Starting phenix.real_space_refine on Sat Aug 10 02:15:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f56_31459/08_2024/7f56_31459_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f56_31459/08_2024/7f56_31459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f56_31459/08_2024/7f56_31459.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f56_31459/08_2024/7f56_31459.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f56_31459/08_2024/7f56_31459_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f56_31459/08_2024/7f56_31459_neut.cif" } resolution = 4.1 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= 0.005 sd= 0.085 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 157 5.16 5 C 17826 2.51 5 N 4601 2.21 5 O 5250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 187": "OE1" <-> "OE2" Residue "A ARG 431": "NH1" <-> "NH2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A GLU 743": "OE1" <-> "OE2" Residue "A GLU 853": "OE1" <-> "OE2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "B GLU 625": "OE1" <-> "OE2" Residue "B GLU 722": "OE1" <-> "OE2" Residue "B GLU 723": "OE1" <-> "OE2" Residue "B GLU 796": "OE1" <-> "OE2" Residue "B GLU 811": "OE1" <-> "OE2" Residue "B GLU 853": "OE1" <-> "OE2" Residue "C GLU 460": "OE1" <-> "OE2" Residue "C ARG 800": "NH1" <-> "NH2" Residue "C GLU 841": "OE1" <-> "OE2" Residue "D ARG 431": "NH1" <-> "NH2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D GLU 469": "OE1" <-> "OE2" Residue "D GLU 743": "OE1" <-> "OE2" Residue "D GLU 806": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 27834 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 6578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 831, 6578 Classifications: {'peptide': 831} Link IDs: {'PTRANS': 33, 'TRANS': 797} Chain: "B" Number of atoms: 6575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 831, 6575 Classifications: {'peptide': 831} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 33, 'TRANS': 797} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 6604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6604 Classifications: {'peptide': 835} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 801} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 6471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6471 Classifications: {'peptide': 818} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 33, 'TRANS': 784} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1226 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 142} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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 Time building chain proxies: 14.78, per 1000 atoms: 0.53 Number of scatterers: 27834 At special positions: 0 Unit cell: (125.12, 161.84, 208.08, 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 157 16.00 O 5250 8.00 N 4601 7.00 C 17826 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.40 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.21 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.39 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.31 Simple disulfide: pdb=" SG CYS E 45 " - pdb=" SG CYS E 72 " 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 F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG A1001 " - " ASN A 430 " " NAG A1002 " - " ASN A 546 " " NAG A1003 " - " ASN A 412 " " NAG B1001 " - " ASN B 751 " " NAG B1002 " - " ASN B 546 " " NAG B1003 " - " ASN B 275 " " NAG B1004 " - " ASN B 412 " " NAG C1001 " - " ASN C 751 " " NAG C1002 " - " ASN C 546 " " NAG C1003 " - " ASN C 275 " " NAG C1004 " - " ASN C 378 " " NAG C1005 " - " ASN C 412 " " NAG D1001 " - " ASN D 751 " " NAG D1002 " - " ASN D 546 " " NAG D1003 " - " ASN D 275 " " NAG D1004 " - " ASN D 412 " " NAG F 1 " - " ASN A 275 " " NAG G 1 " - " ASN A 378 " " NAG H 1 " - " ASN B 378 " " NAG I 1 " - " ASN D 378 " Time building additional restraints: 11.86 Conformation dependent library (CDL) restraints added in 5.0 seconds 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6464 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 45 sheets defined 46.0% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.983A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 Processing helix chain 'A' and resid 179 through 185 removed outlier: 4.127A pdb=" N ILE A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 210 through 222 removed outlier: 4.243A pdb=" N LEU A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 removed outlier: 4.330A pdb=" N GLN A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 272 removed outlier: 4.450A pdb=" N TYR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER A 272 " --> pdb=" O PRO A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 removed outlier: 3.701A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 317 through 335 removed outlier: 3.785A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 removed outlier: 3.996A pdb=" N PHE A 359 " --> pdb=" O PHE A 355 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 560 through 584 Processing helix chain 'A' and resid 607 through 620 Processing helix chain 'A' and resid 631 through 665 removed outlier: 4.026A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 677 Processing helix chain 'A' and resid 690 through 697 Processing helix chain 'A' and resid 699 through 713 Processing helix chain 'A' and resid 721 through 731 Processing helix chain 'A' and resid 739 through 749 Processing helix chain 'A' and resid 772 through 788 removed outlier: 4.441A pdb=" N ASP A 776 " --> pdb=" O SER A 772 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS A 777 " --> pdb=" O PRO A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 799 Processing helix chain 'A' and resid 821 through 850 Processing helix chain 'A' and resid 855 through 863 removed outlier: 3.686A pdb=" N SER A 859 " --> pdb=" O ARG A 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 65 removed outlier: 4.396A pdb=" N ASN B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 102 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.940A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 168 removed outlier: 3.612A pdb=" N LEU B 156 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 190 removed outlier: 3.985A pdb=" N ILE B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLU B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 188 " --> pdb=" O ARG B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 211 through 222 Processing helix chain 'B' and resid 231 through 245 removed outlier: 3.620A pdb=" N ALA B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 269 through 273 removed outlier: 3.954A pdb=" N GLY B 273 " --> pdb=" O ARG B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 removed outlier: 3.501A pdb=" N GLU B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 removed outlier: 3.888A pdb=" N SER B 309 " --> pdb=" O LYS B 306 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY B 310 " --> pdb=" O PRO B 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 306 through 310' Processing helix chain 'B' and resid 317 through 335 removed outlier: 3.666A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 364 removed outlier: 3.581A pdb=" N LEU B 362 " --> pdb=" O ARG B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 418 removed outlier: 3.505A pdb=" N LYS B 418 " --> pdb=" O GLU B 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 415 through 418' Processing helix chain 'B' and resid 424 through 429 removed outlier: 3.937A pdb=" N LEU B 428 " --> pdb=" O ILE B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 454 removed outlier: 4.045A pdb=" N TYR B 454 " --> pdb=" O LYS B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'B' and resid 500 through 507 removed outlier: 3.786A pdb=" N ASP B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 560 through 584 removed outlier: 4.250A pdb=" N TRP B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET B 565 " --> pdb=" O PRO B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 619 Processing helix chain 'B' and resid 631 through 662 removed outlier: 4.012A pdb=" N ILE B 635 " --> pdb=" O LEU B 631 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 677 Processing helix chain 'B' and resid 688 through 695 Processing helix chain 'B' and resid 701 through 712 Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.551A pdb=" N GLY B 724 " --> pdb=" O SER B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 747 Processing helix chain 'B' and resid 773 through 788 removed outlier: 3.955A pdb=" N LYS B 777 " --> pdb=" O PRO B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 Processing helix chain 'B' and resid 816 through 821 Processing helix chain 'B' and resid 821 through 850 removed outlier: 3.912A pdb=" N ILE B 825 " --> pdb=" O GLY B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 863 Processing helix chain 'C' and resid 51 through 67 removed outlier: 3.624A pdb=" N VAL C 61 " --> pdb=" O PHE C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 111 through 125 removed outlier: 4.648A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 168 Processing helix chain 'C' and resid 179 through 185 removed outlier: 3.624A pdb=" N ILE C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 210 through 222 removed outlier: 4.573A pdb=" N LEU C 214 " --> pdb=" O ASP C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 245 removed outlier: 3.571A pdb=" N ALA C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 301 Processing helix chain 'C' and resid 317 through 336 removed outlier: 3.559A pdb=" N VAL C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 366 removed outlier: 3.581A pdb=" N SER C 361 " --> pdb=" O THR C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 475 removed outlier: 3.755A pdb=" N ASP C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 527 Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 563 through 584 removed outlier: 4.018A pdb=" N PHE C 584 " --> pdb=" O VAL C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 Processing helix chain 'C' and resid 630 through 664 Processing helix chain 'C' and resid 670 through 677 Processing helix chain 'C' and resid 689 through 697 removed outlier: 3.665A pdb=" N PHE C 693 " --> pdb=" O ALA C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 713 Processing helix chain 'C' and resid 720 through 731 Processing helix chain 'C' and resid 739 through 748 Processing helix chain 'C' and resid 773 through 789 removed outlier: 4.073A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 800 removed outlier: 3.569A pdb=" N MET C 793 " --> pdb=" O GLY C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 824 through 848 removed outlier: 3.531A pdb=" N ALA C 828 " --> pdb=" O PHE C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 867 Processing helix chain 'D' and resid 51 through 67 removed outlier: 3.959A pdb=" N ASN D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG D 66 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN D 67 " --> pdb=" O THR D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 101 Processing helix chain 'D' and resid 111 through 124 Processing helix chain 'D' and resid 152 through 168 removed outlier: 3.502A pdb=" N LEU D 156 " --> pdb=" O ASP D 152 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 190 removed outlier: 5.197A pdb=" N GLU D 187 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU D 188 " --> pdb=" O ARG D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 194 Processing helix chain 'D' and resid 207 through 210 Processing helix chain 'D' and resid 211 through 222 Processing helix chain 'D' and resid 231 through 245 removed outlier: 3.650A pdb=" N ALA D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 266 through 270 Processing helix chain 'D' and resid 286 through 301 Processing helix chain 'D' and resid 317 through 335 removed outlier: 3.549A pdb=" N ALA D 321 " --> pdb=" O THR D 317 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA D 333 " --> pdb=" O VAL D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 364 removed outlier: 3.920A pdb=" N SER D 361 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 362 " --> pdb=" O ARG D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 417 removed outlier: 3.976A pdb=" N GLN D 417 " --> pdb=" O THR D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 430 Processing helix chain 'D' and resid 461 through 475 Processing helix chain 'D' and resid 500 through 507 removed outlier: 3.511A pdb=" N GLU D 504 " --> pdb=" O GLY D 500 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP D 507 " --> pdb=" O ARG D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 527 removed outlier: 3.760A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL D 526 " --> pdb=" O VAL D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 584 removed outlier: 3.825A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE D 584 " --> pdb=" O VAL D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.580A pdb=" N PHE D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU D 619 " --> pdb=" O GLY D 615 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET D 620 " --> pdb=" O VAL D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 665 removed outlier: 4.370A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 695 Processing helix chain 'D' and resid 701 through 712 removed outlier: 3.570A pdb=" N MET D 705 " --> pdb=" O THR D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 731 Processing helix chain 'D' and resid 739 through 749 Processing helix chain 'D' and resid 772 through 789 removed outlier: 4.367A pdb=" N ASP D 776 " --> pdb=" O SER D 772 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE D 780 " --> pdb=" O ASP D 776 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA D 781 " --> pdb=" O LYS D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 800 removed outlier: 3.628A pdb=" N MET D 793 " --> pdb=" O GLY D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 820 Processing helix chain 'D' and resid 821 through 850 removed outlier: 3.943A pdb=" N ILE D 825 " --> pdb=" O GLY D 821 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 351 Processing helix chain 'E' and resid 354 through 382 removed outlier: 3.804A pdb=" N VAL E 358 " --> pdb=" O THR E 354 " (cutoff:3.500A) Proline residue: E 373 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 removed outlier: 3.681A pdb=" N LEU A 36 " --> pdb=" O THR A 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 83 removed outlier: 5.392A pdb=" N GLY A 40 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 83 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N PHE A 42 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLY A 39 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE A 106 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 203 removed outlier: 7.067A pdb=" N VAL A 172 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ARG A 202 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL A 174 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR A 171 " --> pdb=" O HIS A 225 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ILE A 227 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N THR A 173 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 226 " --> pdb=" O HIS A 253 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE A 255 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N PHE A 279 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N MET A 276 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 394 " --> pdb=" O MET A 276 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP A 390 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N SER A 393 " --> pdb=" O LYS A 401 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LYS A 401 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 368 through 369 Processing sheet with id=AA5, first strand: chain 'A' and resid 477 through 482 removed outlier: 6.257A pdb=" N LEU A 433 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ARG A 481 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL A 435 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 512 " --> pdb=" O ILE A 434 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR A 436 " --> pdb=" O LEU A 512 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA7, first strand: chain 'A' and resid 490 through 492 Processing sheet with id=AA8, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AA9, first strand: chain 'A' and resid 534 through 536 removed outlier: 3.874A pdb=" N MET A 534 " --> pdb=" O TYR A 764 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 737 through 738 removed outlier: 3.710A pdb=" N MET A 737 " --> pdb=" O SER A 539 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 539 " --> pdb=" O MET A 737 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 35 through 38 removed outlier: 5.821A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 106 through 107 removed outlier: 6.357A pdb=" N ILE B 106 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 172 through 176 removed outlier: 3.726A pdb=" N TYR B 176 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 226 through 228 removed outlier: 4.359A pdb=" N PHE B 279 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N MET B 276 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU B 394 " --> pdb=" O MET B 276 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 392 " --> pdb=" O GLY B 278 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP B 390 " --> pdb=" O ARG B 280 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 400 " --> pdb=" O SER B 393 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 369 through 370 Processing sheet with id=AB7, first strand: chain 'B' and resid 403 through 405 removed outlier: 3.546A pdb=" N ASN B 412 " --> pdb=" O THR B 404 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 436 through 437 Processing sheet with id=AB9, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AC1, first strand: chain 'B' and resid 528 through 529 Processing sheet with id=AC2, first strand: chain 'B' and resid 534 through 535 removed outlier: 4.233A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 717 through 718 removed outlier: 7.866A pdb=" N VAL B 718 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA B 684 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU B 681 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N LEU B 736 " --> pdb=" O GLU B 681 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLY B 683 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 9.126A pdb=" N GLU B 738 " --> pdb=" O GLY B 683 " (cutoff:3.500A) removed outlier: 11.067A pdb=" N VAL B 685 " --> pdb=" O GLU B 738 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N TYR B 733 " --> pdb=" O ARG B 543 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ARG B 543 " --> pdb=" O TYR B 733 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET B 737 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 755 " --> pdb=" O ILE B 540 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 39 through 41 removed outlier: 6.562A pdb=" N GLY C 40 " --> pdb=" O GLN C 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 106 through 107 removed outlier: 6.484A pdb=" N ILE C 106 " --> pdb=" O ILE C 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 171 through 176 removed outlier: 7.473A pdb=" N VAL C 172 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N ARG C 202 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 225 through 228 removed outlier: 6.271A pdb=" N VAL C 226 " --> pdb=" O ILE C 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 368 through 370 Processing sheet with id=AC9, first strand: chain 'C' and resid 392 through 395 Processing sheet with id=AD1, first strand: chain 'C' and resid 435 through 437 Processing sheet with id=AD2, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AD3, first strand: chain 'C' and resid 528 through 529 Processing sheet with id=AD4, first strand: chain 'C' and resid 534 through 536 removed outlier: 3.744A pdb=" N MET C 534 " --> pdb=" O TYR C 764 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 737 through 738 removed outlier: 3.501A pdb=" N MET C 737 " --> pdb=" O SER C 539 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 35 through 36 Processing sheet with id=AD7, first strand: chain 'D' and resid 39 through 40 removed outlier: 6.985A pdb=" N GLY D 39 " --> pdb=" O LEU D 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 42 through 43 removed outlier: 6.214A pdb=" N PHE D 42 " --> pdb=" O ILE D 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 173 through 176 removed outlier: 6.204A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 369 through 370 Processing sheet with id=AE2, first strand: chain 'D' and resid 389 through 390 Processing sheet with id=AE3, first strand: chain 'D' and resid 393 through 394 removed outlier: 3.605A pdb=" N GLU D 400 " --> pdb=" O SER D 393 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 433 through 437 removed outlier: 6.302A pdb=" N LEU D 433 " --> pdb=" O GLU D 479 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG D 481 " --> pdb=" O LEU D 433 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL D 435 " --> pdb=" O ARG D 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AE6, first strand: chain 'D' and resid 528 through 529 removed outlier: 3.833A pdb=" N ASP D 528 " --> pdb=" O THR D 768 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 717 through 718 removed outlier: 6.659A pdb=" N ALA D 684 " --> pdb=" O VAL D 718 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY D 683 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N GLU D 738 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N VAL D 685 " --> pdb=" O GLU D 738 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR D 542 " --> pdb=" O THR D 753 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 54 through 58 removed outlier: 3.613A pdb=" N ARG E 153 " --> pdb=" O ASP E 89 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER E 132 " --> pdb=" O ILE E 84 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 72 through 77 removed outlier: 3.506A pdb=" N TRP E 138 " --> pdb=" O ARG E 108 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS E 140 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU E 105 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ARG E 120 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL E 107 " --> pdb=" O ILE E 118 " (cutoff:3.500A) 1144 hydrogen bonds defined for protein. 3291 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: 10.43 Time building geometry restraints manager: 12.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5990 1.33 - 1.45: 6880 1.45 - 1.57: 15324 1.57 - 1.70: 0 1.70 - 1.82: 266 Bond restraints: 28460 Sorted by residual: bond pdb=" CA ASP B 260 " pdb=" C ASP B 260 " ideal model delta sigma weight residual 1.524 1.473 0.051 1.40e-02 5.10e+03 1.31e+01 bond pdb=" CA SER C 179 " pdb=" CB SER C 179 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.64e-02 3.72e+03 1.29e+01 bond pdb=" N VAL A 266 " pdb=" CA VAL A 266 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.16e+01 bond pdb=" N ILE B 473 " pdb=" CA ILE B 473 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.09e-02 8.42e+03 1.10e+01 bond pdb=" C GLU B 267 " pdb=" N PRO B 268 " ideal model delta sigma weight residual 1.337 1.305 0.032 9.80e-03 1.04e+04 1.04e+01 ... (remaining 28455 not shown) Histogram of bond angle deviations from ideal: 95.61 - 103.32: 337 103.32 - 111.04: 11006 111.04 - 118.76: 12083 118.76 - 126.47: 14706 126.47 - 134.19: 410 Bond angle restraints: 38542 Sorted by residual: angle pdb=" N LEU A 619 " pdb=" CA LEU A 619 " pdb=" C LEU A 619 " ideal model delta sigma weight residual 111.28 102.65 8.63 1.09e+00 8.42e-01 6.26e+01 angle pdb=" N ASN C 546 " pdb=" CA ASN C 546 " pdb=" C ASN C 546 " ideal model delta sigma weight residual 111.33 102.21 9.12 1.21e+00 6.83e-01 5.67e+01 angle pdb=" N LEU C 261 " pdb=" CA LEU C 261 " pdb=" C LEU C 261 " ideal model delta sigma weight residual 113.23 104.76 8.47 1.24e+00 6.50e-01 4.66e+01 angle pdb=" N THR D 180 " pdb=" CA THR D 180 " pdb=" C THR D 180 " ideal model delta sigma weight residual 112.87 105.32 7.55 1.20e+00 6.94e-01 3.96e+01 angle pdb=" N ILE A 820 " pdb=" CA ILE A 820 " pdb=" C ILE A 820 " ideal model delta sigma weight residual 111.88 105.28 6.60 1.06e+00 8.90e-01 3.88e+01 ... (remaining 38537 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.20: 16406 23.20 - 46.40: 775 46.40 - 69.60: 92 69.60 - 92.81: 49 92.81 - 116.01: 42 Dihedral angle restraints: 17364 sinusoidal: 7312 harmonic: 10052 Sorted by residual: dihedral pdb=" CA ILE D 363 " pdb=" C ILE D 363 " pdb=" N LYS D 364 " pdb=" CA LYS D 364 " ideal model delta harmonic sigma weight residual -180.00 -151.31 -28.69 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA LYS E 125 " pdb=" C LYS E 125 " pdb=" N SER E 126 " pdb=" CA SER E 126 " ideal model delta harmonic sigma weight residual 180.00 152.96 27.04 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA LEU A 197 " pdb=" C LEU A 197 " pdb=" N ARG A 198 " pdb=" CA ARG A 198 " ideal model delta harmonic sigma weight residual 180.00 153.12 26.88 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 17361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.893: 4373 0.893 - 1.786: 0 1.786 - 2.680: 1 2.680 - 3.573: 0 3.573 - 4.466: 1 Chirality restraints: 4375 Sorted by residual: chirality pdb=" C1 NAG D1003 " pdb=" ND2 ASN D 275 " pdb=" C2 NAG D1003 " pdb=" O5 NAG D1003 " both_signs ideal model delta sigma weight residual False -2.40 2.07 -4.47 2.00e-01 2.50e+01 4.99e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.75e+02 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.32e+02 ... (remaining 4372 not shown) Planarity restraints: 4879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " -0.359 2.00e-02 2.50e+03 3.09e-01 1.19e+03 pdb=" C7 NAG H 2 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " -0.107 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " 0.548 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " -0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 275 " 0.263 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" CG ASN D 275 " -0.100 2.00e-02 2.50e+03 pdb=" OD1 ASN D 275 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN D 275 " -0.510 2.00e-02 2.50e+03 pdb=" C1 NAG D1003 " 0.343 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.347 2.00e-02 2.50e+03 3.00e-01 1.12e+03 pdb=" C7 NAG F 1 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.120 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.535 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.149 2.00e-02 2.50e+03 ... (remaining 4876 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 208 2.44 - 3.06: 21268 3.06 - 3.67: 44145 3.67 - 4.29: 62537 4.29 - 4.90: 96312 Nonbonded interactions: 224470 Sorted by model distance: nonbonded pdb=" CG ASN A 378 " pdb=" C8 NAG G 1 " model vdw 1.831 3.690 nonbonded pdb=" OD1 ASN A 378 " pdb=" C8 NAG G 1 " model vdw 1.928 3.460 nonbonded pdb=" OD1 ASN D 275 " pdb=" O7 NAG D1003 " model vdw 2.145 3.040 nonbonded pdb=" N GLU D 233 " pdb=" OE1 GLU D 233 " model vdw 2.166 3.120 nonbonded pdb=" NH2 ARG A 481 " pdb=" OE2 GLU A 484 " model vdw 2.197 3.120 ... (remaining 224465 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' and (resid 33 through 663 or (resid 664 and (name N or name CA or nam \ e C or name O or name CB )) or resid 665 through 681 or (resid 682 and (name N o \ r name CA or name C or name O or name CB )) or resid 683 through 814 or (resid 8 \ 15 and (name N or name CA or name C or name O or name CB )) or resid 816 through \ 850 or resid 1001 through 1003)) selection = (chain 'B' and (resid 33 through 681 or (resid 682 and (name N or name CA or nam \ e C or name O or name CB )) or resid 683 through 814 or (resid 815 and (name N o \ r name CA or name C or name O or name CB )) or resid 816 through 850 or resid 10 \ 01 through 1003)) selection = (chain 'C' and (resid 33 through 663 or (resid 664 and (name N or name CA or nam \ e C or name O or name CB )) or resid 665 through 850 or resid 1003 through 1005) \ ) selection = (chain 'D' and (resid 33 through 681 or (resid 682 and (name N or name CA or nam \ e C or name O or name CB )) or resid 683 through 814 or (resid 815 and (name N o \ r name CA or name C or name O or name CB )) or resid 816 through 850 or resid 10 \ 02 through 1004)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 2.040 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: 0.970 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 74.030 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.130 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.069 28460 Z= 0.555 Angle : 1.116 9.992 38542 Z= 0.687 Chirality : 0.097 4.466 4375 Planarity : 0.014 0.309 4859 Dihedral : 15.308 116.007 10885 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 27.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 0.50 % Allowed : 1.56 % Favored : 97.94 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.13), residues: 3456 helix: -0.82 (0.13), residues: 1398 sheet: -2.41 (0.27), residues: 383 loop : -2.44 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP E 138 HIS 0.012 0.002 HIS B 225 PHE 0.042 0.003 PHE A 42 TYR 0.043 0.003 TYR A 44 ARG 0.017 0.001 ARG A 431 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 195 time to evaluate : 3.196 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 247 MET cc_start: 0.7700 (tpp) cc_final: 0.6945 (tpp) REVERT: A 394 LEU cc_start: 0.8097 (tp) cc_final: 0.7445 (tp) REVERT: B 360 MET cc_start: 0.8930 (tpt) cc_final: 0.8300 (tpp) REVERT: B 420 LYS cc_start: -0.3847 (OUTLIER) cc_final: -0.4617 (ptpt) REVERT: B 565 MET cc_start: 0.9322 (mpp) cc_final: 0.9068 (mpp) REVERT: B 691 MET cc_start: 0.9069 (tmm) cc_final: 0.8847 (tmm) REVERT: B 794 MET cc_start: 0.8012 (ppp) cc_final: 0.7568 (ppp) REVERT: C 276 MET cc_start: 0.8413 (mpp) cc_final: 0.8143 (mmm) REVERT: C 737 MET cc_start: 0.8977 (ptp) cc_final: 0.8550 (ptp) REVERT: C 793 MET cc_start: 0.9123 (mpp) cc_final: 0.8835 (mpp) REVERT: D 565 MET cc_start: 0.8365 (mtt) cc_final: 0.7610 (mmt) REVERT: D 620 MET cc_start: 0.8813 (mpp) cc_final: 0.8422 (mpp) REVERT: D 737 MET cc_start: 0.8092 (ppp) cc_final: 0.7619 (ppp) outliers start: 15 outliers final: 4 residues processed: 209 average time/residue: 0.3909 time to fit residues: 131.9178 Evaluate side-chains 140 residues out of total 3015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 291 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 chunk 139 optimal weight: 0.0770 chunk 270 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 164 optimal weight: 30.0000 chunk 201 optimal weight: 3.9990 chunk 313 optimal weight: 0.0980 overall best weight: 1.0344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 65 ASN A 137 GLN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS B 129 HIS B 350 HIS ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN D 253 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28460 Z= 0.215 Angle : 0.730 13.951 38542 Z= 0.372 Chirality : 0.046 0.474 4375 Planarity : 0.005 0.053 4859 Dihedral : 10.879 99.738 4323 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.17 % Allowed : 4.62 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.14), residues: 3456 helix: 0.25 (0.13), residues: 1423 sheet: -1.91 (0.27), residues: 382 loop : -2.07 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 296 HIS 0.008 0.001 HIS C 136 PHE 0.048 0.002 PHE C 337 TYR 0.017 0.002 TYR C 44 ARG 0.005 0.001 ARG C 775 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 159 time to evaluate : 3.066 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: A 50 MET cc_start: 0.8483 (ptm) cc_final: 0.7863 (ptm) REVERT: A 247 MET cc_start: 0.8175 (tpp) cc_final: 0.7617 (tpp) REVERT: A 394 LEU cc_start: 0.8189 (tp) cc_final: 0.7692 (tp) REVERT: B 360 MET cc_start: 0.8691 (tpt) cc_final: 0.8375 (tpp) REVERT: B 534 MET cc_start: 0.7683 (tmm) cc_final: 0.7256 (tmm) REVERT: B 565 MET cc_start: 0.9318 (mpp) cc_final: 0.8980 (mpp) REVERT: B 691 MET cc_start: 0.8838 (tmm) cc_final: 0.8338 (tmm) REVERT: B 794 MET cc_start: 0.7943 (ppp) cc_final: 0.7471 (ppp) REVERT: C 247 MET cc_start: 0.7236 (tpp) cc_final: 0.6839 (tpp) REVERT: C 248 MET cc_start: 0.7998 (mmm) cc_final: 0.7666 (tpp) REVERT: C 276 MET cc_start: 0.8285 (mpp) cc_final: 0.8009 (mmm) REVERT: C 559 LEU cc_start: 0.8568 (tp) cc_final: 0.8162 (tt) REVERT: C 565 MET cc_start: 0.9229 (pmm) cc_final: 0.9026 (pmm) REVERT: C 605 ASN cc_start: 0.9366 (t0) cc_final: 0.9057 (t0) REVERT: C 620 MET cc_start: 0.8791 (tpp) cc_final: 0.8443 (tpp) REVERT: C 664 MET cc_start: 0.9222 (ppp) cc_final: 0.8725 (ppp) REVERT: C 793 MET cc_start: 0.9011 (mpp) cc_final: 0.8697 (mpp) REVERT: C 794 MET cc_start: 0.9108 (ttm) cc_final: 0.8871 (ptm) REVERT: D 413 MET cc_start: 0.8278 (ptp) cc_final: 0.8014 (ptp) REVERT: D 565 MET cc_start: 0.8162 (mtt) cc_final: 0.7476 (mmt) REVERT: D 572 LEU cc_start: 0.9392 (mm) cc_final: 0.9096 (mm) REVERT: D 620 MET cc_start: 0.8852 (mpp) cc_final: 0.8571 (mpp) REVERT: D 691 MET cc_start: 0.8109 (pmm) cc_final: 0.7807 (pmm) REVERT: E 137 MET cc_start: 0.8476 (mmt) cc_final: 0.8259 (mmm) outliers start: 5 outliers final: 3 residues processed: 164 average time/residue: 0.3452 time to fit residues: 95.9774 Evaluate side-chains 138 residues out of total 3015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 174 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 260 optimal weight: 2.9990 chunk 213 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 313 optimal weight: 9.9990 chunk 339 optimal weight: 20.0000 chunk 279 optimal weight: 2.9990 chunk 311 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 251 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 GLN B 111 HIS B 136 HIS B 302 GLN B 610 ASN C 34 HIS ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 HIS ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 28460 Z= 0.344 Angle : 0.734 10.970 38542 Z= 0.376 Chirality : 0.046 0.517 4375 Planarity : 0.005 0.060 4859 Dihedral : 9.115 98.202 4323 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.03 % Allowed : 4.39 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.14), residues: 3456 helix: 0.52 (0.13), residues: 1439 sheet: -1.89 (0.25), residues: 446 loop : -1.94 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 706 HIS 0.019 0.002 HIS D 253 PHE 0.035 0.002 PHE C 836 TYR 0.024 0.002 TYR E 92 ARG 0.007 0.001 ARG C 775 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 2.932 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 50 MET cc_start: 0.8609 (ptm) cc_final: 0.7832 (ptm) REVERT: A 247 MET cc_start: 0.8361 (tpp) cc_final: 0.8152 (tpp) REVERT: A 265 ASP cc_start: 0.8196 (t0) cc_final: 0.7701 (m-30) REVERT: A 323 MET cc_start: 0.8319 (tmm) cc_final: 0.8115 (ppp) REVERT: A 413 MET cc_start: 0.8169 (tpp) cc_final: 0.7962 (tpp) REVERT: B 298 MET cc_start: 0.9395 (ptp) cc_final: 0.9043 (ptp) REVERT: B 360 MET cc_start: 0.8938 (tpt) cc_final: 0.8230 (tpp) REVERT: B 565 MET cc_start: 0.9285 (mpp) cc_final: 0.8936 (mpp) REVERT: B 794 MET cc_start: 0.8384 (ppp) cc_final: 0.7935 (ppp) REVERT: C 247 MET cc_start: 0.7370 (tpp) cc_final: 0.7023 (tpp) REVERT: C 276 MET cc_start: 0.8249 (mpp) cc_final: 0.7980 (mmm) REVERT: C 605 ASN cc_start: 0.9413 (t0) cc_final: 0.9145 (t0) REVERT: C 620 MET cc_start: 0.9134 (tpp) cc_final: 0.8772 (mmt) REVERT: C 664 MET cc_start: 0.9198 (ppp) cc_final: 0.8595 (ppp) REVERT: C 705 MET cc_start: 0.7970 (mmm) cc_final: 0.7764 (mmm) REVERT: C 793 MET cc_start: 0.9038 (mpp) cc_final: 0.8732 (mpp) REVERT: D 64 ILE cc_start: 0.8318 (mm) cc_final: 0.7998 (pt) REVERT: D 360 MET cc_start: 0.8315 (mmm) cc_final: 0.7995 (tpp) REVERT: D 565 MET cc_start: 0.8174 (mtt) cc_final: 0.7716 (mmt) REVERT: D 620 MET cc_start: 0.8770 (mpp) cc_final: 0.8432 (mpp) REVERT: D 691 MET cc_start: 0.8341 (pmm) cc_final: 0.7965 (pmm) REVERT: D 794 MET cc_start: 0.9514 (ptm) cc_final: 0.9228 (ptm) REVERT: E 124 MET cc_start: 0.0996 (mmp) cc_final: 0.0315 (mmt) REVERT: E 137 MET cc_start: 0.8460 (mmt) cc_final: 0.8196 (mmm) outliers start: 1 outliers final: 0 residues processed: 147 average time/residue: 0.3656 time to fit residues: 90.8886 Evaluate side-chains 132 residues out of total 3015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 310 optimal weight: 0.9990 chunk 235 optimal weight: 7.9990 chunk 162 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 149 optimal weight: 0.4980 chunk 210 optimal weight: 10.0000 chunk 314 optimal weight: 7.9990 chunk 333 optimal weight: 20.0000 chunk 164 optimal weight: 8.9990 chunk 298 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 28460 Z= 0.290 Angle : 0.669 10.264 38542 Z= 0.343 Chirality : 0.045 0.516 4375 Planarity : 0.004 0.065 4859 Dihedral : 8.225 90.511 4323 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.14), residues: 3456 helix: 0.84 (0.14), residues: 1446 sheet: -1.74 (0.25), residues: 464 loop : -1.91 (0.15), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 706 HIS 0.009 0.001 HIS D 253 PHE 0.035 0.002 PHE C 836 TYR 0.022 0.002 TYR D 252 ARG 0.004 0.000 ARG B 300 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 3015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 3.259 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 50 MET cc_start: 0.8543 (ptm) cc_final: 0.7679 (ptm) REVERT: B 298 MET cc_start: 0.9444 (ptp) cc_final: 0.9177 (ptp) REVERT: B 360 MET cc_start: 0.8987 (tpt) cc_final: 0.8232 (tpp) REVERT: B 534 MET cc_start: 0.7951 (tmm) cc_final: 0.7741 (tmm) REVERT: B 691 MET cc_start: 0.8867 (tmm) cc_final: 0.8431 (tmm) REVERT: B 794 MET cc_start: 0.8335 (ppp) cc_final: 0.7882 (ppp) REVERT: C 33 THR cc_start: 0.7291 (p) cc_final: 0.7004 (t) REVERT: C 247 MET cc_start: 0.7179 (tpp) cc_final: 0.6950 (tpp) REVERT: C 276 MET cc_start: 0.8435 (mpp) cc_final: 0.8081 (mmm) REVERT: C 340 MET cc_start: 0.8214 (tpp) cc_final: 0.7919 (tpp) REVERT: C 605 ASN cc_start: 0.9383 (t0) cc_final: 0.9053 (t0) REVERT: C 620 MET cc_start: 0.9113 (tpp) cc_final: 0.8564 (mmt) REVERT: C 664 MET cc_start: 0.9142 (ppp) cc_final: 0.8772 (ppp) REVERT: C 793 MET cc_start: 0.9185 (mpp) cc_final: 0.8962 (mpp) REVERT: C 794 MET cc_start: 0.9147 (ppp) cc_final: 0.8726 (ppp) REVERT: D 64 ILE cc_start: 0.8300 (mm) cc_final: 0.7898 (pt) REVERT: D 565 MET cc_start: 0.8170 (mtt) cc_final: 0.7680 (mmt) REVERT: D 620 MET cc_start: 0.8770 (mpp) cc_final: 0.8438 (mpp) REVERT: D 691 MET cc_start: 0.8527 (pmm) cc_final: 0.8021 (pmm) REVERT: D 705 MET cc_start: 0.9273 (mmp) cc_final: 0.8771 (mmt) REVERT: D 794 MET cc_start: 0.9468 (ptm) cc_final: 0.9184 (ptm) REVERT: E 124 MET cc_start: 0.1000 (mmp) cc_final: 0.0024 (mmp) REVERT: E 137 MET cc_start: 0.8535 (mmt) cc_final: 0.8324 (mmm) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.3750 time to fit residues: 91.9974 Evaluate side-chains 134 residues out of total 3015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 3.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 277 optimal weight: 9.9990 chunk 189 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 248 optimal weight: 40.0000 chunk 137 optimal weight: 10.0000 chunk 284 optimal weight: 0.7980 chunk 230 optimal weight: 8.9990 chunk 0 optimal weight: 0.9980 chunk 170 optimal weight: 10.0000 chunk 299 optimal weight: 20.0000 chunk 84 optimal weight: 7.9990 overall best weight: 3.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28460 Z= 0.250 Angle : 0.633 10.112 38542 Z= 0.324 Chirality : 0.044 0.492 4375 Planarity : 0.004 0.050 4859 Dihedral : 7.642 83.753 4323 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.03 % Allowed : 2.99 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.15), residues: 3456 helix: 1.04 (0.14), residues: 1453 sheet: -1.76 (0.24), residues: 465 loop : -1.82 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 613 HIS 0.008 0.001 HIS C 253 PHE 0.036 0.002 PHE C 836 TYR 0.020 0.001 TYR D 252 ARG 0.010 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 3015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.8554 (ptm) cc_final: 0.7761 (ptm) REVERT: A 316 MET cc_start: 0.8729 (mtp) cc_final: 0.8476 (tpp) REVERT: A 323 MET cc_start: 0.8616 (tmm) cc_final: 0.8138 (tmm) REVERT: A 705 MET cc_start: 0.9134 (mmp) cc_final: 0.8908 (mmm) REVERT: B 298 MET cc_start: 0.9460 (ptp) cc_final: 0.9166 (ptp) REVERT: B 360 MET cc_start: 0.8988 (tpt) cc_final: 0.8230 (tpp) REVERT: B 565 MET cc_start: 0.9232 (mpp) cc_final: 0.8973 (mpp) REVERT: B 691 MET cc_start: 0.8761 (tmm) cc_final: 0.8384 (tmm) REVERT: B 794 MET cc_start: 0.8290 (ppp) cc_final: 0.7801 (ppp) REVERT: C 33 THR cc_start: 0.6474 (p) cc_final: 0.6218 (t) REVERT: C 276 MET cc_start: 0.8431 (mpp) cc_final: 0.8074 (mmm) REVERT: C 605 ASN cc_start: 0.9415 (t0) cc_final: 0.9106 (t0) REVERT: C 620 MET cc_start: 0.9117 (tpp) cc_final: 0.8664 (mmt) REVERT: C 737 MET cc_start: 0.8776 (ptp) cc_final: 0.8566 (ptp) REVERT: C 793 MET cc_start: 0.9177 (mpp) cc_final: 0.8933 (mpp) REVERT: C 794 MET cc_start: 0.9172 (ppp) cc_final: 0.8812 (ppp) REVERT: D 64 ILE cc_start: 0.8097 (mm) cc_final: 0.7585 (pt) REVERT: D 565 MET cc_start: 0.8158 (mtt) cc_final: 0.7684 (mmt) REVERT: D 620 MET cc_start: 0.8749 (mpp) cc_final: 0.8394 (mpp) REVERT: D 691 MET cc_start: 0.8297 (pmm) cc_final: 0.7996 (pmm) REVERT: D 705 MET cc_start: 0.9237 (mmp) cc_final: 0.8908 (mmp) REVERT: D 709 MET cc_start: 0.8947 (ptp) cc_final: 0.8700 (ptt) REVERT: D 794 MET cc_start: 0.9396 (ptm) cc_final: 0.9132 (ptm) REVERT: E 124 MET cc_start: 0.0626 (mmp) cc_final: -0.0190 (mmp) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.3642 time to fit residues: 90.2055 Evaluate side-chains 132 residues out of total 3015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.0325 > 50: distance: 35 - 41: 33.447 distance: 41 - 42: 67.072 distance: 42 - 43: 55.644 distance: 42 - 45: 57.527 distance: 43 - 44: 57.172 distance: 45 - 46: 27.654 distance: 46 - 47: 9.246 distance: 47 - 48: 23.542 distance: 47 - 49: 43.026 distance: 50 - 51: 28.465 distance: 51 - 52: 27.550 distance: 51 - 54: 47.490 distance: 52 - 53: 52.740 distance: 52 - 55: 56.611 distance: 55 - 56: 38.684 distance: 55 - 61: 49.263 distance: 56 - 57: 40.625 distance: 56 - 59: 49.830 distance: 57 - 62: 56.221 distance: 59 - 60: 41.471 distance: 60 - 61: 58.974 distance: 63 - 64: 39.919 distance: 64 - 65: 5.895 distance: 69 - 70: 57.258 distance: 70 - 71: 38.584 distance: 70 - 73: 45.039 distance: 71 - 72: 17.141 distance: 71 - 78: 57.204 distance: 72 - 93: 45.474 distance: 73 - 74: 60.543 distance: 74 - 75: 46.346 distance: 75 - 76: 43.818 distance: 76 - 77: 16.137 distance: 78 - 79: 38.995 distance: 78 - 84: 50.082 distance: 79 - 80: 56.510 distance: 79 - 82: 27.072 distance: 80 - 81: 56.918 distance: 81 - 99: 67.235 distance: 82 - 83: 41.179 distance: 83 - 84: 9.465 distance: 85 - 86: 40.892 distance: 86 - 87: 33.108 distance: 86 - 89: 40.384 distance: 87 - 88: 51.489 distance: 87 - 93: 33.712 distance: 89 - 90: 40.250 distance: 90 - 91: 39.695 distance: 90 - 92: 55.888 distance: 93 - 94: 55.687 distance: 94 - 95: 40.634 distance: 94 - 97: 39.380 distance: 95 - 96: 38.821 distance: 95 - 99: 40.558 distance: 97 - 98: 57.355 distance: 99 - 100: 69.429 distance: 100 - 101: 28.125 distance: 101 - 102: 22.305 distance: 101 - 103: 13.078 distance: 104 - 105: 53.267 distance: 104 - 107: 41.019 distance: 105 - 106: 21.790 distance: 105 - 111: 32.831 distance: 107 - 108: 6.087 distance: 108 - 109: 55.792 distance: 108 - 110: 56.722