Starting phenix.real_space_refine on Mon Mar 18 08:44:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyn_30501/03_2024/7cyn_30501.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyn_30501/03_2024/7cyn_30501.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/7cyn_30501/03_2024/7cyn_30501.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyn_30501/03_2024/7cyn_30501.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyn_30501/03_2024/7cyn_30501.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyn_30501/03_2024/7cyn_30501.pdb" } 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= 0.000 sd= 0.003 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 110 5.16 5 C 13252 2.51 5 N 3424 2.21 5 O 3646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 93": "OE1" <-> "OE2" Residue "A ASP 95": "OD1" <-> "OD2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A ARG 378": "NH1" <-> "NH2" Residue "A ARG 473": "NH1" <-> "NH2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A GLU 625": "OE1" <-> "OE2" Residue "A GLU 637": "OE1" <-> "OE2" Residue "A GLU 716": "OE1" <-> "OE2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A GLU 769": "OE1" <-> "OE2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B ASP 95": "OD1" <-> "OD2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B ARG 378": "NH1" <-> "NH2" Residue "B ARG 473": "NH1" <-> "NH2" Residue "B GLU 564": "OE1" <-> "OE2" Residue "B ARG 614": "NH1" <-> "NH2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 625": "OE1" <-> "OE2" Residue "B GLU 637": "OE1" <-> "OE2" Residue "B GLU 716": "OE1" <-> "OE2" Residue "B ARG 723": "NH1" <-> "NH2" Residue "B GLU 769": "OE1" <-> "OE2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C ARG 157": "NH1" <-> "NH2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "C TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 207": "NH1" <-> "NH2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 289": "OE1" <-> "OE2" Residue "C ARG 312": "NH1" <-> "NH2" Residue "C ARG 341": "NH1" <-> "NH2" Residue "C ARG 374": "NH1" <-> "NH2" Residue "C TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 513": "NH1" <-> "NH2" Residue "C ARG 520": "NH1" <-> "NH2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D ARG 50": "NH1" <-> "NH2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D ARG 131": "NH1" <-> "NH2" Residue "D ARG 157": "NH1" <-> "NH2" Residue "D ARG 185": "NH1" <-> "NH2" Residue "D TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 207": "NH1" <-> "NH2" Residue "D PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 289": "OE1" <-> "OE2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ARG 341": "NH1" <-> "NH2" Residue "D ARG 374": "NH1" <-> "NH2" Residue "D TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 513": "NH1" <-> "NH2" Residue "D ARG 520": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20432 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6319 Classifications: {'peptide': 786} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 33, 'TRANS': 750} Chain breaks: 2 Chain: "B" Number of atoms: 6319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6319 Classifications: {'peptide': 786} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 33, 'TRANS': 750} Chain breaks: 2 Chain: "C" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3855 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 20, 'TRANS': 462} Chain: "D" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3855 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 20, 'TRANS': 462} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.78, per 1000 atoms: 0.53 Number of scatterers: 20432 At special positions: 0 Unit cell: (97.11, 130.725, 171.81, 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 110 16.00 O 3646 8.00 N 3424 7.00 C 13252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 51 " distance=2.03 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 112 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 189 " distance=2.03 Simple disulfide: pdb=" SG CYS A 263 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 787 " - pdb=" SG CYS A 814 " distance=2.03 Simple disulfide: pdb=" SG CYS A 789 " - pdb=" SG CYS A 833 " distance=2.03 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 51 " distance=2.03 Simple disulfide: pdb=" SG CYS B 98 " - pdb=" SG CYS B 475 " distance=2.03 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 112 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 189 " distance=2.03 Simple disulfide: pdb=" SG CYS B 263 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 787 " - pdb=" SG CYS B 814 " distance=2.03 Simple disulfide: pdb=" SG CYS B 789 " - pdb=" SG CYS B 833 " distance=2.03 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 368 " distance=2.03 Simple disulfide: pdb=" SG CYS D 260 " - pdb=" SG CYS D 368 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 601 " - " ASN C 251 " " NAG D 601 " - " ASN D 251 " " NAG E 1 " - " ASN C 272 " " NAG F 1 " - " ASN D 272 " Time building additional restraints: 8.34 Conformation dependent library (CDL) restraints added in 3.4 seconds 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4828 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 10 sheets defined 39.0% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 168 through 172 removed outlier: 3.804A pdb=" N ALA A 172 " --> pdb=" O THR A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 277 removed outlier: 3.835A pdb=" N ASN A 276 " --> pdb=" O CYS A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 363 through 369 removed outlier: 4.040A pdb=" N LEU A 369 " --> pdb=" O PHE A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 395 Proline residue: A 392 - end of helix removed outlier: 4.329A pdb=" N ASN A 395 " --> pdb=" O PRO A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 removed outlier: 3.632A pdb=" N GLN A 419 " --> pdb=" O MET A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 582 removed outlier: 4.034A pdb=" N PHE A 580 " --> pdb=" O ASN A 576 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 582 " --> pdb=" O HIS A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 673 Processing helix chain 'A' and resid 692 through 698 removed outlier: 3.771A pdb=" N GLN A 696 " --> pdb=" O LYS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 722 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 788 through 790 No H-bonds generated for 'chain 'A' and resid 788 through 790' Processing helix chain 'A' and resid 791 through 798 Processing helix chain 'A' and resid 817 through 821 Processing helix chain 'A' and resid 838 through 864 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.805A pdb=" N ALA B 172 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 277 removed outlier: 3.835A pdb=" N ASN B 276 " --> pdb=" O CYS B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 334 through 339 Processing helix chain 'B' and resid 363 through 369 removed outlier: 4.041A pdb=" N LEU B 369 " --> pdb=" O PHE B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 395 Proline residue: B 392 - end of helix removed outlier: 4.329A pdb=" N ASN B 395 " --> pdb=" O PRO B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 removed outlier: 3.632A pdb=" N GLN B 419 " --> pdb=" O MET B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 582 removed outlier: 4.034A pdb=" N PHE B 580 " --> pdb=" O ASN B 576 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 582 " --> pdb=" O HIS B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 673 Processing helix chain 'B' and resid 692 through 698 removed outlier: 3.770A pdb=" N GLN B 696 " --> pdb=" O LYS B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 722 Processing helix chain 'B' and resid 768 through 773 Processing helix chain 'B' and resid 788 through 790 No H-bonds generated for 'chain 'B' and resid 788 through 790' Processing helix chain 'B' and resid 791 through 798 Processing helix chain 'B' and resid 817 through 821 Processing helix chain 'B' and resid 838 through 864 Processing helix chain 'C' and resid 46 through 89 Processing helix chain 'C' and resid 91 through 99 Processing helix chain 'C' and resid 103 through 117 Processing helix chain 'C' and resid 118 through 134 removed outlier: 3.948A pdb=" N LEU C 124 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR C 125 " --> pdb=" O ALA C 121 " (cutoff:3.500A) Proline residue: C 127 - end of helix removed outlier: 3.542A pdb=" N GLY C 134 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 152 Processing helix chain 'C' and resid 157 through 199 Proline residue: C 163 - end of helix removed outlier: 4.660A pdb=" N VAL C 173 " --> pdb=" O GLY C 169 " (cutoff:3.500A) Proline residue: C 174 - end of helix Processing helix chain 'C' and resid 213 through 235 removed outlier: 3.885A pdb=" N VAL C 219 " --> pdb=" O PRO C 215 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE C 220 " --> pdb=" O TYR C 216 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 223 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE C 232 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA C 233 " --> pdb=" O HIS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 242 Processing helix chain 'C' and resid 249 through 254 removed outlier: 3.955A pdb=" N THR C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 306 Processing helix chain 'C' and resid 312 through 320 removed outlier: 3.534A pdb=" N GLU C 316 " --> pdb=" O ARG C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 335 through 337 No H-bonds generated for 'chain 'C' and resid 335 through 337' Processing helix chain 'C' and resid 339 through 359 Proline residue: C 345 - end of helix Processing helix chain 'C' and resid 365 through 370 removed outlier: 4.486A pdb=" N SER C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 374 through 396 removed outlier: 3.586A pdb=" N LEU C 391 " --> pdb=" O SER C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 422 removed outlier: 3.523A pdb=" N ALA C 407 " --> pdb=" O VAL C 403 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS C 412 " --> pdb=" O GLY C 408 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU C 413 " --> pdb=" O ALA C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 461 removed outlier: 3.690A pdb=" N TYR C 436 " --> pdb=" O SER C 432 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR C 461 " --> pdb=" O LEU C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 488 Processing helix chain 'C' and resid 494 through 518 removed outlier: 3.525A pdb=" N LEU C 518 " --> pdb=" O MET C 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 89 Processing helix chain 'D' and resid 91 through 99 Processing helix chain 'D' and resid 103 through 117 Processing helix chain 'D' and resid 118 through 134 removed outlier: 3.949A pdb=" N LEU D 124 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A) Proline residue: D 127 - end of helix removed outlier: 3.541A pdb=" N GLY D 134 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 152 Processing helix chain 'D' and resid 157 through 199 Proline residue: D 163 - end of helix removed outlier: 4.660A pdb=" N VAL D 173 " --> pdb=" O GLY D 169 " (cutoff:3.500A) Proline residue: D 174 - end of helix Processing helix chain 'D' and resid 213 through 235 removed outlier: 3.886A pdb=" N VAL D 219 " --> pdb=" O PRO D 215 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE D 220 " --> pdb=" O TYR D 216 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE D 223 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE D 232 " --> pdb=" O PHE D 228 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA D 233 " --> pdb=" O HIS D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 242 Processing helix chain 'D' and resid 249 through 254 removed outlier: 3.955A pdb=" N THR D 253 " --> pdb=" O ASP D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 306 Processing helix chain 'D' and resid 312 through 320 removed outlier: 3.534A pdb=" N GLU D 316 " --> pdb=" O ARG D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 335 through 337 No H-bonds generated for 'chain 'D' and resid 335 through 337' Processing helix chain 'D' and resid 339 through 359 Proline residue: D 345 - end of helix Processing helix chain 'D' and resid 365 through 370 removed outlier: 4.487A pdb=" N SER D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 365 through 370' Processing helix chain 'D' and resid 374 through 396 removed outlier: 3.585A pdb=" N LEU D 391 " --> pdb=" O SER D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 422 removed outlier: 3.523A pdb=" N ALA D 407 " --> pdb=" O VAL D 403 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS D 412 " --> pdb=" O GLY D 408 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU D 413 " --> pdb=" O ALA D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 461 removed outlier: 3.691A pdb=" N TYR D 436 " --> pdb=" O SER D 432 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR D 461 " --> pdb=" O LEU D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 488 Processing helix chain 'D' and resid 494 through 518 removed outlier: 3.524A pdb=" N LEU D 518 " --> pdb=" O MET D 514 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 41 removed outlier: 3.626A pdb=" N ASN A 69 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU A 70 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE A 94 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU A 132 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU A 153 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU A 177 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU A 209 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU A 230 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU A 319 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 376 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU A 375 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU A 402 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE A 426 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU A 498 " --> pdb=" O ASN A 523 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU A 522 " --> pdb=" O ASP A 548 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU A 547 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU A 571 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU A 601 " --> pdb=" O GLU A 625 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 162 through 163 removed outlier: 3.530A pdb=" N ILE A 163 " --> pdb=" O SER A 194 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 357 through 359 removed outlier: 6.642A pdb=" N ALA A 358 " --> pdb=" O GLU A 384 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A 411 " --> pdb=" O LYS A 383 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 530 through 531 Processing sheet with id=AA5, first strand: chain 'A' and resid 727 through 729 Processing sheet with id=AA6, first strand: chain 'B' and resid 37 through 41 removed outlier: 3.627A pdb=" N ASN B 69 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU B 70 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE B 94 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU B 132 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU B 153 " --> pdb=" O TYR B 178 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU B 177 " --> pdb=" O SER B 210 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU B 209 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU B 230 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU B 319 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG B 376 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU B 375 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU B 402 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE B 426 " --> pdb=" O ASP B 499 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU B 498 " --> pdb=" O ASN B 523 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU B 522 " --> pdb=" O ASP B 548 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU B 547 " --> pdb=" O ASP B 572 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU B 571 " --> pdb=" O MET B 602 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU B 601 " --> pdb=" O GLU B 625 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 162 through 163 removed outlier: 3.530A pdb=" N ILE B 163 " --> pdb=" O SER B 194 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 357 through 359 removed outlier: 6.642A pdb=" N ALA B 358 " --> pdb=" O GLU B 384 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE B 411 " --> pdb=" O LYS B 383 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 530 through 531 Processing sheet with id=AB1, first strand: chain 'B' and resid 727 through 729 684 hydrogen bonds defined for protein. 1902 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: 5.87 Time building geometry restraints manager: 9.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6425 1.34 - 1.46: 4580 1.46 - 1.58: 9737 1.58 - 1.69: 0 1.69 - 1.81: 170 Bond restraints: 20912 Sorted by residual: bond pdb=" C PRO D 208 " pdb=" N PRO D 209 " ideal model delta sigma weight residual 1.336 1.364 -0.028 1.20e-02 6.94e+03 5.34e+00 bond pdb=" C PRO C 208 " pdb=" N PRO C 209 " ideal model delta sigma weight residual 1.336 1.364 -0.028 1.20e-02 6.94e+03 5.26e+00 bond pdb=" C VAL C 403 " pdb=" N PRO C 404 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.23e-02 6.61e+03 2.26e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.13e+00 ... (remaining 20907 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.13: 618 107.13 - 113.85: 11848 113.85 - 120.56: 8133 120.56 - 127.28: 7549 127.28 - 133.99: 226 Bond angle restraints: 28374 Sorted by residual: angle pdb=" N ILE A 573 " pdb=" CA ILE A 573 " pdb=" C ILE A 573 " ideal model delta sigma weight residual 111.88 108.05 3.83 1.06e+00 8.90e-01 1.30e+01 angle pdb=" N ILE B 573 " pdb=" CA ILE B 573 " pdb=" C ILE B 573 " ideal model delta sigma weight residual 111.88 108.07 3.81 1.06e+00 8.90e-01 1.29e+01 angle pdb=" C VAL D 117 " pdb=" N THR D 118 " pdb=" CA THR D 118 " ideal model delta sigma weight residual 120.06 123.71 -3.65 1.19e+00 7.06e-01 9.42e+00 angle pdb=" C VAL C 117 " pdb=" N THR C 118 " pdb=" CA THR C 118 " ideal model delta sigma weight residual 120.06 123.71 -3.65 1.19e+00 7.06e-01 9.39e+00 angle pdb=" CA LEU B 786 " pdb=" CB LEU B 786 " pdb=" CG LEU B 786 " ideal model delta sigma weight residual 116.30 125.79 -9.49 3.50e+00 8.16e-02 7.36e+00 ... (remaining 28369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 11560 17.22 - 34.44: 870 34.44 - 51.66: 174 51.66 - 68.88: 20 68.88 - 86.10: 18 Dihedral angle restraints: 12642 sinusoidal: 5172 harmonic: 7470 Sorted by residual: dihedral pdb=" CB CYS B 789 " pdb=" SG CYS B 789 " pdb=" SG CYS B 833 " pdb=" CB CYS B 833 " ideal model delta sinusoidal sigma weight residual -86.00 -161.71 75.71 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CB CYS A 789 " pdb=" SG CYS A 789 " pdb=" SG CYS A 833 " pdb=" CB CYS A 833 " ideal model delta sinusoidal sigma weight residual -86.00 -161.68 75.68 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CB CYS D 260 " pdb=" SG CYS D 260 " pdb=" SG CYS D 368 " pdb=" CB CYS D 368 " ideal model delta sinusoidal sigma weight residual 93.00 143.76 -50.76 1 1.00e+01 1.00e-02 3.53e+01 ... (remaining 12639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1878 0.028 - 0.057: 974 0.057 - 0.085: 258 0.085 - 0.113: 124 0.113 - 0.141: 30 Chirality restraints: 3264 Sorted by residual: chirality pdb=" CA THR D 126 " pdb=" N THR D 126 " pdb=" C THR D 126 " pdb=" CB THR D 126 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE A 142 " pdb=" N ILE A 142 " pdb=" C ILE A 142 " pdb=" CB ILE A 142 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" C1 NAG D 601 " pdb=" ND2 ASN D 251 " pdb=" C2 NAG D 601 " pdb=" O5 NAG D 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 3261 not shown) Planarity restraints: 3552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 118 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.98e+00 pdb=" N PRO D 119 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 118 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO C 119 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 119 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 119 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 207 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.47e+00 pdb=" N PRO D 208 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 208 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 208 " 0.026 5.00e-02 4.00e+02 ... (remaining 3549 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1515 2.74 - 3.28: 20870 3.28 - 3.82: 34244 3.82 - 4.36: 40363 4.36 - 4.90: 67848 Nonbonded interactions: 164840 Sorted by model distance: nonbonded pdb=" OD1 ASN A 733 " pdb=" ND2 ASN A 757 " model vdw 2.204 2.520 nonbonded pdb=" OD1 ASN B 733 " pdb=" ND2 ASN B 757 " model vdw 2.204 2.520 nonbonded pdb=" O ASN B 431 " pdb=" ND2 ASN B 503 " model vdw 2.218 2.520 nonbonded pdb=" O ASN A 431 " pdb=" ND2 ASN A 503 " model vdw 2.218 2.520 nonbonded pdb=" OH TYR D 99 " pdb=" OE1 GLU D 156 " model vdw 2.227 2.440 ... (remaining 164835 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.990 Check model and map are aligned: 0.320 Set scattering table: 0.180 Process input model: 52.920 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 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 : 0.002 0.050 20912 Z= 0.136 Angle : 0.519 9.492 28374 Z= 0.289 Chirality : 0.039 0.141 3264 Planarity : 0.003 0.050 3548 Dihedral : 12.509 86.102 7760 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.55 % Favored : 94.37 % Rotamer: Outliers : 0.09 % Allowed : 3.42 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.16), residues: 2522 helix: -0.50 (0.17), residues: 870 sheet: -2.68 (0.33), residues: 260 loop : -2.24 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP A 793 HIS 0.004 0.000 HIS C 475 PHE 0.013 0.001 PHE C 346 TYR 0.014 0.001 TYR D 190 ARG 0.001 0.000 ARG C 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 453 time to evaluate : 2.454 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: A 498 LEU cc_start: 0.8641 (tp) cc_final: 0.8438 (tp) REVERT: A 500 LEU cc_start: 0.9139 (mt) cc_final: 0.8745 (mt) REVERT: A 690 PHE cc_start: 0.6363 (t80) cc_final: 0.6023 (t80) REVERT: A 779 LEU cc_start: 0.7682 (mp) cc_final: 0.7308 (mp) REVERT: A 848 SER cc_start: 0.8940 (m) cc_final: 0.8661 (p) REVERT: B 302 LEU cc_start: 0.8745 (mt) cc_final: 0.8503 (mt) REVERT: B 779 LEU cc_start: 0.7996 (mp) cc_final: 0.7732 (mp) REVERT: C 128 VAL cc_start: 0.8460 (m) cc_final: 0.8191 (p) REVERT: C 170 MET cc_start: 0.5838 (tpt) cc_final: 0.5407 (tpt) REVERT: D 128 VAL cc_start: 0.8501 (m) cc_final: 0.8288 (p) REVERT: D 384 LEU cc_start: 0.8725 (mt) cc_final: 0.8409 (pp) outliers start: 2 outliers final: 0 residues processed: 453 average time/residue: 0.3079 time to fit residues: 222.7341 Evaluate side-chains 287 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 20.0000 chunk 191 optimal weight: 30.0000 chunk 105 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 120 optimal weight: 30.0000 chunk 147 optimal weight: 5.9990 chunk 228 optimal weight: 10.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 ASN ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 HIS ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 20912 Z= 0.368 Angle : 0.831 11.640 28374 Z= 0.406 Chirality : 0.046 0.217 3264 Planarity : 0.005 0.055 3548 Dihedral : 4.601 24.065 2872 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.76 % Favored : 95.20 % Rotamer: Outliers : 0.13 % Allowed : 5.09 % Favored : 94.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % 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: -1.35 (0.17), residues: 2522 helix: 0.39 (0.17), residues: 900 sheet: -2.34 (0.32), residues: 272 loop : -1.48 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 476 HIS 0.009 0.002 HIS B 587 PHE 0.024 0.002 PHE C 228 TYR 0.025 0.002 TYR D 474 ARG 0.007 0.001 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 309 time to evaluate : 2.654 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: A 498 LEU cc_start: 0.8766 (tp) cc_final: 0.8521 (tp) REVERT: A 500 LEU cc_start: 0.9238 (mt) cc_final: 0.8946 (mt) REVERT: B 248 LEU cc_start: 0.8125 (mt) cc_final: 0.7742 (mp) REVERT: B 369 LEU cc_start: 0.8296 (mp) cc_final: 0.7853 (tp) REVERT: B 372 LEU cc_start: 0.7975 (tp) cc_final: 0.7451 (tp) REVERT: B 498 LEU cc_start: 0.8703 (tp) cc_final: 0.8436 (tp) REVERT: B 500 LEU cc_start: 0.9027 (mt) cc_final: 0.8820 (mt) REVERT: B 547 LEU cc_start: 0.8531 (tp) cc_final: 0.7360 (tp) REVERT: C 168 LEU cc_start: 0.7992 (tp) cc_final: 0.7765 (tp) outliers start: 3 outliers final: 0 residues processed: 310 average time/residue: 0.2927 time to fit residues: 146.4456 Evaluate side-chains 203 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 190 optimal weight: 20.0000 chunk 155 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 229 optimal weight: 9.9990 chunk 247 optimal weight: 5.9990 chunk 204 optimal weight: 20.0000 chunk 227 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 overall best weight: 6.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 HIS ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** D 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20912 Z= 0.279 Angle : 0.657 7.100 28374 Z= 0.328 Chirality : 0.043 0.205 3264 Planarity : 0.004 0.050 3548 Dihedral : 4.367 25.547 2872 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % 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: -0.87 (0.17), residues: 2522 helix: 0.92 (0.18), residues: 888 sheet: -2.37 (0.32), residues: 270 loop : -1.20 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 692 HIS 0.007 0.001 HIS B 587 PHE 0.021 0.002 PHE C 483 TYR 0.018 0.002 TYR B 546 ARG 0.007 0.001 ARG B 784 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 2.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.4747 (mmm) cc_final: 0.4542 (mmm) REVERT: A 498 LEU cc_start: 0.8868 (tp) cc_final: 0.8654 (tp) REVERT: A 500 LEU cc_start: 0.9197 (mt) cc_final: 0.8972 (mt) REVERT: A 662 LEU cc_start: 0.8186 (tp) cc_final: 0.7916 (tt) REVERT: B 369 LEU cc_start: 0.8389 (mp) cc_final: 0.7837 (tp) REVERT: B 372 LEU cc_start: 0.7945 (tp) cc_final: 0.7505 (tp) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.2851 time to fit residues: 127.1290 Evaluate side-chains 192 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 5.9990 chunk 172 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 chunk 25 optimal weight: 30.0000 chunk 109 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 230 optimal weight: 8.9990 chunk 243 optimal weight: 20.0000 chunk 120 optimal weight: 7.9990 chunk 218 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN A 337 HIS ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 ASN ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 ASN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 ASN ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20912 Z= 0.279 Angle : 0.667 7.416 28374 Z= 0.332 Chirality : 0.043 0.233 3264 Planarity : 0.004 0.048 3548 Dihedral : 4.548 26.236 2872 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.13 % Allowed : 4.25 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % 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: -0.71 (0.17), residues: 2522 helix: 1.01 (0.18), residues: 890 sheet: -2.46 (0.31), residues: 270 loop : -1.04 (0.18), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 796 HIS 0.008 0.001 HIS B 587 PHE 0.019 0.002 PHE C 346 TYR 0.017 0.002 TYR D 349 ARG 0.003 0.000 ARG D 519 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 256 time to evaluate : 2.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 146 TYR cc_start: 0.8585 (m-80) cc_final: 0.8190 (m-80) outliers start: 3 outliers final: 2 residues processed: 259 average time/residue: 0.2713 time to fit residues: 116.5284 Evaluate side-chains 185 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 183 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 20.0000 chunk 138 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 181 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 0 optimal weight: 0.0470 chunk 124 optimal weight: 20.0000 chunk 218 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 overall best weight: 4.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS A 138 GLN ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 HIS B 138 GLN ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20912 Z= 0.218 Angle : 0.621 8.683 28374 Z= 0.307 Chirality : 0.043 0.278 3264 Planarity : 0.004 0.047 3548 Dihedral : 4.444 25.816 2872 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % 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: -0.58 (0.17), residues: 2522 helix: 1.24 (0.18), residues: 874 sheet: -2.47 (0.31), residues: 272 loop : -1.01 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 793 HIS 0.006 0.001 HIS A 781 PHE 0.027 0.002 PHE C 483 TYR 0.014 0.001 TYR C 349 ARG 0.004 0.000 ARG B 784 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 2.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 LEU cc_start: 0.8810 (tp) cc_final: 0.8596 (tp) REVERT: A 616 MET cc_start: 0.6064 (mmp) cc_final: 0.5819 (mmp) REVERT: B 549 PHE cc_start: 0.8501 (m-80) cc_final: 0.8278 (m-10) REVERT: B 847 ILE cc_start: 0.9300 (pt) cc_final: 0.9088 (pt) REVERT: D 146 TYR cc_start: 0.8560 (m-80) cc_final: 0.8161 (m-80) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.2792 time to fit residues: 119.0889 Evaluate side-chains 180 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 7.9990 chunk 219 optimal weight: 30.0000 chunk 48 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 243 optimal weight: 5.9990 chunk 202 optimal weight: 40.0000 chunk 112 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 128 optimal weight: 0.5980 overall best weight: 6.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN A 304 HIS ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 HIS B 138 GLN B 304 HIS ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN C 265 HIS ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20912 Z= 0.272 Angle : 0.663 6.966 28374 Z= 0.331 Chirality : 0.043 0.231 3264 Planarity : 0.004 0.044 3548 Dihedral : 4.602 26.012 2872 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 21.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % 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: -0.63 (0.17), residues: 2522 helix: 1.07 (0.18), residues: 896 sheet: -2.52 (0.32), residues: 246 loop : -1.01 (0.18), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 793 HIS 0.008 0.001 HIS A 587 PHE 0.030 0.002 PHE C 297 TYR 0.020 0.001 TYR B 751 ARG 0.003 0.000 ARG A 717 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 LEU cc_start: 0.8758 (tp) cc_final: 0.8522 (tp) REVERT: B 498 LEU cc_start: 0.8663 (tp) cc_final: 0.8419 (tp) REVERT: D 139 MET cc_start: 0.8687 (mmm) cc_final: 0.8137 (mmt) REVERT: D 146 TYR cc_start: 0.8525 (m-80) cc_final: 0.8132 (m-80) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2695 time to fit residues: 102.6656 Evaluate side-chains 169 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 178 optimal weight: 20.0000 chunk 137 optimal weight: 7.9990 chunk 205 optimal weight: 20.0000 chunk 136 optimal weight: 8.9990 chunk 242 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 112 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 GLN ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20912 Z= 0.210 Angle : 0.620 10.028 28374 Z= 0.306 Chirality : 0.042 0.175 3264 Planarity : 0.004 0.049 3548 Dihedral : 4.507 25.596 2872 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % 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: -0.51 (0.17), residues: 2522 helix: 1.22 (0.18), residues: 884 sheet: -2.50 (0.32), residues: 246 loop : -0.95 (0.18), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 793 HIS 0.006 0.001 HIS A 781 PHE 0.031 0.001 PHE D 297 TYR 0.026 0.001 TYR D 146 ARG 0.009 0.000 ARG A 784 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 LEU cc_start: 0.8716 (tp) cc_final: 0.8475 (tp) REVERT: A 500 LEU cc_start: 0.9331 (mt) cc_final: 0.9088 (mt) REVERT: A 856 MET cc_start: 0.7347 (ppp) cc_final: 0.7132 (ppp) REVERT: B 498 LEU cc_start: 0.8582 (tp) cc_final: 0.8328 (tp) REVERT: B 549 PHE cc_start: 0.8326 (m-80) cc_final: 0.8102 (m-10) REVERT: C 168 LEU cc_start: 0.8143 (tp) cc_final: 0.7836 (tp) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.2603 time to fit residues: 102.6897 Evaluate side-chains 165 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 120 optimal weight: 20.0000 chunk 22 optimal weight: 40.0000 chunk 190 optimal weight: 20.0000 chunk 220 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN B 167 ASN ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 GLN ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.5829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20912 Z= 0.242 Angle : 0.667 10.344 28374 Z= 0.326 Chirality : 0.043 0.352 3264 Planarity : 0.004 0.046 3548 Dihedral : 4.600 25.958 2872 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 21.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % 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: -0.52 (0.17), residues: 2522 helix: 1.21 (0.18), residues: 862 sheet: -2.52 (0.32), residues: 248 loop : -0.91 (0.18), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 796 HIS 0.007 0.001 HIS A 587 PHE 0.027 0.001 PHE C 297 TYR 0.015 0.001 TYR B 751 ARG 0.002 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 2.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 LEU cc_start: 0.8681 (tp) cc_final: 0.8451 (tp) REVERT: A 856 MET cc_start: 0.7436 (ppp) cc_final: 0.7080 (ppp) REVERT: B 498 LEU cc_start: 0.8588 (tp) cc_final: 0.8309 (tp) REVERT: C 168 LEU cc_start: 0.8309 (tp) cc_final: 0.7884 (tp) REVERT: D 139 MET cc_start: 0.8717 (mmm) cc_final: 0.8318 (mmt) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.2578 time to fit residues: 96.9722 Evaluate side-chains 167 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 9.9990 chunk 212 optimal weight: 7.9990 chunk 226 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 177 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 204 optimal weight: 20.0000 chunk 214 optimal weight: 0.9990 chunk 225 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN C 181 ASN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.5878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20912 Z= 0.183 Angle : 0.614 7.991 28374 Z= 0.301 Chirality : 0.042 0.345 3264 Planarity : 0.004 0.052 3548 Dihedral : 4.475 25.427 2872 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % 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: -0.51 (0.17), residues: 2522 helix: 1.20 (0.18), residues: 878 sheet: -2.35 (0.32), residues: 244 loop : -0.95 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 796 HIS 0.005 0.001 HIS A 781 PHE 0.027 0.001 PHE D 297 TYR 0.021 0.001 TYR A 751 ARG 0.016 0.000 ARG B 784 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 LEU cc_start: 0.9319 (mt) cc_final: 0.9107 (mt) REVERT: B 498 LEU cc_start: 0.8561 (tp) cc_final: 0.8290 (tp) REVERT: B 549 PHE cc_start: 0.8400 (m-80) cc_final: 0.8166 (m-10) REVERT: D 139 MET cc_start: 0.8611 (mmm) cc_final: 0.8146 (mmt) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.2909 time to fit residues: 116.4652 Evaluate side-chains 170 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.8980 chunk 146 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 251 optimal weight: 30.0000 chunk 231 optimal weight: 8.9990 chunk 199 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 154 optimal weight: 0.2980 chunk 122 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 HIS ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.5985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20912 Z= 0.184 Angle : 0.641 11.658 28374 Z= 0.311 Chirality : 0.043 0.302 3264 Planarity : 0.004 0.050 3548 Dihedral : 4.475 25.385 2872 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % 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: -0.58 (0.17), residues: 2522 helix: 1.10 (0.18), residues: 880 sheet: -2.33 (0.32), residues: 244 loop : -0.99 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 793 HIS 0.008 0.001 HIS C 475 PHE 0.024 0.001 PHE D 297 TYR 0.022 0.001 TYR C 474 ARG 0.003 0.000 ARG B 784 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 LEU cc_start: 0.8638 (tp) cc_final: 0.8408 (tp) REVERT: A 500 LEU cc_start: 0.9268 (mt) cc_final: 0.9024 (mt) REVERT: A 785 PHE cc_start: 0.7611 (m-80) cc_final: 0.7201 (m-80) REVERT: B 498 LEU cc_start: 0.8687 (tp) cc_final: 0.8452 (tp) REVERT: B 549 PHE cc_start: 0.8385 (m-80) cc_final: 0.8156 (m-10) REVERT: C 139 MET cc_start: 0.8639 (mmm) cc_final: 0.8209 (mmt) REVERT: D 139 MET cc_start: 0.8599 (mmm) cc_final: 0.8180 (mmt) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.2553 time to fit residues: 102.0286 Evaluate side-chains 169 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 6.9990 chunk 61 optimal weight: 0.0010 chunk 184 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 55 optimal weight: 20.0000 chunk 200 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 205 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 175 optimal weight: 1.9990 overall best weight: 3.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.047816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.037536 restraints weight = 171592.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.038345 restraints weight = 124961.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.038959 restraints weight = 100921.611| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.6094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 20912 Z= 0.194 Angle : 0.645 15.137 28374 Z= 0.315 Chirality : 0.043 0.290 3264 Planarity : 0.004 0.052 3548 Dihedral : 4.495 24.975 2872 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.63 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.08 % 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: -0.57 (0.17), residues: 2522 helix: 1.14 (0.18), residues: 870 sheet: -2.32 (0.31), residues: 244 loop : -0.99 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 796 HIS 0.005 0.001 HIS A 781 PHE 0.024 0.001 PHE D 297 TYR 0.016 0.001 TYR C 474 ARG 0.003 0.000 ARG B 784 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3441.41 seconds wall clock time: 65 minutes 58.29 seconds (3958.29 seconds total)