optimal weight: 0.7980 chunk 173 optimal weight: 0.3980 chunk 135 optimal weight: 9.9990 chunk 198 optimal weight: 30.0000 chunk 298 optimal weight: 7.9990 chunk 275 optimal weight: 20.0000 chunk 237 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 overall best weight: 4.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 37 GLN D 90 GLN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 37 GLN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 24234 Z= 0.325 Angle : 0.672 14.153 32922 Z= 0.357 Chirality : 0.045 0.184 3780 Planarity : 0.004 0.075 4170 Dihedral : 6.037 56.262 3603 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.43 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.34 (0.15), residues: 2982 helix: -0.19 (0.25), residues: 435 sheet: 0.22 (0.16), residues: 996 loop : -0.45 (0.17), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 427 HIS 0.013 0.002 HIS C 100D PHE 0.016 0.002 PHE G 63 TYR 0.033 0.002 TYR K 32 ARG 0.014 0.001 ARG D 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7673 (ppp) cc_final: 0.7421 (ppp) REVERT: F 530 MET cc_start: 0.6879 (mpp) cc_final: 0.6391 (mpp) REVERT: F 626 MET cc_start: 0.8468 (tpp) cc_final: 0.8186 (tpp) REVERT: J 530 MET cc_start: 0.7054 (mpp) cc_final: 0.6802 (mpp) REVERT: J 626 MET cc_start: 0.8576 (tpp) cc_final: 0.8289 (tpp) REVERT: K 34 MET cc_start: 0.7090 (mmt) cc_final: 0.6838 (mmp) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.3434 time to fit residues: 71.1262 Evaluate side-chains 93 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 6.9990 chunk 253 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 219 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 238 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.049216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.036640 restraints weight = 183793.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.037665 restraints weight = 108843.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.038327 restraints weight = 78450.159| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24234 Z= 0.206 Angle : 0.614 14.122 32922 Z= 0.328 Chirality : 0.044 0.171 3780 Planarity : 0.004 0.047 4170 Dihedral : 5.810 51.564 3603 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.59 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.30 (0.16), residues: 2982 helix: -0.33 (0.24), residues: 453 sheet: 0.20 (0.16), residues: 1005 loop : -0.33 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 427 HIS 0.009 0.001 HIS C 100D PHE 0.019 0.001 PHE C 63 TYR 0.030 0.002 TYR L 91 ARG 0.007 0.000 ARG D 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3459.92 seconds wall clock time: 64 minutes 36.95 seconds (3876.95 seconds total)