Starting phenix.real_space_refine on Sun Mar 10 21:38:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgr_10182/03_2024/6sgr_10182.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgr_10182/03_2024/6sgr_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_10182/03_2024/6sgr_10182.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgr_10182/03_2024/6sgr_10182.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgr_10182/03_2024/6sgr_10182.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgr_10182/03_2024/6sgr_10182.pdb" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 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. 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-5265/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: 17.25, per 1000 atoms: 0.32 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: 31.71 Conformation dependent library (CDL) restraints added in 4.0 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: 3.40 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: 21.19 Time building geometry restraints manager: 33.52 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: 22657 17.84 - 35.68: 2152 35.68 - 53.53: 598 53.53 - 71.37: 158 71.37 - 89.21: 35 Dihedral angle restraints: 25600 sinusoidal: 14002 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 25597 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 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: 1.030 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: 0.670 Extract box with map and model: 7.760 Check model and map are aligned: 0.580 Set scattering table: 0.370 Process input model: 128.240 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 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 % Allowed : 1.26 % Favored : 98.74 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 895 HIS 0.003 0.001 HIS E 85 PHE 0.017 0.001 PHE B 11 TYR 0.013 0.001 TYR C 327 ARG 0.003 0.000 ARG A 363 *********************** 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 : 3.152 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 REVERT: A 626 ILE cc_start: 0.8862 (mt) cc_final: 0.8637 (tt) REVERT: B 69 MET cc_start: 0.8131 (mmp) cc_final: 0.7903 (mmp) REVERT: B 361 ASN cc_start: 0.7700 (p0) cc_final: 0.7275 (p0) REVERT: B 417 GLU cc_start: 0.6949 (tp30) cc_final: 0.6744 (tp30) REVERT: B 527 TYR cc_start: 0.8741 (t80) cc_final: 0.8497 (t80) REVERT: B 648 THR cc_start: 0.8600 (m) cc_final: 0.8382 (m) REVERT: B 686 ASP cc_start: 0.7773 (p0) cc_final: 0.7221 (p0) REVERT: C 813 SER cc_start: 0.8218 (m) cc_final: 0.7681 (p) REVERT: E 144 LYS cc_start: 0.8100 (ptmt) cc_final: 0.7776 (ttpp) outliers start: 0 outliers final: 0 residues processed: 622 average time/residue: 0.8586 time to fit residues: 806.1434 Evaluate side-chains 434 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 434 time to evaluate : 3.049 ------------------------------------------------------------------------------- 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: 0.5980 chunk 264 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 273 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 chunk 316 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.8200 moved from start: 0.2020 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= 0.245 Angle : 0.531 6.363 37090 Z= 0.278 Chirality : 0.041 0.155 4378 Planarity : 0.004 0.059 4744 Dihedral : 4.125 24.009 3730 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.80 % Allowed : 6.22 % Favored : 92.97 % 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: 0.10 (0.11), residues: 2007 sheet: -1.49 (0.24), residues: 410 loop : -2.18 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 789 HIS 0.005 0.001 HIS E 125 PHE 0.022 0.001 PHE B 666 TYR 0.013 0.001 TYR A 157 ARG 0.004 0.000 ARG A 653 *********************** 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 475 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 452 time to evaluate : 3.113 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: A 626 ILE cc_start: 0.9112 (mt) cc_final: 0.8843 (tt) REVERT: A 657 GLN cc_start: 0.6779 (tm-30) cc_final: 0.6437 (tm-30) REVERT: B 573 MET cc_start: 0.7643 (mtp) cc_final: 0.7203 (mtt) REVERT: B 648 THR cc_start: 0.8695 (m) cc_final: 0.8480 (m) REVERT: B 686 ASP cc_start: 0.7799 (p0) cc_final: 0.7380 (p0) REVERT: B 953 MET cc_start: 0.8733 (mtp) cc_final: 0.8517 (mtp) REVERT: C 813 SER cc_start: 0.8364 (m) cc_final: 0.7907 (p) REVERT: D 109 LYS cc_start: 0.8399 (mtpt) cc_final: 0.8128 (mmmt) REVERT: E 144 LYS cc_start: 0.8268 (ptmt) cc_final: 0.7889 (ttpp) outliers start: 23 outliers final: 20 residues processed: 468 average time/residue: 0.8152 time to fit residues: 588.5501 Evaluate side-chains 433 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 413 time to evaluate : 3.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 817 GLU Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 860 THR Chi-restraints excluded: chain H residue 1 MET 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: 1.9990 chunk 215 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 317 optimal weight: 6.9990 chunk 342 optimal weight: 1.9990 chunk 282 optimal weight: 4.9990 chunk 314 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 254 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 194 ASN C 228 GLN C 274 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27314 Z= 0.242 Angle : 0.509 6.208 37090 Z= 0.266 Chirality : 0.041 0.150 4378 Planarity : 0.004 0.047 4744 Dihedral : 3.989 23.649 3730 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.01 % Allowed : 7.76 % Favored : 91.22 % 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: -0.30 (0.14), residues: 3512 helix: 0.82 (0.12), residues: 2010 sheet: -1.28 (0.24), residues: 418 loop : -1.59 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 754 HIS 0.003 0.001 HIS E 52 PHE 0.017 0.001 PHE B 352 TYR 0.011 0.001 TYR A 157 ARG 0.007 0.000 ARG A 653 *********************** 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 468 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 439 time to evaluate : 3.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 ARG cc_start: 0.8071 (ttt180) cc_final: 0.7649 (tmm-80) REVERT: A 626 ILE cc_start: 0.9092 (mt) cc_final: 0.8843 (tt) REVERT: A 657 GLN cc_start: 0.6791 (tm-30) cc_final: 0.6517 (tm-30) REVERT: A 937 LEU cc_start: 0.8733 (mt) cc_final: 0.8402 (mp) REVERT: B 648 THR cc_start: 0.8785 (m) cc_final: 0.8539 (m) REVERT: B 953 MET cc_start: 0.8774 (mtp) cc_final: 0.8444 (mtp) REVERT: C 163 LYS cc_start: 0.9068 (tttt) cc_final: 0.8775 (tttm) REVERT: C 813 SER cc_start: 0.8560 (m) cc_final: 0.8301 (p) REVERT: E 144 LYS cc_start: 0.8326 (ptmt) cc_final: 0.7946 (ttpp) outliers start: 29 outliers final: 24 residues processed: 461 average time/residue: 0.7854 time to fit residues: 557.8585 Evaluate side-chains 424 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 400 time to evaluate : 3.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain H residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 313 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 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: 2.5388 ------------------------------------------------------------------------------- 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 B 588 GLN C 700 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 27314 Z= 0.328 Angle : 0.536 6.340 37090 Z= 0.282 Chirality : 0.042 0.152 4378 Planarity : 0.004 0.045 4744 Dihedral : 4.044 23.923 3730 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.43 % Allowed : 8.67 % Favored : 89.90 % 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: 0.99 (0.12), residues: 2009 sheet: -1.18 (0.24), residues: 418 loop : -1.36 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 789 HIS 0.004 0.001 HIS D 89 PHE 0.017 0.001 PHE A 682 TYR 0.014 0.001 TYR A 157 ARG 0.004 0.000 ARG A1030 *********************** 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 474 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 433 time to evaluate : 3.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 ASN cc_start: 0.7048 (t0) cc_final: 0.6798 (t0) REVERT: A 657 GLN cc_start: 0.6853 (tm-30) cc_final: 0.6522 (tm-30) REVERT: B 69 MET cc_start: 0.8429 (mmp) cc_final: 0.8152 (mmt) REVERT: B 648 THR cc_start: 0.8873 (m) cc_final: 0.8602 (m) REVERT: B 673 GLU cc_start: 0.7572 (pm20) cc_final: 0.7351 (mp0) REVERT: B 1011 MET cc_start: 0.8838 (mmp) cc_final: 0.8592 (mmp) REVERT: C 21 LEU cc_start: 0.8819 (tp) cc_final: 0.8611 (mp) REVERT: C 112 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.6651 (mp10) REVERT: C 163 LYS cc_start: 0.9100 (tttt) cc_final: 0.8825 (tttm) REVERT: E 144 LYS cc_start: 0.8372 (ptmt) cc_final: 0.7993 (ttpp) outliers start: 41 outliers final: 31 residues processed: 463 average time/residue: 0.7587 time to fit residues: 545.7127 Evaluate side-chains 444 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 412 time to evaluate : 3.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 540 ARG Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 817 GLU Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 519 MET Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain C residue 977 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 82 THR 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: 0.7980 chunk 4 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 287 optimal weight: 0.9990 chunk 233 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 302 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3505 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= 0.278 Angle : 0.515 6.164 37090 Z= 0.269 Chirality : 0.041 0.154 4378 Planarity : 0.004 0.046 4744 Dihedral : 4.006 22.988 3730 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.57 % Allowed : 9.79 % Favored : 88.64 % 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: 0.29 (0.15), residues: 3512 helix: 1.21 (0.12), residues: 2011 sheet: -1.05 (0.25), residues: 425 loop : -1.12 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 515 HIS 0.003 0.001 HIS E 52 PHE 0.017 0.001 PHE A 682 TYR 0.011 0.001 TYR C 892 ARG 0.003 0.000 ARG A1030 *********************** 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 469 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 424 time to evaluate : 3.051 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: A 192 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7507 (mm-30) REVERT: A 657 GLN cc_start: 0.6878 (tm-30) cc_final: 0.6592 (tm-30) REVERT: B 648 THR cc_start: 0.8894 (m) cc_final: 0.8595 (m) REVERT: B 673 GLU cc_start: 0.7544 (pm20) cc_final: 0.7324 (mp0) REVERT: B 1011 MET cc_start: 0.8844 (mmp) cc_final: 0.8547 (mmp) REVERT: C 21 LEU cc_start: 0.8892 (tp) cc_final: 0.8626 (mp) REVERT: C 163 LYS cc_start: 0.9100 (tttt) cc_final: 0.8800 (tttm) REVERT: C 226 LYS cc_start: 0.8416 (mptt) cc_final: 0.8178 (mmtp) REVERT: C 676 THR cc_start: 0.8390 (OUTLIER) cc_final: 0.8086 (m) REVERT: C 774 MET cc_start: 0.8932 (ttt) cc_final: 0.8567 (ttt) REVERT: E 144 LYS cc_start: 0.8379 (ptmt) cc_final: 0.8031 (ttpp) outliers start: 45 outliers final: 37 residues processed: 458 average time/residue: 0.7668 time to fit residues: 547.0414 Evaluate side-chains 441 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 403 time to evaluate : 3.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 540 ARG Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 817 GLU Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 714 THR Chi-restraints excluded: chain C residue 860 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain C residue 977 MET Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 82 THR 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: 3.9990 chunk 66 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 337 optimal weight: 10.0000 chunk 280 optimal weight: 8.9990 chunk 156 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 177 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN B 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 27314 Z= 0.344 Angle : 0.545 6.354 37090 Z= 0.287 Chirality : 0.042 0.152 4378 Planarity : 0.004 0.049 4744 Dihedral : 4.097 23.218 3730 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.78 % Allowed : 10.35 % Favored : 87.87 % 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: 0.32 (0.15), residues: 3512 helix: 1.20 (0.12), residues: 2016 sheet: -1.04 (0.25), residues: 424 loop : -1.05 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 789 HIS 0.005 0.001 HIS D 89 PHE 0.019 0.001 PHE B 11 TYR 0.014 0.001 TYR A 157 ARG 0.009 0.000 ARG C 432 *********************** 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 458 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 407 time to evaluate : 3.635 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: A 192 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7531 (mm-30) REVERT: A 447 MET cc_start: 0.8427 (mmm) cc_final: 0.8000 (mmm) REVERT: A 657 GLN cc_start: 0.6916 (tm-30) cc_final: 0.6630 (tm-30) REVERT: B 192 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7180 (mp0) REVERT: B 648 THR cc_start: 0.8930 (m) cc_final: 0.8619 (m) REVERT: B 673 GLU cc_start: 0.7506 (pm20) cc_final: 0.7268 (mp0) REVERT: B 1011 MET cc_start: 0.8971 (mmp) cc_final: 0.8623 (mmp) REVERT: C 21 LEU cc_start: 0.8849 (tp) cc_final: 0.8561 (mp) REVERT: C 163 LYS cc_start: 0.9139 (tttt) cc_final: 0.8821 (tttm) REVERT: C 676 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8078 (m) REVERT: C 774 MET cc_start: 0.8985 (ttt) cc_final: 0.8691 (ttt) REVERT: E 144 LYS cc_start: 0.8407 (ptmt) cc_final: 0.8083 (ttpp) outliers start: 51 outliers final: 41 residues processed: 445 average time/residue: 0.7739 time to fit residues: 535.7927 Evaluate side-chains 436 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 393 time to evaluate : 3.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 540 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 817 GLU Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 714 THR Chi-restraints excluded: chain C residue 860 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain C residue 977 MET Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain F residue 4 LEU 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: 0.7980 chunk 284 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 chunk 336 optimal weight: 7.9990 chunk 210 optimal weight: 0.7980 chunk 205 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 27314 Z= 0.234 Angle : 0.501 6.060 37090 Z= 0.262 Chirality : 0.040 0.150 4378 Planarity : 0.003 0.046 4744 Dihedral : 3.979 23.305 3730 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.50 % Allowed : 11.26 % Favored : 87.24 % 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: 0.62 (0.15), residues: 3512 helix: 1.42 (0.12), residues: 2017 sheet: -0.86 (0.25), residues: 424 loop : -0.90 (0.20), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 789 HIS 0.003 0.001 HIS E 52 PHE 0.016 0.001 PHE B 682 TYR 0.011 0.001 TYR B 790 ARG 0.006 0.000 ARG C 432 *********************** 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 454 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 411 time to evaluate : 3.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASP cc_start: 0.8846 (t70) cc_final: 0.8585 (t0) REVERT: A 447 MET cc_start: 0.8448 (mmm) cc_final: 0.8034 (mmm) REVERT: A 657 GLN cc_start: 0.6906 (tm-30) cc_final: 0.6636 (tm-30) REVERT: B 153 ASP cc_start: 0.7759 (m-30) cc_final: 0.7307 (m-30) REVERT: B 335 ILE cc_start: 0.8671 (tp) cc_final: 0.8339 (tp) REVERT: B 648 THR cc_start: 0.8912 (m) cc_final: 0.8601 (m) REVERT: B 673 GLU cc_start: 0.7463 (pm20) cc_final: 0.7199 (mp0) REVERT: B 1011 MET cc_start: 0.8951 (mmp) cc_final: 0.8600 (mmp) REVERT: C 21 LEU cc_start: 0.8852 (tp) cc_final: 0.8592 (mp) REVERT: C 163 LYS cc_start: 0.9119 (tttt) cc_final: 0.8808 (tttm) REVERT: C 537 SER cc_start: 0.8253 (m) cc_final: 0.7715 (p) REVERT: C 676 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8082 (m) REVERT: C 774 MET cc_start: 0.8997 (ttt) cc_final: 0.8710 (ttt) REVERT: E 144 LYS cc_start: 0.8382 (ptmt) cc_final: 0.8063 (ttpp) outliers start: 43 outliers final: 41 residues processed: 442 average time/residue: 0.7922 time to fit residues: 548.1170 Evaluate side-chains 444 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 402 time to evaluate : 3.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 540 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 817 GLU Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 471 SER Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 860 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain C residue 977 MET Chi-restraints excluded: chain C residue 993 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain F residue 4 LEU 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: 1.9990 chunk 200 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 213 optimal weight: 4.9990 chunk 229 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 264 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 830 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 27314 Z= 0.187 Angle : 0.484 6.063 37090 Z= 0.251 Chirality : 0.040 0.150 4378 Planarity : 0.003 0.046 4744 Dihedral : 3.844 21.742 3730 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.43 % Allowed : 11.64 % Favored : 86.92 % 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: 0.89 (0.15), residues: 3512 helix: 1.62 (0.12), residues: 2017 sheet: -0.73 (0.26), residues: 412 loop : -0.77 (0.20), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 515 HIS 0.003 0.001 HIS E 52 PHE 0.021 0.001 PHE G 33 TYR 0.013 0.001 TYR A 892 ARG 0.005 0.000 ARG C 432 *********************** 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 458 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 417 time to evaluate : 3.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASP cc_start: 0.8808 (t70) cc_final: 0.8561 (t0) REVERT: A 447 MET cc_start: 0.8477 (mmm) cc_final: 0.8084 (mmm) REVERT: A 657 GLN cc_start: 0.6881 (tm-30) cc_final: 0.6613 (tm-30) REVERT: B 84 SER cc_start: 0.8243 (p) cc_final: 0.7977 (t) REVERT: B 335 ILE cc_start: 0.8652 (tp) cc_final: 0.8320 (tp) REVERT: B 648 THR cc_start: 0.8895 (m) cc_final: 0.8589 (m) REVERT: B 673 GLU cc_start: 0.7498 (pm20) cc_final: 0.7206 (mp0) REVERT: C 21 LEU cc_start: 0.8839 (tp) cc_final: 0.8581 (mp) REVERT: C 112 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.6902 (mp10) REVERT: C 163 LYS cc_start: 0.9109 (tttt) cc_final: 0.8812 (tttm) REVERT: C 537 SER cc_start: 0.8234 (m) cc_final: 0.7708 (p) REVERT: C 774 MET cc_start: 0.8997 (ttt) cc_final: 0.8701 (ttt) REVERT: E 144 LYS cc_start: 0.8390 (ptmt) cc_final: 0.8067 (ttpp) outliers start: 41 outliers final: 34 residues processed: 446 average time/residue: 0.7852 time to fit residues: 546.2102 Evaluate side-chains 439 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 404 time to evaluate : 3.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 540 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 817 GLU Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 471 SER Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain C residue 977 MET Chi-restraints excluded: chain C residue 993 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain H residue 29 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 305 optimal weight: 2.9990 chunk 322 optimal weight: 2.9990 chunk 294 optimal weight: 0.9980 chunk 313 optimal weight: 0.1980 chunk 188 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 246 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 283 optimal weight: 1.9990 chunk 296 optimal weight: 3.9990 chunk 312 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 692 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27314 Z= 0.187 Angle : 0.483 6.056 37090 Z= 0.250 Chirality : 0.040 0.149 4378 Planarity : 0.003 0.046 4744 Dihedral : 3.794 21.159 3730 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.33 % Allowed : 12.06 % Favored : 86.61 % 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: 1.75 (0.12), residues: 2017 sheet: -0.63 (0.26), residues: 420 loop : -0.64 (0.20), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 789 HIS 0.003 0.001 HIS E 52 PHE 0.016 0.001 PHE B 682 TYR 0.011 0.001 TYR B 790 ARG 0.005 0.000 ARG C 432 *********************** 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 447 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 409 time to evaluate : 3.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASP cc_start: 0.8816 (t70) cc_final: 0.8600 (t0) REVERT: A 657 GLN cc_start: 0.6887 (tm-30) cc_final: 0.6624 (tm-30) REVERT: B 335 ILE cc_start: 0.8653 (tp) cc_final: 0.8331 (tp) REVERT: B 648 THR cc_start: 0.8909 (m) cc_final: 0.8595 (m) REVERT: B 902 MET cc_start: 0.8560 (mtm) cc_final: 0.8352 (mtp) REVERT: C 21 LEU cc_start: 0.8847 (tp) cc_final: 0.8590 (mp) REVERT: C 112 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.6907 (mp10) REVERT: C 163 LYS cc_start: 0.9112 (tttt) cc_final: 0.8826 (tttm) REVERT: C 537 SER cc_start: 0.8248 (m) cc_final: 0.7722 (p) REVERT: C 676 THR cc_start: 0.8390 (OUTLIER) cc_final: 0.8080 (m) REVERT: C 774 MET cc_start: 0.8998 (ttt) cc_final: 0.8697 (ttt) outliers start: 38 outliers final: 35 residues processed: 436 average time/residue: 0.7481 time to fit residues: 510.8275 Evaluate side-chains 437 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 400 time to evaluate : 3.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 540 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 817 GLU Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 471 SER Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain C residue 977 MET Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain H residue 29 LEU 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: 4.9990 chunk 202 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 347 optimal weight: 0.6980 chunk 320 optimal weight: 4.9990 chunk 276 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 27314 Z= 0.335 Angle : 0.538 6.272 37090 Z= 0.282 Chirality : 0.042 0.162 4378 Planarity : 0.004 0.043 4744 Dihedral : 3.989 22.315 3730 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.36 % Allowed : 11.75 % Favored : 86.89 % 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: 0.88 (0.15), residues: 3512 helix: 1.58 (0.12), residues: 2018 sheet: -0.77 (0.26), residues: 431 loop : -0.68 (0.20), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 789 HIS 0.004 0.001 HIS D 89 PHE 0.020 0.001 PHE B 11 TYR 0.016 0.001 TYR B 790 ARG 0.005 0.000 ARG C 432 ********************** 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 437 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 398 time to evaluate : 3.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASP cc_start: 0.8908 (t70) cc_final: 0.8682 (t0) REVERT: A 657 GLN cc_start: 0.6932 (tm-30) cc_final: 0.6690 (tm-30) REVERT: B 84 SER cc_start: 0.8329 (p) cc_final: 0.8062 (t) REVERT: B 335 ILE cc_start: 0.8802 (tp) cc_final: 0.8450 (tp) REVERT: B 648 THR cc_start: 0.8961 (m) cc_final: 0.8635 (m) REVERT: C 21 LEU cc_start: 0.8825 (tp) cc_final: 0.8496 (mp) REVERT: C 163 LYS cc_start: 0.9146 (tttt) cc_final: 0.8837 (tttm) REVERT: C 537 SER cc_start: 0.8469 (m) cc_final: 0.7891 (p) REVERT: C 676 THR cc_start: 0.8390 (OUTLIER) cc_final: 0.8090 (m) REVERT: C 774 MET cc_start: 0.9005 (ttt) cc_final: 0.8699 (ttt) REVERT: E 144 LYS cc_start: 0.8601 (ptpt) cc_final: 0.8332 (ttpp) outliers start: 39 outliers final: 36 residues processed: 427 average time/residue: 0.7912 time to fit residues: 529.3718 Evaluate side-chains 430 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 393 time to evaluate : 3.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 540 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 817 GLU Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 471 SER Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain C residue 977 MET Chi-restraints excluded: chain C residue 993 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain H residue 29 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 219 optimal weight: 3.9990 chunk 294 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 chunk 255 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 277 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 284 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.108907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.085671 restraints weight = 106018.101| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.63 r_work: 0.2809 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27314 Z= 0.214 Angle : 0.498 6.071 37090 Z= 0.259 Chirality : 0.040 0.147 4378 Planarity : 0.003 0.044 4744 Dihedral : 3.897 21.593 3730 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.26 % Allowed : 12.13 % Favored : 86.61 % 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: 1.72 (0.12), residues: 2019 sheet: -0.69 (0.26), residues: 431 loop : -0.58 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 515 HIS 0.003 0.001 HIS E 52 PHE 0.017 0.001 PHE B 682 TYR 0.017 0.001 TYR B 790 ARG 0.005 0.000 ARG C 432 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10736.91 seconds wall clock time: 186 minutes 5.96 seconds (11165.96 seconds total)