Starting phenix.real_space_refine (version: dev) on Tue Feb 21 23:30:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgr_10182/02_2023/6sgr_10182.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgr_10182/02_2023/6sgr_10182.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgr_10182/02_2023/6sgr_10182.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgr_10182/02_2023/6sgr_10182.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgr_10182/02_2023/6sgr_10182.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgr_10182/02_2023/6sgr_10182.pdb" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 Process input model Symmetric amino acids flipped Residue "A GLU 130": "OE1" <-> "OE2" Residue "A ARG 307": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 673": "OE1" <-> "OE2" Residue "A GLU 839": "OE1" <-> "OE2" Residue "A GLU 893": "OE1" <-> "OE2" Residue "B GLU 121": "OE1" <-> "OE2" Residue "B ARG 185": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 673": "OE1" <-> "OE2" Residue "B ARG 780": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 363": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 792": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 893": "OE1" <-> "OE2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 130": "OE1" <-> "OE2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "E ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 29": "OE1" <-> "OE2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "F GLU 3": "OE1" <-> "OE2" Residue "H GLU 3": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 54142 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 16027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 16027 Classifications: {'peptide': 1044} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 998} Chain: "B" Number of atoms: 15850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 15850 Classifications: {'peptide': 1033} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 987} Chain: "C" Number of atoms: 15850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 15850 Classifications: {'peptide': 1033} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 987} Chain: "D" Number of atoms: 2336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2336 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 3, 'TRANS': 152} Chain: "E" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2287 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 3, 'TRANS': 148} Chain: "F" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 601 Classifications: {'peptide': 37} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "G" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 590 Classifications: {'peptide': 36} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "H" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 601 Classifications: {'peptide': 37} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 35} Time building chain proxies: 18.13, per 1000 atoms: 0.33 Number of scatterers: 54142 At special positions: 0 Unit cell: (151.232, 133.824, 146.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 143 16.00 O 4978 8.00 N 4429 7.00 C 17262 6.00 H 27330 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 34.98 Conformation dependent library (CDL) restraints added in 3.4 seconds 7024 Ramachandran restraints generated. 3512 Oldfield, 0 Emsley, 3512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6446 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 24 sheets defined 59.9% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 removed outlier: 3.590A pdb=" N PHE A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 29 removed outlier: 3.691A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 162 through 167 removed outlier: 3.550A pdb=" N ILE A 166 " --> pdb=" O MET A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 199 through 211 removed outlier: 3.628A pdb=" N ILE A 207 " --> pdb=" O VAL A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 298 through 312 Processing helix chain 'A' and resid 329 through 360 removed outlier: 3.705A pdb=" N VAL A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE A 337 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 387 removed outlier: 4.504A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 392 through 424 removed outlier: 3.756A pdb=" N MET A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 454 removed outlier: 5.916A pdb=" N GLY A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.639A pdb=" N PHE A 459 " --> pdb=" O MET A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 488 removed outlier: 3.764A pdb=" N TYR A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 496 Processing helix chain 'A' and resid 511 through 536 Processing helix chain 'A' and resid 539 through 558 removed outlier: 3.788A pdb=" N VAL A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 601 Processing helix chain 'A' and resid 633 through 637 Processing helix chain 'A' and resid 643 through 657 removed outlier: 3.858A pdb=" N ARG A 653 " --> pdb=" O MET A 649 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA A 654 " --> pdb=" O ARG A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 708 removed outlier: 3.544A pdb=" N LEU A 695 " --> pdb=" O GLY A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 Processing helix chain 'A' and resid 742 through 755 Processing helix chain 'A' and resid 782 through 786 Processing helix chain 'A' and resid 836 through 849 removed outlier: 3.905A pdb=" N ALA A 840 " --> pdb=" O SER A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 869 removed outlier: 3.884A pdb=" N GLN A 865 " --> pdb=" O GLY A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 892 removed outlier: 3.893A pdb=" N LEU A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 903 Processing helix chain 'A' and resid 904 through 918 removed outlier: 3.766A pdb=" N GLY A 908 " --> pdb=" O VAL A 904 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 957 Processing helix chain 'A' and resid 959 through 991 removed outlier: 4.929A pdb=" N ARG A 973 " --> pdb=" O ARG A 969 " (cutoff:3.500A) Proline residue: A 974 - end of helix Proline residue: A 988 - end of helix Processing helix chain 'A' and resid 996 through 1033 removed outlier: 3.827A pdb=" N GLY A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE A1019 " --> pdb=" O THR A1015 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N PHE A1020 " --> pdb=" O VAL A1016 " (cutoff:3.500A) Proline residue: A1023 - end of helix Processing helix chain 'A' and resid 1037 through 1041 removed outlier: 3.517A pdb=" N ILE A1040 " --> pdb=" O ASN A1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 7 removed outlier: 3.825A pdb=" N ASP B 7 " --> pdb=" O ASN B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 29 removed outlier: 3.618A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.590A pdb=" N ALA B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 163 through 169 Processing helix chain 'B' and resid 189 through 196 removed outlier: 4.005A pdb=" N PHE B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.620A pdb=" N VAL B 203 " --> pdb=" O THR B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.545A pdb=" N PHE B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 265 removed outlier: 4.213A pdb=" N VAL B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 261 through 265' Processing helix chain 'B' and resid 298 through 313 removed outlier: 3.641A pdb=" N MET B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 360 removed outlier: 3.623A pdb=" N VAL B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 366 removed outlier: 3.571A pdb=" N THR B 365 " --> pdb=" O ASN B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 387 Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 391 through 423 removed outlier: 4.096A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 454 removed outlier: 5.395A pdb=" N GLY B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 459 removed outlier: 3.743A pdb=" N PHE B 459 " --> pdb=" O MET B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 494 removed outlier: 3.861A pdb=" N ALA B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N THR B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Proline residue: B 490 - end of helix Processing helix chain 'B' and resid 511 through 535 removed outlier: 3.784A pdb=" N ARG B 518 " --> pdb=" O GLY B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 558 removed outlier: 4.016A pdb=" N LEU B 544 " --> pdb=" O ARG B 540 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 601 removed outlier: 3.584A pdb=" N THR B 587 " --> pdb=" O THR B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 637 Processing helix chain 'B' and resid 643 through 656 Processing helix chain 'B' and resid 691 through 708 removed outlier: 3.704A pdb=" N LEU B 695 " --> pdb=" O GLY B 691 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS B 708 " --> pdb=" O ALA B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 739 removed outlier: 3.661A pdb=" N ALA B 736 " --> pdb=" O ASP B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 755 Processing helix chain 'B' and resid 777 through 780 Processing helix chain 'B' and resid 782 through 786 Processing helix chain 'B' and resid 802 through 804 No H-bonds generated for 'chain 'B' and resid 802 through 804' Processing helix chain 'B' and resid 836 through 849 Processing helix chain 'B' and resid 860 through 867 Processing helix chain 'B' and resid 872 through 893 Processing helix chain 'B' and resid 896 through 901 Processing helix chain 'B' and resid 905 through 920 removed outlier: 4.392A pdb=" N GLY B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 955 Processing helix chain 'B' and resid 959 through 992 removed outlier: 4.798A pdb=" N ARG B 973 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Proline residue: B 974 - end of helix Proline residue: B 988 - end of helix Processing helix chain 'B' and resid 996 through 1033 removed outlier: 4.048A pdb=" N GLY B1006 " --> pdb=" O ALA B1002 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE B1019 " --> pdb=" O THR B1015 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE B1020 " --> pdb=" O VAL B1016 " (cutoff:3.500A) Proline residue: B1023 - end of helix Processing helix chain 'C' and resid 2 through 8 removed outlier: 3.867A pdb=" N ASP C 7 " --> pdb=" O ASN C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 30 removed outlier: 3.742A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 28 " --> pdb=" O GLY C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.560A pdb=" N ILE C 72 " --> pdb=" O MET C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 111 Processing helix chain 'C' and resid 112 through 118 removed outlier: 4.188A pdb=" N MET C 115 " --> pdb=" O GLN C 112 " (cutoff:3.500A) Proline residue: C 116 - end of helix No H-bonds generated for 'chain 'C' and resid 112 through 118' Processing helix chain 'C' and resid 119 through 126 removed outlier: 3.511A pdb=" N GLN C 123 " --> pdb=" O PRO C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 162 removed outlier: 3.732A pdb=" N ILE C 154 " --> pdb=" O THR C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 189 through 195 Processing helix chain 'C' and resid 199 through 210 Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.502A pdb=" N PHE C 246 " --> pdb=" O SER C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'C' and resid 298 through 312 Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 329 through 360 removed outlier: 3.706A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 370 Proline residue: C 368 - end of helix Processing helix chain 'C' and resid 370 through 387 removed outlier: 3.740A pdb=" N VAL C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 405 removed outlier: 3.532A pdb=" N MET C 395 " --> pdb=" O ASN C 391 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 423 removed outlier: 4.117A pdb=" N VAL C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 451 removed outlier: 4.449A pdb=" N GLY C 436 " --> pdb=" O ARG C 432 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN C 437 " --> pdb=" O LYS C 433 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN C 439 " --> pdb=" O MET C 435 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLY C 440 " --> pdb=" O GLY C 436 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ALA C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 458 Processing helix chain 'C' and resid 461 through 496 removed outlier: 3.565A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Proline residue: C 490 - end of helix Processing helix chain 'C' and resid 511 through 535 removed outlier: 3.912A pdb=" N TRP C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 539 removed outlier: 6.207A pdb=" N GLY C 539 " --> pdb=" O ARG C 536 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 536 through 539' Processing helix chain 'C' and resid 540 through 558 removed outlier: 3.922A pdb=" N LEU C 544 " --> pdb=" O ARG C 540 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU C 546 " --> pdb=" O LEU C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 601 Processing helix chain 'C' and resid 643 through 655 Processing helix chain 'C' and resid 691 through 707 removed outlier: 3.569A pdb=" N LEU C 695 " --> pdb=" O GLY C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 740 Processing helix chain 'C' and resid 742 through 754 removed outlier: 3.564A pdb=" N LEU C 750 " --> pdb=" O ILE C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 777 through 780 Processing helix chain 'C' and resid 783 through 788 Processing helix chain 'C' and resid 836 through 850 removed outlier: 3.671A pdb=" N ALA C 840 " --> pdb=" O SER C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 892 removed outlier: 3.560A pdb=" N TYR C 864 " --> pdb=" O THR C 860 " (cutoff:3.500A) Proline residue: C 874 - end of helix removed outlier: 4.085A pdb=" N VAL C 884 " --> pdb=" O SER C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 903 Processing helix chain 'C' and resid 905 through 920 removed outlier: 4.210A pdb=" N GLY C 911 " --> pdb=" O LEU C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 955 removed outlier: 4.310A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 991 removed outlier: 5.085A pdb=" N ARG C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Proline residue: C 974 - end of helix Proline residue: C 988 - end of helix Processing helix chain 'C' and resid 996 through 1017 removed outlier: 3.512A pdb=" N GLN C1000 " --> pdb=" O GLY C 996 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY C1006 " --> pdb=" O ALA C1002 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL C1007 " --> pdb=" O VAL C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1033 Proline residue: C1023 - end of helix Processing helix chain 'D' and resid 12 through 25 Processing helix chain 'D' and resid 26 through 36 Processing helix chain 'D' and resid 49 through 57 Processing helix chain 'D' and resid 60 through 69 Processing helix chain 'D' and resid 82 through 89 removed outlier: 3.589A pdb=" N LEU D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N HIS D 89 " --> pdb=" O HIS D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 removed outlier: 3.744A pdb=" N VAL D 96 " --> pdb=" O HIS D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 123 Processing helix chain 'D' and resid 126 through 135 removed outlier: 3.725A pdb=" N TYR D 135 " --> pdb=" O VAL D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 157 Processing helix chain 'D' and resid 158 through 165 removed outlier: 3.745A pdb=" N ALA D 162 " --> pdb=" O ASN D 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 25 removed outlier: 4.556A pdb=" N GLU E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 49 through 57 Processing helix chain 'E' and resid 59 through 68 Processing helix chain 'E' and resid 82 through 89 removed outlier: 3.730A pdb=" N LEU E 86 " --> pdb=" O THR E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 102 removed outlier: 3.721A pdb=" N GLU E 97 " --> pdb=" O LEU E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 123 removed outlier: 3.671A pdb=" N LEU E 119 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG E 123 " --> pdb=" O LEU E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 135 Processing helix chain 'E' and resid 148 through 157 Processing helix chain 'E' and resid 158 through 165 Processing helix chain 'F' and resid 2 through 36 Proline residue: F 16 - end of helix Processing helix chain 'G' and resid 2 through 35 removed outlier: 3.839A pdb=" N SER G 7 " --> pdb=" O GLU G 3 " (cutoff:3.500A) Proline residue: G 16 - end of helix Processing helix chain 'H' and resid 2 through 36 Proline residue: H 16 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 130 removed outlier: 12.342A pdb=" N ARG A 815 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N GLU A 826 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU A 817 " --> pdb=" O SER A 824 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLN A 830 " --> pdb=" O SER A 715 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N SER A 715 " --> pdb=" O GLN A 830 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 130 removed outlier: 12.342A pdb=" N ARG A 815 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N GLU A 826 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU A 817 " --> pdb=" O SER A 824 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 7.006A pdb=" N VAL A 172 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ALA A 294 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASN A 144 " --> pdb=" O PRO A 285 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET A 138 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU A 293 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N PHE A 136 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N LEU A 137 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASP A 328 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL A 139 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 177 removed outlier: 7.006A pdb=" N VAL A 172 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ALA A 294 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 286 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 608 " --> pdb=" O SER A 630 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N THR A 624 " --> pdb=" O GLY A 614 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 272 removed outlier: 7.582A pdb=" N TYR A 182 " --> pdb=" O LYS A 770 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N TYR A 772 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N MET A 184 " --> pdb=" O TYR A 772 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N MET A 774 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ILE A 186 " --> pdb=" O MET A 774 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASN A 760 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL A 773 " --> pdb=" O TYR A 758 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TYR A 758 " --> pdb=" O VAL A 773 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 218 through 219 removed outlier: 4.184A pdb=" N SER A 233 " --> pdb=" O PRO B 725 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 250 through 253 removed outlier: 6.961A pdb=" N VAL A 260 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 805 through 812 removed outlier: 4.524A pdb=" N SER C 233 " --> pdb=" O PRO A 725 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLY C 217 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ALA C 236 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ALA C 215 " --> pdb=" O ALA C 236 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 790 through 792 Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 131 removed outlier: 4.193A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 12.431A pdb=" N ARG B 815 " --> pdb=" O GLU B 826 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N GLU B 826 " --> pdb=" O ARG B 815 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU B 817 " --> pdb=" O SER B 824 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 822 " --> pdb=" O TYR B 819 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLN B 830 " --> pdb=" O SER B 715 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N SER B 715 " --> pdb=" O GLN B 830 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 128 through 131 removed outlier: 4.193A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 12.431A pdb=" N ARG B 815 " --> pdb=" O GLU B 826 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N GLU B 826 " --> pdb=" O ARG B 815 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU B 817 " --> pdb=" O SER B 824 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 822 " --> pdb=" O TYR B 819 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 138 through 143 removed outlier: 3.780A pdb=" N MET B 138 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP B 174 " --> pdb=" O LYS B 292 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 266 through 272 removed outlier: 7.784A pdb=" N TYR B 182 " --> pdb=" O LYS B 770 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N TYR B 772 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N MET B 184 " --> pdb=" O TYR B 772 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N MET B 774 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE B 186 " --> pdb=" O MET B 774 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN B 760 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL B 773 " --> pdb=" O TYR B 758 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TYR B 758 " --> pdb=" O VAL B 773 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 218 through 219 removed outlier: 6.826A pdb=" N SER B 233 " --> pdb=" O PHE C 727 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE C 729 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE B 235 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE C 731 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 252 through 253 removed outlier: 3.901A pdb=" N LYS B 252 " --> pdb=" O VAL B 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 278 through 281 removed outlier: 6.852A pdb=" N SER B 630 " --> pdb=" O GLU B 607 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL B 609 " --> pdb=" O PHE B 628 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE B 628 " --> pdb=" O VAL B 609 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA B 611 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE B 626 " --> pdb=" O ALA B 611 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ASN B 613 " --> pdb=" O THR B 624 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N THR B 624 " --> pdb=" O ASN B 613 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N PHE B 615 " --> pdb=" O GLN B 622 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N GLN B 622 " --> pdb=" O PHE B 615 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 790 through 792 Processing sheet with id=AB9, first strand: chain 'C' and resid 128 through 131 removed outlier: 12.282A pdb=" N ARG C 815 " --> pdb=" O GLU C 826 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N GLU C 826 " --> pdb=" O ARG C 815 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU C 817 " --> pdb=" O SER C 824 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 822 " --> pdb=" O TYR C 819 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLN C 830 " --> pdb=" O SER C 715 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N SER C 715 " --> pdb=" O GLN C 830 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 128 through 131 removed outlier: 12.282A pdb=" N ARG C 815 " --> pdb=" O GLU C 826 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N GLU C 826 " --> pdb=" O ARG C 815 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU C 817 " --> pdb=" O SER C 824 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 822 " --> pdb=" O TYR C 819 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.851A pdb=" N ASN C 144 " --> pdb=" O PRO C 285 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL C 139 " --> pdb=" O PRO C 326 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.244A pdb=" N ALA C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 267 through 272 removed outlier: 7.607A pdb=" N TYR C 182 " --> pdb=" O LYS C 770 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N TYR C 772 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N MET C 184 " --> pdb=" O TYR C 772 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N MET C 774 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ILE C 186 " --> pdb=" O MET C 774 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN C 760 " --> pdb=" O VAL C 771 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL C 773 " --> pdb=" O TYR C 758 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR C 758 " --> pdb=" O VAL C 773 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 250 through 253 removed outlier: 7.232A pdb=" N VAL C 260 " --> pdb=" O LEU C 251 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 790 through 792 1741 hydrogen bonds defined for protein. 5043 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: 19.88 Time building geometry restraints manager: 36.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 27324 1.03 - 1.23: 7 1.23 - 1.42: 11005 1.42 - 1.61: 16028 1.61 - 1.81: 280 Bond restraints: 54644 Sorted by residual: bond pdb=" N GLY C 821 " pdb=" H GLY C 821 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.51e+00 bond pdb=" CA SER C 481 " pdb=" CB SER C 481 " ideal model delta sigma weight residual 1.528 1.490 0.038 1.59e-02 3.96e+03 5.80e+00 bond pdb=" N GLN C 928 " pdb=" H GLN C 928 " ideal model delta sigma weight residual 0.860 0.907 -0.047 2.00e-02 2.50e+03 5.63e+00 bond pdb=" C GLN C 928 " pdb=" O GLN C 928 " ideal model delta sigma weight residual 1.237 1.211 0.026 1.17e-02 7.31e+03 4.92e+00 bond pdb=" N SER C 481 " pdb=" H SER C 481 " ideal model delta sigma weight residual 0.860 0.903 -0.043 2.00e-02 2.50e+03 4.59e+00 ... (remaining 54639 not shown) Histogram of bond angle deviations from ideal: 98.62 - 105.71: 590 105.71 - 112.79: 65249 112.79 - 119.88: 13793 119.88 - 126.96: 19268 126.96 - 134.05: 250 Bond angle restraints: 99150 Sorted by residual: angle pdb=" N ILE B 370 " pdb=" CA ILE B 370 " pdb=" C ILE B 370 " ideal model delta sigma weight residual 112.96 108.52 4.44 1.00e+00 1.00e+00 1.97e+01 angle pdb=" C GLN C 928 " pdb=" N VAL C 929 " pdb=" CA VAL C 929 " ideal model delta sigma weight residual 120.46 125.90 -5.44 1.37e+00 5.33e-01 1.57e+01 angle pdb=" CA GLN C 928 " pdb=" C GLN C 928 " pdb=" O GLN C 928 " ideal model delta sigma weight residual 120.55 116.38 4.17 1.06e+00 8.90e-01 1.55e+01 angle pdb=" CA SER C 481 " pdb=" C SER C 481 " pdb=" O SER C 481 " ideal model delta sigma weight residual 120.42 116.51 3.91 1.06e+00 8.90e-01 1.36e+01 angle pdb=" CA GLY C 821 " pdb=" C GLY C 821 " pdb=" O GLY C 821 " ideal model delta sigma weight residual 119.25 114.95 4.30 1.28e+00 6.10e-01 1.13e+01 ... (remaining 99145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 19336 17.84 - 35.68: 1851 35.68 - 53.53: 327 53.53 - 71.37: 58 71.37 - 89.21: 35 Dihedral angle restraints: 21607 sinusoidal: 10009 harmonic: 11598 Sorted by residual: dihedral pdb=" CA GLN A 437 " pdb=" C GLN A 437 " pdb=" N ILE A 438 " pdb=" CA ILE A 438 " ideal model delta harmonic sigma weight residual 180.00 -155.81 -24.19 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA PHE C 680 " pdb=" C PHE C 680 " pdb=" N ASP C 681 " pdb=" CA ASP C 681 " ideal model delta harmonic sigma weight residual 180.00 156.54 23.46 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA GLN B 437 " pdb=" C GLN B 437 " pdb=" N ILE B 438 " pdb=" CA ILE B 438 " ideal model delta harmonic sigma weight residual -180.00 -158.64 -21.36 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 21604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2551 0.028 - 0.056: 1167 0.056 - 0.084: 421 0.084 - 0.112: 187 0.112 - 0.139: 52 Chirality restraints: 4378 Sorted by residual: chirality pdb=" CA ILE C 45 " pdb=" N ILE C 45 " pdb=" C ILE C 45 " pdb=" CB ILE C 45 " 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=" CA VAL A 88 " pdb=" N VAL A 88 " pdb=" C VAL A 88 " pdb=" CB VAL A 88 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA VAL C 576 " pdb=" N VAL C 576 " pdb=" C VAL C 576 " pdb=" CB VAL C 576 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 4375 not shown) Planarity restraints: 8120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 821 " 0.024 2.00e-02 2.50e+03 4.63e-02 2.15e+01 pdb=" N LEU C 822 " -0.080 2.00e-02 2.50e+03 pdb=" CA LEU C 822 " 0.021 2.00e-02 2.50e+03 pdb=" H LEU C 822 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 928 " -0.028 2.00e-02 2.50e+03 3.10e-02 1.45e+01 pdb=" CD GLN C 928 " -0.004 2.00e-02 2.50e+03 pdb=" OE1 GLN C 928 " 0.031 2.00e-02 2.50e+03 pdb=" NE2 GLN C 928 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN C 928 " 0.045 2.00e-02 2.50e+03 pdb="HE22 GLN C 928 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 481 " 0.014 2.00e-02 2.50e+03 2.67e-02 7.11e+00 pdb=" N VAL C 482 " -0.046 2.00e-02 2.50e+03 pdb=" CA VAL C 482 " 0.012 2.00e-02 2.50e+03 pdb=" H VAL C 482 " 0.020 2.00e-02 2.50e+03 ... (remaining 8117 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 634 2.06 - 2.70: 88062 2.70 - 3.33: 158994 3.33 - 3.97: 202965 3.97 - 4.60: 328477 Nonbonded interactions: 779132 Sorted by model distance: nonbonded pdb=" HB3 ALA B 457 " pdb=" HG SER B 471 " model vdw 1.427 2.270 nonbonded pdb=" HH TYR B 527 " pdb=" O ILE B1019 " model vdw 1.605 1.850 nonbonded pdb=" OD1 ASP D 143 " pdb=" H LYS D 144 " model vdw 1.619 1.850 nonbonded pdb=" HH TYR A 527 " pdb=" O ILE A1019 " model vdw 1.628 1.850 nonbonded pdb=" H THR C 241 " pdb=" OE1 GLU C 245 " model vdw 1.631 1.850 ... (remaining 779127 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' and resid 1 through 1033) selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and ((resid 15 and (name N or name CA or name C or name O or name HA2 \ or name HA3)) or resid 16 through 166)) selection = chain 'E' } ncs_group { reference = (chain 'F' and resid 1 through 36) selection = chain 'G' selection = (chain 'H' and resid 1 through 36) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 143 5.16 5 C 17262 2.51 5 N 4429 2.21 5 O 4978 1.98 5 H 27330 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.610 Extract box with map and model: 9.220 Check model and map are aligned: 0.600 Process input model: 128.910 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.370 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 : 0.004 0.046 27314 Z= 0.284 Angle : 0.539 6.372 37090 Z= 0.304 Chirality : 0.040 0.139 4378 Planarity : 0.004 0.053 4744 Dihedral : 13.558 89.212 9845 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.12), residues: 3512 helix: -1.38 (0.10), residues: 1986 sheet: -1.89 (0.24), residues: 396 loop : -3.02 (0.15), residues: 1130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7024 Ramachandran restraints generated. 3512 Oldfield, 0 Emsley, 3512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7024 Ramachandran restraints generated. 3512 Oldfield, 0 Emsley, 3512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 622 time to evaluate : 3.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 622 average time/residue: 0.8682 time to fit residues: 814.6959 Evaluate side-chains 432 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 3.106 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 294 optimal weight: 0.7980 chunk 264 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 273 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 203 optimal weight: 6.9990 chunk 316 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 274 ASN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 ASN A 605 ASN A 692 HIS A 733 GLN A1001 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 GLN B 360 GLN B 592 ASN B1001 ASN C 231 ASN C 298 ASN C 941 ASN C1000 GLN D 102 ASN E 118 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 27314 Z= 0.250 Angle : 0.536 6.415 37090 Z= 0.281 Chirality : 0.041 0.152 4378 Planarity : 0.004 0.051 4744 Dihedral : 4.128 24.054 3730 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.25 (0.14), residues: 3512 helix: 0.11 (0.11), residues: 2008 sheet: -1.56 (0.24), residues: 422 loop : -2.15 (0.18), residues: 1082 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7024 Ramachandran restraints generated. 3512 Oldfield, 0 Emsley, 3512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7024 Ramachandran restraints generated. 3512 Oldfield, 0 Emsley, 3512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 448 time to evaluate : 3.133 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 outliers start: 23 outliers final: 20 residues processed: 464 average time/residue: 0.8408 time to fit residues: 599.8901 Evaluate side-chains 431 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 411 time to evaluate : 3.133 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.5151 time to fit residues: 23.3469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 176 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 263 optimal weight: 0.7980 chunk 215 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 317 optimal weight: 6.9990 chunk 342 optimal weight: 3.9990 chunk 282 optimal weight: 3.9990 chunk 314 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 254 optimal weight: 3.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN C 228 GLN C 274 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 27314 Z= 0.263 Angle : 0.520 6.272 37090 Z= 0.272 Chirality : 0.041 0.150 4378 Planarity : 0.003 0.048 4744 Dihedral : 4.021 23.944 3730 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.31 (0.14), residues: 3512 helix: 0.82 (0.12), residues: 2010 sheet: -1.32 (0.24), residues: 426 loop : -1.58 (0.19), residues: 1076 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7024 Ramachandran restraints generated. 3512 Oldfield, 0 Emsley, 3512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7024 Ramachandran restraints generated. 3512 Oldfield, 0 Emsley, 3512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 446 time to evaluate : 3.189 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 outliers start: 15 outliers final: 11 residues processed: 457 average time/residue: 0.8278 time to fit residues: 583.2028 Evaluate side-chains 411 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 400 time to evaluate : 3.106 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.6071 time to fit residues: 15.2783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 313 optimal weight: 5.9990 chunk 238 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 151 optimal weight: 0.6980 chunk 213 optimal weight: 3.9990 chunk 318 optimal weight: 4.9990 chunk 337 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 301 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN C 700 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 27314 Z= 0.294 Angle : 0.531 6.337 37090 Z= 0.278 Chirality : 0.041 0.163 4378 Planarity : 0.003 0.047 4744 Dihedral : 4.025 23.563 3730 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.03 (0.14), residues: 3512 helix: 1.05 (0.12), residues: 2009 sheet: -1.25 (0.24), residues: 435 loop : -1.30 (0.19), residues: 1068 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7024 Ramachandran restraints generated. 3512 Oldfield, 0 Emsley, 3512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7024 Ramachandran restraints generated. 3512 Oldfield, 0 Emsley, 3512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 430 time to evaluate : 3.154 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 outliers start: 19 outliers final: 10 residues processed: 443 average time/residue: 0.8048 time to fit residues: 548.9279 Evaluate side-chains 415 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 405 time to evaluate : 3.162 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4968 time to fit residues: 13.0848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 280 optimal weight: 8.9990 chunk 191 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 287 optimal weight: 0.9990 chunk 233 optimal weight: 0.0270 chunk 0 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 302 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN B 194 ASN E 112 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 27314 Z= 0.200 Angle : 0.490 6.102 37090 Z= 0.254 Chirality : 0.040 0.150 4378 Planarity : 0.003 0.047 4744 Dihedral : 3.898 22.630 3730 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.41 (0.15), residues: 3512 helix: 1.32 (0.12), residues: 2009 sheet: -1.00 (0.25), residues: 418 loop : -1.09 (0.20), residues: 1085 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7024 Ramachandran restraints generated. 3512 Oldfield, 0 Emsley, 3512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7024 Ramachandran restraints generated. 3512 Oldfield, 0 Emsley, 3512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 427 time to evaluate : 3.126 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 outliers start: 13 outliers final: 9 residues processed: 435 average time/residue: 0.8233 time to fit residues: 554.9540 Evaluate side-chains 415 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 406 time to evaluate : 3.144 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.5559 time to fit residues: 12.9340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 113 optimal weight: 2.9990 chunk 303 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 337 optimal weight: 9.9990 chunk 280 optimal weight: 8.9990 chunk 156 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 GLN B 120 GLN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 27314 Z= 0.291 Angle : 0.522 6.257 37090 Z= 0.273 Chirality : 0.041 0.151 4378 Planarity : 0.003 0.049 4744 Dihedral : 3.977 22.917 3730 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.47 (0.15), residues: 3512 helix: 1.33 (0.12), residues: 2017 sheet: -1.01 (0.25), residues: 433 loop : -1.00 (0.20), residues: 1062 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7024 Ramachandran restraints generated. 3512 Oldfield, 0 Emsley, 3512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7024 Ramachandran restraints generated. 3512 Oldfield, 0 Emsley, 3512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 406 time to evaluate : 3.178 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 outliers start: 12 outliers final: 9 residues processed: 413 average time/residue: 0.8550 time to fit residues: 547.8380 Evaluate side-chains 403 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 394 time to evaluate : 3.195 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.5163 time to fit residues: 12.7442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 325 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 284 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 336 optimal weight: 2.9990 chunk 210 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 27314 Z= 0.321 Angle : 0.533 6.185 37090 Z= 0.279 Chirality : 0.041 0.151 4378 Planarity : 0.003 0.046 4744 Dihedral : 4.065 25.384 3730 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.53 (0.15), residues: 3512 helix: 1.35 (0.12), residues: 2018 sheet: -0.99 (0.25), residues: 433 loop : -0.92 (0.20), residues: 1061 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7024 Ramachandran restraints generated. 3512 Oldfield, 0 Emsley, 3512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7024 Ramachandran restraints generated. 3512 Oldfield, 0 Emsley, 3512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 403 time to evaluate : 3.191 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 outliers start: 12 outliers final: 8 residues processed: 413 average time/residue: 0.8409 time to fit residues: 539.5682 Evaluate side-chains 404 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 396 time to evaluate : 3.141 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.5519 time to fit residues: 12.0046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 208 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 200 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 213 optimal weight: 3.9990 chunk 229 optimal weight: 0.5980 chunk 166 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 264 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 27314 Z= 0.149 Angle : 0.476 5.980 37090 Z= 0.246 Chirality : 0.040 0.149 4378 Planarity : 0.003 0.047 4744 Dihedral : 3.808 22.294 3730 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.94 (0.15), residues: 3512 helix: 1.68 (0.12), residues: 2018 sheet: -0.78 (0.25), residues: 421 loop : -0.74 (0.20), residues: 1073 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7024 Ramachandran restraints generated. 3512 Oldfield, 0 Emsley, 3512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7024 Ramachandran restraints generated. 3512 Oldfield, 0 Emsley, 3512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 419 time to evaluate : 3.223 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 outliers start: 7 outliers final: 5 residues processed: 422 average time/residue: 0.8333 time to fit residues: 542.0315 Evaluate side-chains 407 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 402 time to evaluate : 3.140 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4975 time to fit residues: 8.6947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 305 optimal weight: 0.8980 chunk 322 optimal weight: 0.0980 chunk 294 optimal weight: 0.9980 chunk 313 optimal weight: 8.9990 chunk 188 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 283 optimal weight: 1.9990 chunk 296 optimal weight: 3.9990 chunk 312 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 27314 Z= 0.203 Angle : 0.488 6.091 37090 Z= 0.252 Chirality : 0.040 0.150 4378 Planarity : 0.003 0.047 4744 Dihedral : 3.799 21.776 3730 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.06 (0.15), residues: 3512 helix: 1.76 (0.12), residues: 2016 sheet: -0.69 (0.26), residues: 415 loop : -0.70 (0.20), residues: 1081 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7024 Ramachandran restraints generated. 3512 Oldfield, 0 Emsley, 3512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7024 Ramachandran restraints generated. 3512 Oldfield, 0 Emsley, 3512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 402 time to evaluate : 3.134 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 outliers start: 3 outliers final: 2 residues processed: 402 average time/residue: 0.8259 time to fit residues: 515.9037 Evaluate side-chains 395 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 393 time to evaluate : 3.201 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4922 time to fit residues: 5.9162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 205 optimal weight: 2.9990 chunk 331 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 347 optimal weight: 0.9990 chunk 320 optimal weight: 4.9990 chunk 276 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 213 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 27314 Z= 0.233 Angle : 0.500 6.306 37090 Z= 0.259 Chirality : 0.040 0.150 4378 Planarity : 0.003 0.046 4744 Dihedral : 3.817 21.725 3730 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.09 (0.15), residues: 3512 helix: 1.78 (0.12), residues: 2018 sheet: -0.73 (0.26), residues: 415 loop : -0.63 (0.20), residues: 1079 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7024 Ramachandran restraints generated. 3512 Oldfield, 0 Emsley, 3512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7024 Ramachandran restraints generated. 3512 Oldfield, 0 Emsley, 3512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 401 time to evaluate : 3.252 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 outliers start: 4 outliers final: 2 residues processed: 404 average time/residue: 0.8624 time to fit residues: 544.8447 Evaluate side-chains 395 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 393 time to evaluate : 3.172 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5128 time to fit residues: 5.9714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 219 optimal weight: 4.9990 chunk 294 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 255 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 277 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.109387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.086063 restraints weight = 105640.307| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.60 r_work: 0.2789 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 27314 Z= 0.270 Angle : 0.513 6.238 37090 Z= 0.268 Chirality : 0.040 0.149 4378 Planarity : 0.003 0.083 4744 Dihedral : 3.899 22.056 3730 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.08 (0.15), residues: 3512 helix: 1.76 (0.12), residues: 2019 sheet: -0.72 (0.26), residues: 420 loop : -0.63 (0.20), residues: 1073 =============================================================================== Job complete usr+sys time: 10828.69 seconds wall clock time: 187 minutes 26.98 seconds (11246.98 seconds total)