Starting phenix.real_space_refine on Tue Mar 19 07:49:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tw1_26147/03_2024/7tw1_26147.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tw1_26147/03_2024/7tw1_26147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tw1_26147/03_2024/7tw1_26147.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tw1_26147/03_2024/7tw1_26147.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tw1_26147/03_2024/7tw1_26147.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tw1_26147/03_2024/7tw1_26147.pdb" } resolution = 4.6 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 15249 2.51 5 N 4037 2.21 5 O 4243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 669": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23625 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6582 Classifications: {'peptide': 833} Link IDs: {'PTRANS': 50, 'TRANS': 782} Chain breaks: 3 Chain: "A" Number of atoms: 6563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 830, 6563 Classifications: {'peptide': 830} Link IDs: {'PTRANS': 49, 'TRANS': 780} Chain breaks: 3 Chain: "E" Number of atoms: 5240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5240 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 31, 'TRANS': 633} Chain breaks: 2 Chain: "F" Number of atoms: 5240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5240 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 31, 'TRANS': 633} Chain breaks: 2 Time building chain proxies: 11.97, per 1000 atoms: 0.51 Number of scatterers: 23625 At special positions: 0 Unit cell: (146.3, 155.1, 185.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 4243 8.00 N 4037 7.00 C 15249 6.00 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: 8.25 Conformation dependent library (CDL) restraints added in 4.1 seconds 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5606 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 29 sheets defined 43.0% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'B' and resid 42 through 47 removed outlier: 3.639A pdb=" N HIS B 47 " --> pdb=" O THR B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 115 Processing helix chain 'B' and resid 127 through 142 Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 149 through 158 removed outlier: 3.553A pdb=" N ARG B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 277 through 291 removed outlier: 3.738A pdb=" N GLU B 291 " --> pdb=" O THR B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 303 through 317 removed outlier: 4.262A pdb=" N LEU B 307 " --> pdb=" O SER B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 333 Processing helix chain 'B' and resid 335 through 347 removed outlier: 4.058A pdb=" N GLN B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 390 Processing helix chain 'B' and resid 392 through 399 Processing helix chain 'B' and resid 402 through 431 removed outlier: 3.774A pdb=" N LEU B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Proline residue: B 419 - end of helix Processing helix chain 'B' and resid 437 through 455 removed outlier: 3.815A pdb=" N PHE B 451 " --> pdb=" O GLN B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 483 Processing helix chain 'B' and resid 488 through 507 removed outlier: 4.305A pdb=" N TRP B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 516 removed outlier: 4.267A pdb=" N PHE B 511 " --> pdb=" O GLU B 508 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU B 512 " --> pdb=" O GLY B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 547 removed outlier: 3.500A pdb=" N GLN B 521 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 593 removed outlier: 4.102A pdb=" N ASN B 593 " --> pdb=" O ARG B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 607 Processing helix chain 'B' and resid 608 through 624 Processing helix chain 'B' and resid 660 through 667 Processing helix chain 'B' and resid 668 through 690 removed outlier: 3.612A pdb=" N LEU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER B 690 " --> pdb=" O THR B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 695 removed outlier: 3.585A pdb=" N LYS B 695 " --> pdb=" O PRO B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 720 removed outlier: 3.687A pdb=" N LEU B 706 " --> pdb=" O PHE B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 738 removed outlier: 3.508A pdb=" N LEU B 738 " --> pdb=" O HIS B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 773 removed outlier: 3.561A pdb=" N LEU B 764 " --> pdb=" O ARG B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 784 through 799 removed outlier: 4.402A pdb=" N LEU B 788 " --> pdb=" O PRO B 784 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 789 " --> pdb=" O LEU B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 812 Processing helix chain 'B' and resid 815 through 819 removed outlier: 3.543A pdb=" N TYR B 818 " --> pdb=" O PRO B 815 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS B 819 " --> pdb=" O PRO B 816 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 815 through 819' Processing helix chain 'B' and resid 822 through 827 Processing helix chain 'B' and resid 829 through 853 Processing helix chain 'B' and resid 855 through 857 No H-bonds generated for 'chain 'B' and resid 855 through 857' Processing helix chain 'B' and resid 858 through 873 removed outlier: 3.746A pdb=" N VAL B 862 " --> pdb=" O ALA B 858 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 863 " --> pdb=" O LEU B 859 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL B 867 " --> pdb=" O LEU B 863 " (cutoff:3.500A) Proline residue: B 868 - end of helix removed outlier: 3.992A pdb=" N ARG B 871 " --> pdb=" O VAL B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 877 Processing helix chain 'B' and resid 879 through 887 removed outlier: 3.666A pdb=" N ASP B 887 " --> pdb=" O LEU B 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 removed outlier: 3.504A pdb=" N ASP A 45 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS A 47 " --> pdb=" O THR A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 116 removed outlier: 4.180A pdb=" N LYS A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 149 through 158 Processing helix chain 'A' and resid 164 through 171 removed outlier: 4.439A pdb=" N GLU A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 201 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 277 through 290 Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 303 through 317 removed outlier: 3.920A pdb=" N LEU A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 334 Processing helix chain 'A' and resid 335 through 347 removed outlier: 3.687A pdb=" N TYR A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 390 Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 402 through 431 removed outlier: 3.813A pdb=" N LEU A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 437 through 455 Processing helix chain 'A' and resid 465 through 483 Processing helix chain 'A' and resid 488 through 507 removed outlier: 4.186A pdb=" N TRP A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 517 through 547 removed outlier: 3.548A pdb=" N GLN A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 593 removed outlier: 4.035A pdb=" N ASN A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 608 removed outlier: 4.234A pdb=" N PHE A 608 " --> pdb=" O VAL A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 624 Processing helix chain 'A' and resid 660 through 667 Processing helix chain 'A' and resid 668 through 690 removed outlier: 3.574A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 695 removed outlier: 3.615A pdb=" N ARG A 694 " --> pdb=" O LYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 719 removed outlier: 3.503A pdb=" N LEU A 706 " --> pdb=" O PHE A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 738 Processing helix chain 'A' and resid 760 through 773 Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 784 through 799 removed outlier: 4.172A pdb=" N LEU A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 removed outlier: 4.096A pdb=" N PHE A 813 " --> pdb=" O ILE A 809 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 819 removed outlier: 3.530A pdb=" N HIS A 819 " --> pdb=" O PRO A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 827 removed outlier: 3.678A pdb=" N LYS A 826 " --> pdb=" O VAL A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 853 Processing helix chain 'A' and resid 855 through 857 No H-bonds generated for 'chain 'A' and resid 855 through 857' Processing helix chain 'A' and resid 858 through 865 removed outlier: 3.741A pdb=" N VAL A 862 " --> pdb=" O ALA A 858 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 872 removed outlier: 3.652A pdb=" N LEU A 869 " --> pdb=" O LEU A 865 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG A 871 " --> pdb=" O VAL A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 877 Processing helix chain 'A' and resid 879 through 887 removed outlier: 3.558A pdb=" N ASP A 887 " --> pdb=" O LEU A 883 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 21 removed outlier: 3.513A pdb=" N ASN E 17 " --> pdb=" O GLN E 13 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N GLU E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 58 removed outlier: 3.628A pdb=" N LYS E 58 " --> pdb=" O PRO E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 159 Processing helix chain 'E' and resid 187 through 197 Processing helix chain 'E' and resid 201 through 205 Processing helix chain 'E' and resid 207 through 227 removed outlier: 3.596A pdb=" N VAL E 211 " --> pdb=" O GLN E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 242 Processing helix chain 'E' and resid 248 through 258 Processing helix chain 'E' and resid 269 through 283 removed outlier: 4.329A pdb=" N ALA E 273 " --> pdb=" O TRP E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 374 Processing helix chain 'E' and resid 382 through 388 Processing helix chain 'E' and resid 432 through 435 Processing helix chain 'E' and resid 441 through 458 removed outlier: 3.640A pdb=" N LYS E 445 " --> pdb=" O SER E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 550 through 552 No H-bonds generated for 'chain 'E' and resid 550 through 552' Processing helix chain 'F' and resid 13 through 21 removed outlier: 3.509A pdb=" N ASN F 17 " --> pdb=" O GLN F 13 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLU F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 58 removed outlier: 3.625A pdb=" N LYS F 58 " --> pdb=" O PRO F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 159 Processing helix chain 'F' and resid 187 through 197 Processing helix chain 'F' and resid 201 through 205 Processing helix chain 'F' and resid 207 through 227 Processing helix chain 'F' and resid 238 through 242 Processing helix chain 'F' and resid 248 through 258 Processing helix chain 'F' and resid 269 through 283 removed outlier: 4.282A pdb=" N ALA F 273 " --> pdb=" O TRP F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 374 Processing helix chain 'F' and resid 382 through 388 Processing helix chain 'F' and resid 432 through 435 Processing helix chain 'F' and resid 441 through 458 removed outlier: 3.635A pdb=" N LYS F 445 " --> pdb=" O SER F 441 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU F 457 " --> pdb=" O LYS F 453 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 552 No H-bonds generated for 'chain 'F' and resid 550 through 552' Processing sheet with id=AA1, first strand: chain 'B' and resid 35 through 36 removed outlier: 3.941A pdb=" N ALA B 35 " --> pdb=" O ARG F 638 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA F 598 " --> pdb=" O VAL F 685 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 85 through 87 removed outlier: 7.199A pdb=" N LEU B 61 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG B 80 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 59 " --> pdb=" O ARG B 80 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N SER B 224 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N PHE B 264 " --> pdb=" O SER B 224 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA B 226 " --> pdb=" O PHE B 264 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N PHE B 266 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU B 228 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU B 268 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU B 230 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ARG B 263 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL B 119 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ARG B 246 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU B 121 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLN B 248 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU B 123 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ALA B 250 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 85 through 87 removed outlier: 7.199A pdb=" N LEU B 61 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG B 80 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 59 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 103 removed outlier: 3.523A pdb=" N VAL A 320 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 462 through 463 Processing sheet with id=AA6, first strand: chain 'B' and resid 739 through 740 Processing sheet with id=AA7, first strand: chain 'A' and resid 35 through 37 removed outlier: 4.002A pdb=" N ALA A 35 " --> pdb=" O ARG E 638 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER E 636 " --> pdb=" O HIS A 37 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ALA E 598 " --> pdb=" O VAL E 685 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 86 through 87 removed outlier: 7.164A pdb=" N LEU A 61 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ARG A 80 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL A 59 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LYS A 56 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR A 227 " --> pdb=" O LYS A 56 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N TYR A 58 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N VAL A 229 " --> pdb=" O TYR A 58 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU A 60 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N VAL A 231 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLN A 62 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ARG A 263 " --> pdb=" O SER A 224 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ALA A 226 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU A 265 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU A 228 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL A 267 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU A 230 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU A 269 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N PHE A 264 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 10.888A pdb=" N GLU A 249 " --> pdb=" O PHE A 264 " (cutoff:3.500A) removed outlier: 11.970A pdb=" N PHE A 266 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 11.764A pdb=" N LEU A 247 " --> pdb=" O PHE A 266 " (cutoff:3.500A) removed outlier: 11.448A pdb=" N LEU A 268 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 12.460A pdb=" N VAL A 245 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLN A 248 " --> pdb=" O ASP A 122 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 86 through 87 removed outlier: 7.164A pdb=" N LEU A 61 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ARG A 80 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL A 59 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AB2, first strand: chain 'A' and resid 739 through 741 Processing sheet with id=AB3, first strand: chain 'E' and resid 7 through 11 removed outlier: 6.884A pdb=" N SER E 101 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ARG E 97 " --> pdb=" O SER E 101 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR E 103 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL E 93 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER E 91 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 32 through 34 removed outlier: 6.607A pdb=" N GLN E 128 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL E 123 " --> pdb=" O GLN E 128 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU E 130 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU E 121 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY E 132 " --> pdb=" O LEU E 119 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 163 through 169 Processing sheet with id=AB6, first strand: chain 'E' and resid 362 through 367 removed outlier: 3.611A pdb=" N SER E 362 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N THR E 330 " --> pdb=" O LEU E 349 " (cutoff:3.500A) removed outlier: 12.180A pdb=" N THR E 328 " --> pdb=" O PRO E 351 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE E 323 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA E 295 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE E 325 " --> pdb=" O ALA E 293 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N VAL E 288 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LYS E 421 " --> pdb=" O VAL E 288 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N PHE E 292 " --> pdb=" O ASN E 417 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ASN E 417 " --> pdb=" O PHE E 292 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 303 through 308 removed outlier: 3.864A pdb=" N GLU E 405 " --> pdb=" O LYS E 397 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 408 through 409 removed outlier: 6.796A pdb=" N ASP E 408 " --> pdb=" O PHE E 578 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N GLN E 580 " --> pdb=" O ASP E 408 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU E 485 " --> pdb=" O CYS E 586 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 408 through 409 removed outlier: 6.796A pdb=" N ASP E 408 " --> pdb=" O PHE E 578 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N GLN E 580 " --> pdb=" O ASP E 408 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ALA E 515 " --> pdb=" O LYS E 525 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N LYS E 525 " --> pdb=" O ALA E 515 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 475 through 480 Processing sheet with id=AC2, first strand: chain 'E' and resid 591 through 593 Processing sheet with id=AC3, first strand: chain 'F' and resid 7 through 11 removed outlier: 6.899A pdb=" N SER F 101 " --> pdb=" O ARG F 97 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ARG F 97 " --> pdb=" O SER F 101 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR F 103 " --> pdb=" O GLU F 95 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL F 93 " --> pdb=" O SER F 105 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER F 91 " --> pdb=" O THR F 107 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 32 through 34 removed outlier: 6.606A pdb=" N GLN F 128 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL F 123 " --> pdb=" O GLN F 128 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU F 130 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU F 121 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY F 132 " --> pdb=" O LEU F 119 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 163 through 169 Processing sheet with id=AC6, first strand: chain 'F' and resid 362 through 367 removed outlier: 3.612A pdb=" N SER F 362 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N THR F 330 " --> pdb=" O LEU F 349 " (cutoff:3.500A) removed outlier: 12.197A pdb=" N THR F 328 " --> pdb=" O PRO F 351 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE F 323 " --> pdb=" O ALA F 295 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA F 295 " --> pdb=" O ILE F 323 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE F 325 " --> pdb=" O ALA F 293 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N VAL F 288 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LYS F 421 " --> pdb=" O VAL F 288 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE F 292 " --> pdb=" O ASN F 417 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ASN F 417 " --> pdb=" O PHE F 292 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 303 through 308 removed outlier: 3.813A pdb=" N GLU F 405 " --> pdb=" O LYS F 397 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 408 through 409 removed outlier: 6.716A pdb=" N ASP F 408 " --> pdb=" O PHE F 578 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N GLN F 580 " --> pdb=" O ASP F 408 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU F 485 " --> pdb=" O CYS F 586 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 408 through 409 removed outlier: 6.716A pdb=" N ASP F 408 " --> pdb=" O PHE F 578 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N GLN F 580 " --> pdb=" O ASP F 408 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA F 515 " --> pdb=" O LYS F 525 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LYS F 525 " --> pdb=" O ALA F 515 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 475 through 480 Processing sheet with id=AD2, first strand: chain 'F' and resid 590 through 593 1127 hydrogen bonds defined for protein. 3195 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.19 Time building geometry restraints manager: 8.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7487 1.34 - 1.46: 4703 1.46 - 1.58: 11816 1.58 - 1.70: 0 1.70 - 1.82: 152 Bond restraints: 24158 Sorted by residual: bond pdb=" N VAL B 640 " pdb=" CA VAL B 640 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.20e-02 6.94e+03 9.29e+00 bond pdb=" N VAL E 249 " pdb=" CA VAL E 249 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.23e-02 6.61e+03 7.21e+00 bond pdb=" N SER B 643 " pdb=" CA SER B 643 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.02e+00 bond pdb=" N SER E 248 " pdb=" CA SER E 248 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.28e-02 6.10e+03 5.76e+00 bond pdb=" N ASN B 642 " pdb=" CA ASN B 642 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.32e+00 ... (remaining 24153 not shown) Histogram of bond angle deviations from ideal: 94.48 - 102.41: 57 102.41 - 110.34: 5617 110.34 - 118.27: 13181 118.27 - 126.20: 13540 126.20 - 134.12: 423 Bond angle restraints: 32818 Sorted by residual: angle pdb=" N GLU F 452 " pdb=" CA GLU F 452 " pdb=" CB GLU F 452 " ideal model delta sigma weight residual 110.16 115.74 -5.58 1.48e+00 4.57e-01 1.42e+01 angle pdb=" N GLU A 312 " pdb=" CA GLU A 312 " pdb=" CB GLU A 312 " ideal model delta sigma weight residual 110.16 115.64 -5.48 1.48e+00 4.57e-01 1.37e+01 angle pdb=" CB MET B 435 " pdb=" CG MET B 435 " pdb=" SD MET B 435 " ideal model delta sigma weight residual 112.70 123.78 -11.08 3.00e+00 1.11e-01 1.36e+01 angle pdb=" C ASP A 369 " pdb=" N ASP A 370 " pdb=" CA ASP A 370 " ideal model delta sigma weight residual 120.67 125.56 -4.89 1.34e+00 5.57e-01 1.33e+01 angle pdb=" C GLN A 754 " pdb=" N GLU A 755 " pdb=" CA GLU A 755 " ideal model delta sigma weight residual 122.10 116.31 5.79 1.66e+00 3.63e-01 1.22e+01 ... (remaining 32813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 13133 17.86 - 35.71: 1140 35.71 - 53.57: 159 53.57 - 71.42: 31 71.42 - 89.28: 23 Dihedral angle restraints: 14486 sinusoidal: 5831 harmonic: 8655 Sorted by residual: dihedral pdb=" CA MET B 31 " pdb=" C MET B 31 " pdb=" N GLU B 32 " pdb=" CA GLU B 32 " ideal model delta harmonic sigma weight residual 180.00 155.70 24.30 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA HIS F 632 " pdb=" C HIS F 632 " pdb=" N ARG F 633 " pdb=" CA ARG F 633 " ideal model delta harmonic sigma weight residual -180.00 -160.35 -19.65 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA GLN F 225 " pdb=" C GLN F 225 " pdb=" N ARG F 226 " pdb=" CA ARG F 226 " ideal model delta harmonic sigma weight residual -180.00 -160.56 -19.44 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 14483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 3492 0.085 - 0.170: 274 0.170 - 0.255: 11 0.255 - 0.340: 0 0.340 - 0.425: 2 Chirality restraints: 3779 Sorted by residual: chirality pdb=" CB ILE E 284 " pdb=" CA ILE E 284 " pdb=" CG1 ILE E 284 " pdb=" CG2 ILE E 284 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" CB ILE F 284 " pdb=" CA ILE F 284 " pdb=" CG1 ILE F 284 " pdb=" CG2 ILE F 284 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CG LEU B 844 " pdb=" CB LEU B 844 " pdb=" CD1 LEU B 844 " pdb=" CD2 LEU B 844 " both_signs ideal model delta sigma weight residual False -2.59 -2.82 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 3776 not shown) Planarity restraints: 4178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 496 " -0.022 2.00e-02 2.50e+03 2.44e-02 1.49e+01 pdb=" CG TRP A 496 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP A 496 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP A 496 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 496 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 496 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 496 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 496 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 496 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 496 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 496 " 0.012 2.00e-02 2.50e+03 1.44e-02 5.18e+00 pdb=" CG TRP B 496 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP B 496 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 496 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 496 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 496 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 496 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 496 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 496 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 496 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 662 " -0.014 2.00e-02 2.50e+03 1.29e-02 4.15e+00 pdb=" CG TRP A 662 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 662 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 662 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 662 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 662 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 662 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 662 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 662 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 662 " -0.001 2.00e-02 2.50e+03 ... (remaining 4175 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 445 2.67 - 3.23: 21795 3.23 - 3.79: 36398 3.79 - 4.34: 46445 4.34 - 4.90: 76249 Nonbonded interactions: 181332 Sorted by model distance: nonbonded pdb=" O ASN B 642 " pdb=" OG SER B 643 " model vdw 2.117 2.440 nonbonded pdb=" O ALA B 571 " pdb=" OG SER B 574 " model vdw 2.221 2.440 nonbonded pdb=" O ALA A 571 " pdb=" OG SER A 574 " model vdw 2.221 2.440 nonbonded pdb=" OG1 THR B 42 " pdb=" OE2 GLU F 634 " model vdw 2.238 2.440 nonbonded pdb=" OG1 THR A 42 " pdb=" OE2 GLU E 634 " model vdw 2.256 2.440 ... (remaining 181327 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 30 through 348 or resid 369 through 894)) } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.440 Check model and map are aligned: 0.330 Set scattering table: 0.180 Process input model: 60.690 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 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 : 0.003 0.051 24158 Z= 0.201 Angle : 0.741 11.079 32818 Z= 0.376 Chirality : 0.046 0.425 3779 Planarity : 0.005 0.049 4178 Dihedral : 13.825 89.278 8880 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.08 % Allowed : 0.66 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.15), residues: 2965 helix: 0.62 (0.15), residues: 1120 sheet: 0.17 (0.20), residues: 604 loop : -0.92 (0.17), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP A 496 HIS 0.007 0.001 HIS B 55 PHE 0.033 0.001 PHE A 792 TYR 0.026 0.001 TYR A 390 ARG 0.005 0.000 ARG A 656 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 155 time to evaluate : 2.649 Fit side-chains revert: symmetry clash REVERT: B 66 MET cc_start: 0.7605 (ptp) cc_final: 0.7258 (ptp) REVERT: B 776 MET cc_start: 0.8254 (mpp) cc_final: 0.7807 (mpp) REVERT: B 787 VAL cc_start: 0.9424 (t) cc_final: 0.8851 (p) REVERT: B 792 PHE cc_start: 0.9091 (m-10) cc_final: 0.8804 (m-80) REVERT: A 471 PHE cc_start: 0.9042 (t80) cc_final: 0.8818 (t80) REVERT: A 776 MET cc_start: 0.8269 (mpp) cc_final: 0.7817 (mpp) REVERT: A 792 PHE cc_start: 0.9434 (m-80) cc_final: 0.8840 (m-80) REVERT: E 618 MET cc_start: 0.7949 (tpt) cc_final: 0.7356 (tpt) REVERT: E 667 GLU cc_start: 0.8454 (pp20) cc_final: 0.8176 (pm20) outliers start: 2 outliers final: 0 residues processed: 157 average time/residue: 0.2682 time to fit residues: 73.2757 Evaluate side-chains 124 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 251 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 125 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 152 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 233 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 270 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 559 ASN E 675 ASN ** F 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 559 ASN F 675 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24158 Z= 0.241 Angle : 0.594 7.920 32818 Z= 0.302 Chirality : 0.040 0.159 3779 Planarity : 0.004 0.043 4178 Dihedral : 4.377 19.826 3221 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 2965 helix: 0.95 (0.15), residues: 1146 sheet: 0.06 (0.20), residues: 584 loop : -0.97 (0.17), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 496 HIS 0.004 0.001 HIS F 220 PHE 0.016 0.002 PHE A 294 TYR 0.010 0.001 TYR A 390 ARG 0.004 0.001 ARG B 432 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 2.943 Fit side-chains revert: symmetry clash REVERT: B 66 MET cc_start: 0.8041 (ptp) cc_final: 0.7502 (ptp) REVERT: B 776 MET cc_start: 0.8447 (mpp) cc_final: 0.7877 (mpp) REVERT: B 792 PHE cc_start: 0.9048 (m-10) cc_final: 0.8682 (m-80) REVERT: A 696 MET cc_start: 0.4055 (tpp) cc_final: 0.3737 (tpt) REVERT: A 776 MET cc_start: 0.8419 (mpp) cc_final: 0.7853 (mpp) REVERT: A 792 PHE cc_start: 0.9308 (m-80) cc_final: 0.8913 (m-80) REVERT: E 618 MET cc_start: 0.8376 (tpt) cc_final: 0.7947 (tpp) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2754 time to fit residues: 67.4735 Evaluate side-chains 111 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 150 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 184 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 271 optimal weight: 20.0000 chunk 292 optimal weight: 8.9990 chunk 241 optimal weight: 7.9990 chunk 268 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 217 optimal weight: 0.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 593 ASN ** B 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 GLN A 642 ASN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 HIS ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 517 HIS F 220 HIS ** F 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 417 ASN ** F 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 517 HIS ** F 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24158 Z= 0.327 Angle : 0.674 13.077 32818 Z= 0.342 Chirality : 0.042 0.172 3779 Planarity : 0.005 0.040 4178 Dihedral : 4.716 21.891 3221 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.16 % Allowed : 6.48 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 2965 helix: 0.70 (0.15), residues: 1137 sheet: -0.17 (0.20), residues: 582 loop : -1.14 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 496 HIS 0.006 0.001 HIS F 220 PHE 0.020 0.002 PHE A 659 TYR 0.021 0.002 TYR B 390 ARG 0.005 0.001 ARG B 827 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 135 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 MET cc_start: 0.7981 (ptp) cc_final: 0.7675 (ppp) REVERT: B 776 MET cc_start: 0.8490 (mpp) cc_final: 0.7908 (mpp) REVERT: B 792 PHE cc_start: 0.9079 (m-10) cc_final: 0.8650 (m-80) REVERT: A 66 MET cc_start: 0.7686 (tmm) cc_final: 0.6982 (tmm) REVERT: A 776 MET cc_start: 0.8427 (mpp) cc_final: 0.7856 (mpp) REVERT: E 618 MET cc_start: 0.8210 (tpt) cc_final: 0.7898 (tpt) outliers start: 4 outliers final: 3 residues processed: 139 average time/residue: 0.2872 time to fit residues: 69.1029 Evaluate side-chains 101 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 267 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 chunk 272 optimal weight: 0.5980 chunk 288 optimal weight: 10.0000 chunk 142 optimal weight: 0.0570 chunk 257 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 683 GLN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 GLN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24158 Z= 0.142 Angle : 0.560 9.994 32818 Z= 0.274 Chirality : 0.040 0.197 3779 Planarity : 0.004 0.047 4178 Dihedral : 4.246 20.781 3221 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.04 % Allowed : 3.76 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 2965 helix: 1.09 (0.16), residues: 1149 sheet: -0.04 (0.20), residues: 582 loop : -0.96 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 496 HIS 0.004 0.001 HIS A 55 PHE 0.015 0.001 PHE A 675 TYR 0.027 0.001 TYR B 299 ARG 0.004 0.000 ARG A 656 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 2.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 MET cc_start: 0.7963 (ptp) cc_final: 0.7681 (ppp) REVERT: B 776 MET cc_start: 0.8466 (mpp) cc_final: 0.7864 (mpp) REVERT: B 792 PHE cc_start: 0.9084 (m-10) cc_final: 0.8653 (m-80) REVERT: A 66 MET cc_start: 0.7690 (tmm) cc_final: 0.7032 (tmm) REVERT: A 776 MET cc_start: 0.8520 (mpp) cc_final: 0.7900 (mpp) REVERT: A 792 PHE cc_start: 0.9520 (m-80) cc_final: 0.9007 (m-80) REVERT: E 618 MET cc_start: 0.8062 (tpt) cc_final: 0.7673 (tpt) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.2921 time to fit residues: 78.9687 Evaluate side-chains 115 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 239 optimal weight: 6.9990 chunk 163 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 245 optimal weight: 9.9990 chunk 199 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 chunk 258 optimal weight: 0.9990 chunk 72 optimal weight: 0.0070 overall best weight: 3.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24158 Z= 0.240 Angle : 0.595 11.090 32818 Z= 0.297 Chirality : 0.041 0.161 3779 Planarity : 0.004 0.039 4178 Dihedral : 4.337 21.139 3221 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 2965 helix: 1.03 (0.16), residues: 1150 sheet: -0.19 (0.20), residues: 580 loop : -1.04 (0.17), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 662 HIS 0.006 0.001 HIS A 101 PHE 0.016 0.001 PHE A 294 TYR 0.010 0.001 TYR B 299 ARG 0.004 0.000 ARG A 656 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 MET cc_start: 0.7975 (ptp) cc_final: 0.7677 (ppp) REVERT: B 776 MET cc_start: 0.8489 (mpp) cc_final: 0.7858 (mpp) REVERT: B 792 PHE cc_start: 0.9046 (m-10) cc_final: 0.8590 (m-80) REVERT: A 776 MET cc_start: 0.8472 (mpp) cc_final: 0.7871 (mpp) REVERT: A 792 PHE cc_start: 0.9527 (m-80) cc_final: 0.8848 (m-80) REVERT: E 618 MET cc_start: 0.8086 (tpt) cc_final: 0.7624 (tpt) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.3037 time to fit residues: 72.7855 Evaluate side-chains 109 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 96 optimal weight: 20.0000 chunk 259 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 288 optimal weight: 7.9990 chunk 239 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 GLN ** B 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 GLN ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 122 GLN ** F 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 532 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 24158 Z= 0.350 Angle : 0.709 13.573 32818 Z= 0.357 Chirality : 0.044 0.305 3779 Planarity : 0.005 0.041 4178 Dihedral : 4.862 22.827 3221 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.15), residues: 2965 helix: 0.58 (0.15), residues: 1134 sheet: -0.34 (0.20), residues: 566 loop : -1.33 (0.16), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP A 496 HIS 0.009 0.002 HIS A 101 PHE 0.019 0.002 PHE A 294 TYR 0.023 0.002 TYR A 390 ARG 0.005 0.001 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 2.832 Fit side-chains revert: symmetry clash REVERT: B 66 MET cc_start: 0.8279 (ptp) cc_final: 0.7764 (ppp) REVERT: B 776 MET cc_start: 0.8502 (mpp) cc_final: 0.7877 (mpp) REVERT: B 792 PHE cc_start: 0.9085 (m-10) cc_final: 0.8643 (m-80) REVERT: A 776 MET cc_start: 0.8500 (mpp) cc_final: 0.7905 (mpp) REVERT: A 792 PHE cc_start: 0.9444 (m-80) cc_final: 0.8915 (m-80) REVERT: E 618 MET cc_start: 0.8184 (tpt) cc_final: 0.7804 (tpt) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.2994 time to fit residues: 68.1512 Evaluate side-chains 99 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 277 optimal weight: 6.9990 chunk 32 optimal weight: 20.0000 chunk 164 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 163 optimal weight: 0.0570 chunk 242 optimal weight: 0.0770 chunk 161 optimal weight: 7.9990 chunk 287 optimal weight: 0.9990 chunk 179 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 overall best weight: 2.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 GLN ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24158 Z= 0.173 Angle : 0.593 10.783 32818 Z= 0.291 Chirality : 0.041 0.180 3779 Planarity : 0.004 0.042 4178 Dihedral : 4.448 22.332 3221 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.15), residues: 2965 helix: 1.02 (0.15), residues: 1136 sheet: -0.33 (0.21), residues: 582 loop : -1.07 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP B 496 HIS 0.004 0.001 HIS E 589 PHE 0.018 0.001 PHE A 294 TYR 0.016 0.001 TYR A 390 ARG 0.004 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 MET cc_start: 0.8268 (ptp) cc_final: 0.7733 (ptt) REVERT: B 586 MET cc_start: 0.6822 (mmp) cc_final: 0.5866 (ppp) REVERT: B 776 MET cc_start: 0.8505 (mpp) cc_final: 0.7874 (mpp) REVERT: B 792 PHE cc_start: 0.9035 (m-10) cc_final: 0.8570 (m-80) REVERT: A 471 PHE cc_start: 0.9018 (t80) cc_final: 0.8790 (t80) REVERT: A 776 MET cc_start: 0.8525 (mpp) cc_final: 0.7923 (mpp) REVERT: A 792 PHE cc_start: 0.9436 (m-80) cc_final: 0.8882 (m-80) REVERT: E 618 MET cc_start: 0.8137 (tpt) cc_final: 0.7733 (tpt) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2754 time to fit residues: 67.4495 Evaluate side-chains 104 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 177 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 182 optimal weight: 7.9990 chunk 195 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 225 optimal weight: 0.7980 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24158 Z= 0.248 Angle : 0.625 8.402 32818 Z= 0.312 Chirality : 0.042 0.187 3779 Planarity : 0.004 0.044 4178 Dihedral : 4.545 22.316 3221 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 2965 helix: 0.90 (0.15), residues: 1140 sheet: -0.39 (0.20), residues: 564 loop : -1.14 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 496 HIS 0.006 0.001 HIS A 101 PHE 0.019 0.002 PHE A 294 TYR 0.012 0.001 TYR A 390 ARG 0.005 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 2.995 Fit side-chains revert: symmetry clash REVERT: B 66 MET cc_start: 0.8241 (ptp) cc_final: 0.7836 (ptt) REVERT: B 586 MET cc_start: 0.6934 (mmp) cc_final: 0.6023 (tmm) REVERT: B 776 MET cc_start: 0.8501 (mpp) cc_final: 0.7889 (mpp) REVERT: B 792 PHE cc_start: 0.9041 (m-10) cc_final: 0.8560 (m-80) REVERT: A 776 MET cc_start: 0.8507 (mpp) cc_final: 0.7940 (mpp) REVERT: A 792 PHE cc_start: 0.9413 (m-80) cc_final: 0.8836 (m-80) REVERT: E 618 MET cc_start: 0.8154 (tpt) cc_final: 0.7698 (tpt) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.3110 time to fit residues: 70.9487 Evaluate side-chains 101 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 261 optimal weight: 0.0670 chunk 275 optimal weight: 5.9990 chunk 251 optimal weight: 2.9990 chunk 267 optimal weight: 20.0000 chunk 161 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 210 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 241 optimal weight: 9.9990 chunk 253 optimal weight: 5.9990 chunk 266 optimal weight: 4.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24158 Z= 0.212 Angle : 0.607 8.265 32818 Z= 0.302 Chirality : 0.041 0.246 3779 Planarity : 0.004 0.045 4178 Dihedral : 4.476 22.446 3221 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.15), residues: 2965 helix: 0.94 (0.15), residues: 1139 sheet: -0.44 (0.20), residues: 576 loop : -1.12 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 496 HIS 0.003 0.001 HIS E 500 PHE 0.019 0.001 PHE A 294 TYR 0.014 0.001 TYR A 58 ARG 0.004 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 2.790 Fit side-chains revert: symmetry clash REVERT: B 66 MET cc_start: 0.8235 (ptp) cc_final: 0.7822 (ptt) REVERT: B 586 MET cc_start: 0.6919 (mmp) cc_final: 0.6012 (tmm) REVERT: B 776 MET cc_start: 0.8500 (mpp) cc_final: 0.7867 (mpp) REVERT: B 792 PHE cc_start: 0.8996 (m-10) cc_final: 0.8478 (m-80) REVERT: A 289 MET cc_start: 0.8219 (mmm) cc_final: 0.7776 (mmm) REVERT: A 471 PHE cc_start: 0.9079 (t80) cc_final: 0.8847 (t80) REVERT: A 776 MET cc_start: 0.8519 (mpp) cc_final: 0.7916 (mpp) REVERT: A 792 PHE cc_start: 0.9382 (m-80) cc_final: 0.8802 (m-80) REVERT: E 618 MET cc_start: 0.8236 (tpt) cc_final: 0.7817 (tpt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2830 time to fit residues: 65.7236 Evaluate side-chains 104 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 175 optimal weight: 5.9990 chunk 283 optimal weight: 7.9990 chunk 172 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 196 optimal weight: 4.9990 chunk 296 optimal weight: 0.0050 chunk 273 optimal weight: 6.9990 chunk 236 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 GLN ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 675 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24158 Z= 0.157 Angle : 0.581 8.278 32818 Z= 0.283 Chirality : 0.041 0.247 3779 Planarity : 0.004 0.052 4178 Dihedral : 4.224 21.306 3221 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 2965 helix: 1.15 (0.16), residues: 1137 sheet: -0.41 (0.20), residues: 576 loop : -0.99 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 496 HIS 0.003 0.001 HIS A 55 PHE 0.018 0.001 PHE A 294 TYR 0.012 0.001 TYR A 390 ARG 0.003 0.000 ARG A 656 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 2.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 MET cc_start: 0.8115 (ptp) cc_final: 0.7753 (ptt) REVERT: B 586 MET cc_start: 0.6875 (mmp) cc_final: 0.5957 (tmm) REVERT: B 696 MET cc_start: 0.4447 (ptm) cc_final: 0.2046 (tpt) REVERT: B 776 MET cc_start: 0.8487 (mpp) cc_final: 0.7857 (mpp) REVERT: A 471 PHE cc_start: 0.8970 (t80) cc_final: 0.8735 (t80) REVERT: A 586 MET cc_start: 0.7096 (mmp) cc_final: 0.5827 (tmm) REVERT: A 776 MET cc_start: 0.8504 (mpp) cc_final: 0.7907 (mpp) REVERT: A 792 PHE cc_start: 0.9396 (m-80) cc_final: 0.8813 (m-80) REVERT: E 618 MET cc_start: 0.8238 (tpt) cc_final: 0.7828 (tpt) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2820 time to fit residues: 69.2057 Evaluate side-chains 108 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 187 optimal weight: 0.9990 chunk 251 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 217 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 236 optimal weight: 6.9990 chunk 99 optimal weight: 30.0000 chunk 243 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 675 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.048007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.033703 restraints weight = 205253.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.034663 restraints weight = 129340.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.035285 restraints weight = 96631.757| |-----------------------------------------------------------------------------| r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24158 Z= 0.291 Angle : 0.664 8.593 32818 Z= 0.334 Chirality : 0.043 0.252 3779 Planarity : 0.005 0.049 4178 Dihedral : 4.627 22.622 3221 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 2965 helix: 0.81 (0.15), residues: 1130 sheet: -0.47 (0.20), residues: 562 loop : -1.21 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 496 HIS 0.006 0.001 HIS A 101 PHE 0.024 0.002 PHE F 79 TYR 0.020 0.002 TYR B 390 ARG 0.006 0.001 ARG A 388 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3272.80 seconds wall clock time: 61 minutes 22.96 seconds (3682.96 seconds total)