Starting phenix.real_space_refine on Mon Feb 19 07:02:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gk0_40177/02_2024/8gk0_40177_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gk0_40177/02_2024/8gk0_40177.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gk0_40177/02_2024/8gk0_40177_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gk0_40177/02_2024/8gk0_40177_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gk0_40177/02_2024/8gk0_40177_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gk0_40177/02_2024/8gk0_40177.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gk0_40177/02_2024/8gk0_40177.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gk0_40177/02_2024/8gk0_40177_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gk0_40177/02_2024/8gk0_40177_trim_updated.pdb" } resolution = 3.44 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= 0.027 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 84 5.16 5 C 15494 2.51 5 N 3844 2.21 5 O 4460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 67": "OE1" <-> "OE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B GLU 274": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B GLU 415": "OE1" <-> "OE2" Residue "B GLU 635": "OE1" <-> "OE2" Residue "B GLU 860": "OE1" <-> "OE2" Residue "B GLU 887": "OE1" <-> "OE2" Residue "B GLU 946": "OE1" <-> "OE2" Residue "A GLU 34": "OE1" <-> "OE2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A GLU 635": "OE1" <-> "OE2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "A GLU 887": "OE1" <-> "OE2" Residue "A GLU 941": "OE1" <-> "OE2" Residue "A GLU 945": "OE1" <-> "OE2" Residue "A GLU 956": "OE1" <-> "OE2" Residue "A GLU 1028": "OE1" <-> "OE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C GLU 415": "OE1" <-> "OE2" Residue "C GLU 467": "OE1" <-> "OE2" Residue "C GLU 564": "OE1" <-> "OE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C GLU 635": "OE1" <-> "OE2" Residue "C GLU 675": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23882 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 7877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 7877 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 985} Chain breaks: 2 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "A" Number of atoms: 7975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7975 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 990} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 8030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8030 Unusual residues: {'ERY': 1} Classifications: {'peptide': 1032, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 990, None: 1} Not linked: pdbres="LYS C1032 " pdbres="ERY C1101 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.08, per 1000 atoms: 0.55 Number of scatterers: 23882 At special positions: 0 Unit cell: (116.63, 130.54, 154.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 4460 8.00 N 3844 7.00 C 15494 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: 9.78 Conformation dependent library (CDL) restraints added in 4.2 seconds 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5834 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 101 helices and 25 sheets defined 54.2% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.97 Creating SS restraints... Processing helix chain 'B' and resid 2 through 8 removed outlier: 3.815A pdb=" N PHE B 6 " --> pdb=" O PHE B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 30 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 63 through 69 Processing helix chain 'B' and resid 100 through 117 removed outlier: 4.395A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA B 114 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 151 through 168 removed outlier: 4.734A pdb=" N LEU B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ASP B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B 165 " --> pdb=" O ASN B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 197 Processing helix chain 'B' and resid 201 through 211 Processing helix chain 'B' and resid 244 through 247 No H-bonds generated for 'chain 'B' and resid 244 through 247' Processing helix chain 'B' and resid 263 through 266 No H-bonds generated for 'chain 'B' and resid 263 through 266' Processing helix chain 'B' and resid 300 through 317 removed outlier: 3.881A pdb=" N ASN B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 359 removed outlier: 4.009A pdb=" N VAL B 334 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 387 Proline residue: B 369 - end of helix removed outlier: 3.805A pdb=" N ALA B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Proline residue: B 374 - end of helix removed outlier: 3.654A pdb=" N PHE B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 423 removed outlier: 4.932A pdb=" N GLY B 404 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP B 409 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA B 410 " --> pdb=" O VAL B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 460 removed outlier: 5.582A pdb=" N SER B 442 " --> pdb=" O ASN B 438 " (cutoff:3.500A) Proline residue: B 443 - end of helix Proline residue: B 457 - end of helix removed outlier: 4.104A pdb=" N PHE B 460 " --> pdb=" O ILE B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 488 removed outlier: 3.547A pdb=" N GLN B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR B 475 " --> pdb=" O GLN B 471 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B 481 " --> pdb=" O ALA B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 497 Processing helix chain 'B' and resid 508 through 533 Processing helix chain 'B' and resid 535 through 555 removed outlier: 4.025A pdb=" N VAL B 539 " --> pdb=" O THR B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 597 removed outlier: 3.777A pdb=" N GLN B 597 " --> pdb=" O LYS B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 648 Processing helix chain 'B' and resid 686 through 702 removed outlier: 4.130A pdb=" N THR B 702 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 731 Processing helix chain 'B' and resid 736 through 746 Processing helix chain 'B' and resid 830 through 845 Processing helix chain 'B' and resid 856 through 862 Processing helix chain 'B' and resid 870 through 886 removed outlier: 4.345A pdb=" N MET B 875 " --> pdb=" O PHE B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 913 removed outlier: 4.031A pdb=" N VAL B 899 " --> pdb=" O ILE B 896 " (cutoff:3.500A) Proline residue: B 900 - end of helix removed outlier: 3.596A pdb=" N ARG B 913 " --> pdb=" O VAL B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 949 Processing helix chain 'B' and resid 954 through 964 Processing helix chain 'B' and resid 966 through 979 Processing helix chain 'B' and resid 981 through 985 Processing helix chain 'B' and resid 991 through 1031 removed outlier: 3.691A pdb=" N ALA B1012 " --> pdb=" O ALA B1008 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ILE B1013 " --> pdb=" O SER B1009 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE B1014 " --> pdb=" O THR B1010 " (cutoff:3.500A) Proline residue: B1017 - end of helix Processing helix chain 'A' and resid 2 through 8 removed outlier: 3.772A pdb=" N PHE A 6 " --> pdb=" O PHE A 2 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A 8 " --> pdb=" O LYS A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 30 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 63 through 70 removed outlier: 3.702A pdb=" N ALA A 69 " --> pdb=" O PRO A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 117 removed outlier: 5.168A pdb=" N ALA A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LYS A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 151 through 168 removed outlier: 4.548A pdb=" N LEU A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ASP A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU A 165 " --> pdb=" O ASN A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 197 Processing helix chain 'A' and resid 201 through 211 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 263 through 266 No H-bonds generated for 'chain 'A' and resid 263 through 266' Processing helix chain 'A' and resid 300 through 317 removed outlier: 3.934A pdb=" N ASN A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 360 Processing helix chain 'A' and resid 363 through 387 removed outlier: 3.503A pdb=" N ILE A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) Proline residue: A 369 - end of helix removed outlier: 4.115A pdb=" N ALA A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL A 373 " --> pdb=" O PRO A 369 " (cutoff:3.500A) Proline residue: A 374 - end of helix Processing helix chain 'A' and resid 393 through 423 removed outlier: 4.466A pdb=" N GLY A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL A 407 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASP A 409 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ALA A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 453 removed outlier: 5.604A pdb=" N SER A 442 " --> pdb=" O ASN A 438 " (cutoff:3.500A) Proline residue: A 443 - end of helix Processing helix chain 'A' and resid 456 through 460 removed outlier: 4.089A pdb=" N PHE A 460 " --> pdb=" O ILE A 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 456 through 460' Processing helix chain 'A' and resid 464 through 498 removed outlier: 3.758A pdb=" N GLN A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE A 472 " --> pdb=" O ILE A 468 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N THR A 491 " --> pdb=" O ALA A 487 " (cutoff:3.500A) Proline residue: A 492 - end of helix Processing helix chain 'A' and resid 508 through 533 Processing helix chain 'A' and resid 536 through 555 Processing helix chain 'A' and resid 581 through 596 Processing helix chain 'A' and resid 638 through 648 Processing helix chain 'A' and resid 686 through 702 Processing helix chain 'A' and resid 726 through 732 Processing helix chain 'A' and resid 736 through 746 Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 794 through 796 No H-bonds generated for 'chain 'A' and resid 794 through 796' Processing helix chain 'A' and resid 830 through 844 Processing helix chain 'A' and resid 856 through 862 Processing helix chain 'A' and resid 866 through 886 removed outlier: 3.650A pdb=" N PHE A 871 " --> pdb=" O GLY A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 913 removed outlier: 3.755A pdb=" N VAL A 899 " --> pdb=" O VAL A 895 " (cutoff:3.500A) Proline residue: A 900 - end of helix Processing helix chain 'A' and resid 919 through 950 removed outlier: 4.241A pdb=" N PHE A 942 " --> pdb=" O LEU A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 984 removed outlier: 4.970A pdb=" N ARG A 967 " --> pdb=" O LYS A 963 " (cutoff:3.500A) Proline residue: A 968 - end of helix Proline residue: A 982 - end of helix Processing helix chain 'A' and resid 991 through 1010 Processing helix chain 'A' and resid 1012 through 1031 Proline residue: A1017 - end of helix Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 10 through 30 Processing helix chain 'C' and resid 55 through 70 removed outlier: 4.255A pdb=" N THR C 64 " --> pdb=" O SER C 60 " (cutoff:3.500A) Proline residue: C 65 - end of helix Processing helix chain 'C' and resid 100 through 117 removed outlier: 3.505A pdb=" N ALA C 114 " --> pdb=" O ARG C 110 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ALA C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LYS C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 124 Processing helix chain 'C' and resid 151 through 160 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 191 through 197 Processing helix chain 'C' and resid 201 through 211 Processing helix chain 'C' and resid 244 through 248 Processing helix chain 'C' and resid 263 through 266 No H-bonds generated for 'chain 'C' and resid 263 through 266' Processing helix chain 'C' and resid 300 through 317 removed outlier: 3.868A pdb=" N ASN C 317 " --> pdb=" O GLU C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 359 Processing helix chain 'C' and resid 364 through 386 removed outlier: 3.534A pdb=" N ILE C 367 " --> pdb=" O LYS C 364 " (cutoff:3.500A) Proline residue: C 369 - end of helix removed outlier: 4.999A pdb=" N VAL C 373 " --> pdb=" O MET C 370 " (cutoff:3.500A) Proline residue: C 374 - end of helix Processing helix chain 'C' and resid 393 through 423 removed outlier: 4.028A pdb=" N GLY C 404 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE C 405 " --> pdb=" O LEU C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 460 removed outlier: 5.268A pdb=" N SER C 442 " --> pdb=" O ASN C 438 " (cutoff:3.500A) Proline residue: C 443 - end of helix Proline residue: C 457 - end of helix Processing helix chain 'C' and resid 463 through 498 removed outlier: 3.518A pdb=" N PHE C 472 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR C 491 " --> pdb=" O ALA C 487 " (cutoff:3.500A) Proline residue: C 492 - end of helix Processing helix chain 'C' and resid 508 through 533 Processing helix chain 'C' and resid 537 through 555 Processing helix chain 'C' and resid 581 through 596 Processing helix chain 'C' and resid 638 through 647 Processing helix chain 'C' and resid 686 through 702 removed outlier: 4.124A pdb=" N THR C 702 " --> pdb=" O GLU C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 731 Processing helix chain 'C' and resid 736 through 746 Processing helix chain 'C' and resid 770 through 773 No H-bonds generated for 'chain 'C' and resid 770 through 773' Processing helix chain 'C' and resid 830 through 844 Processing helix chain 'C' and resid 856 through 861 Processing helix chain 'C' and resid 866 through 886 Processing helix chain 'C' and resid 891 through 912 Proline residue: C 900 - end of helix Processing helix chain 'C' and resid 919 through 948 Processing helix chain 'C' and resid 954 through 984 removed outlier: 4.470A pdb=" N ARG C 967 " --> pdb=" O LYS C 963 " (cutoff:3.500A) Proline residue: C 968 - end of helix Proline residue: C 982 - end of helix Processing helix chain 'C' and resid 991 through 1031 removed outlier: 3.755A pdb=" N GLY C1000 " --> pdb=" O SER C 996 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA C1012 " --> pdb=" O ALA C1008 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE C1013 " --> pdb=" O SER C1009 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE C1014 " --> pdb=" O THR C1010 " (cutoff:3.500A) Proline residue: C1017 - end of helix Processing sheet with id= A, first strand: chain 'B' and resid 127 through 130 Processing sheet with id= B, first strand: chain 'B' and resid 322 through 325 removed outlier: 6.757A pdb=" N ILE B 292 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL B 139 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE B 290 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER B 141 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL B 288 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 267 through 273 removed outlier: 8.253A pdb=" N ASN B 761 " --> pdb=" O TYR B 183 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N MET B 185 " --> pdb=" O ASN B 761 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLN B 763 " --> pdb=" O MET B 185 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ILE B 187 " --> pdb=" O GLN B 763 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASN B 765 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU B 189 " --> pdb=" O ASN B 765 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG B 767 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 279 through 282 removed outlier: 7.163A pdb=" N ILE B 627 " --> pdb=" O SER B 602 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER B 604 " --> pdb=" O PHE B 625 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N PHE B 625 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER B 606 " --> pdb=" O ALA B 623 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA B 623 " --> pdb=" O SER B 606 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE B 608 " --> pdb=" O ALA B 621 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ALA B 621 " --> pdb=" O ILE B 608 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE B 572 " --> pdb=" O TYR B 658 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 849 through 854 removed outlier: 3.600A pdb=" N SER B 854 " --> pdb=" O GLU B 675 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLU B 675 " --> pdb=" O SER B 854 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B 818 " --> pdb=" O ALA B 678 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 718 through 724 Processing sheet with id= G, first strand: chain 'B' and resid 783 through 785 Processing sheet with id= H, first strand: chain 'B' and resid 251 through 254 removed outlier: 7.096A pdb=" N LEU B 261 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 128 through 132 removed outlier: 4.289A pdb=" N THR A 43 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS A 810 " --> pdb=" O ALA A 817 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA A 818 " --> pdb=" O ALA A 678 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 822 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 322 through 325 removed outlier: 3.625A pdb=" N GLU A 138 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 267 through 273 Processing sheet with id= L, first strand: chain 'A' and resid 285 through 287 removed outlier: 3.705A pdb=" N GLY A 280 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE A 627 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER A 604 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N PHE A 625 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N SER A 606 " --> pdb=" O ALA A 623 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ALA A 623 " --> pdb=" O SER A 606 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILE A 608 " --> pdb=" O ALA A 621 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ALA A 621 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 718 through 724 Processing sheet with id= N, first strand: chain 'A' and resid 754 through 756 Processing sheet with id= O, first strand: chain 'A' and resid 783 through 785 Processing sheet with id= P, first strand: chain 'C' and resid 128 through 131 removed outlier: 3.890A pdb=" N TYR C 78 " --> pdb=" O TYR C 93 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL C 809 " --> pdb=" O SER C 83 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 267 through 273 Processing sheet with id= R, first strand: chain 'C' and resid 216 through 220 removed outlier: 3.572A pdb=" N ILE C 233 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 279 through 282 removed outlier: 6.645A pdb=" N ILE C 627 " --> pdb=" O SER C 602 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N SER C 604 " --> pdb=" O PHE C 625 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE C 625 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N SER C 606 " --> pdb=" O ALA C 623 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA C 623 " --> pdb=" O SER C 606 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ILE C 608 " --> pdb=" O ALA C 621 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ALA C 621 " --> pdb=" O ILE C 608 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 674 through 679 removed outlier: 3.571A pdb=" N ALA C 678 " --> pdb=" O ALA C 818 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 818 " --> pdb=" O ALA C 678 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 718 through 724 removed outlier: 3.604A pdb=" N THR C 799 " --> pdb=" O ILE C 723 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 754 through 757 Processing sheet with id= W, first strand: chain 'C' and resid 783 through 785 Processing sheet with id= X, first strand: chain 'C' and resid 322 through 329 removed outlier: 6.712A pdb=" N VAL C 139 " --> pdb=" O PRO C 327 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP C 329 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N LEU C 137 " --> pdb=" O ASP C 329 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE C 292 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL C 139 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ILE C 290 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER C 141 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL C 288 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 251 through 254 removed outlier: 7.146A pdb=" N LEU C 261 " --> pdb=" O LEU C 252 " (cutoff:3.500A) 1355 hydrogen bonds defined for protein. 3876 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: 8.78 Time building geometry restraints manager: 10.55 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: 7422 1.34 - 1.46: 3424 1.46 - 1.57: 13332 1.57 - 1.69: 0 1.69 - 1.81: 162 Bond restraints: 24340 Sorted by residual: bond pdb=" C14 ERY C1101 " pdb=" O4 ERY C1101 " ideal model delta sigma weight residual 1.512 1.418 0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C22 ERY C1101 " pdb=" O9 ERY C1101 " ideal model delta sigma weight residual 1.489 1.428 0.061 2.00e-02 2.50e+03 9.38e+00 bond pdb=" C14 ERY C1101 " pdb=" O3 ERY C1101 " ideal model delta sigma weight residual 1.364 1.424 -0.060 2.00e-02 2.50e+03 9.07e+00 bond pdb=" C16 ERY C1101 " pdb=" C19 ERY C1101 " ideal model delta sigma weight residual 1.581 1.524 0.057 2.00e-02 2.50e+03 8.17e+00 bond pdb=" C1 ERY C1101 " pdb=" C2 ERY C1101 " ideal model delta sigma weight residual 1.558 1.502 0.056 2.00e-02 2.50e+03 7.91e+00 ... (remaining 24335 not shown) Histogram of bond angle deviations from ideal: 96.91 - 104.33: 346 104.33 - 111.75: 11803 111.75 - 119.17: 8018 119.17 - 126.58: 12707 126.58 - 134.00: 201 Bond angle restraints: 33075 Sorted by residual: angle pdb=" C ILE B 456 " pdb=" CA ILE B 456 " pdb=" CB ILE B 456 " ideal model delta sigma weight residual 114.35 109.26 5.09 1.06e+00 8.90e-01 2.31e+01 angle pdb=" N THR B 977 " pdb=" CA THR B 977 " pdb=" C THR B 977 " ideal model delta sigma weight residual 111.07 106.29 4.78 1.07e+00 8.73e-01 1.99e+01 angle pdb=" CA GLU A 587 " pdb=" CB GLU A 587 " pdb=" CG GLU A 587 " ideal model delta sigma weight residual 114.10 122.80 -8.70 2.00e+00 2.50e-01 1.89e+01 angle pdb=" CA GLN C 737 " pdb=" CB GLN C 737 " pdb=" CG GLN C 737 " ideal model delta sigma weight residual 114.10 122.27 -8.17 2.00e+00 2.50e-01 1.67e+01 angle pdb=" C10 ERY C1101 " pdb=" C9 ERY C1101 " pdb=" C8 ERY C1101 " ideal model delta sigma weight residual 109.61 121.14 -11.53 3.00e+00 1.11e-01 1.48e+01 ... (remaining 33070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.50: 14022 29.50 - 59.00: 570 59.00 - 88.50: 26 88.50 - 118.00: 2 118.00 - 147.50: 2 Dihedral angle restraints: 14622 sinusoidal: 5603 harmonic: 9019 Sorted by residual: dihedral pdb=" CA GLN C 648 " pdb=" C GLN C 648 " pdb=" N TYR C 649 " pdb=" CA TYR C 649 " ideal model delta harmonic sigma weight residual 180.00 -153.96 -26.04 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" C10 ERY C1101 " pdb=" C8 ERY C1101 " pdb=" C9 ERY C1101 " pdb=" C7 ERY C1101 " ideal model delta sinusoidal sigma weight residual 222.86 75.36 147.50 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" C11 ERY C1101 " pdb=" C10 ERY C1101 " pdb=" C9 ERY C1101 " pdb=" C8 ERY C1101 " ideal model delta sinusoidal sigma weight residual -71.83 72.83 -144.66 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 14619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.070: 3947 1.070 - 2.140: 0 2.140 - 3.210: 0 3.210 - 4.280: 0 4.280 - 5.350: 4 Chirality restraints: 3951 Sorted by residual: chirality pdb=" C12 ERY C1101 " pdb=" C11 ERY C1101 " pdb=" C13 ERY C1101 " pdb=" C35 ERY C1101 " both_signs ideal model delta sigma weight residual False -2.75 2.60 -5.35 2.00e-01 2.50e+01 7.16e+02 chirality pdb=" C6 ERY C1101 " pdb=" C32 ERY C1101 " pdb=" C5 ERY C1101 " pdb=" C7 ERY C1101 " both_signs ideal model delta sigma weight residual False -2.75 2.57 -5.33 2.00e-01 2.50e+01 7.10e+02 chirality pdb=" C16 ERY C1101 " pdb=" C15 ERY C1101 " pdb=" C17 ERY C1101 " pdb=" C19 ERY C1101 " both_signs ideal model delta sigma weight residual False 2.68 -2.54 5.22 2.00e-01 2.50e+01 6.82e+02 ... (remaining 3948 not shown) Planarity restraints: 4182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 256 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.50e+00 pdb=" C GLU A 256 " 0.044 2.00e-02 2.50e+03 pdb=" O GLU A 256 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP A 257 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 368 " -0.039 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO B 369 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 369 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 369 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 891 " -0.039 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO A 892 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 892 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 892 " -0.033 5.00e-02 4.00e+02 ... (remaining 4179 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2593 2.74 - 3.28: 25762 3.28 - 3.82: 41890 3.82 - 4.36: 47762 4.36 - 4.90: 83049 Nonbonded interactions: 201056 Sorted by model distance: nonbonded pdb=" OD2 ASP A 692 " pdb=" OH TYR A 849 " model vdw 2.205 2.440 nonbonded pdb=" OG SER C 559 " pdb=" OD2 ASP C 916 " model vdw 2.207 2.440 nonbonded pdb=" N GLU B 467 " pdb=" OE1 GLU B 467 " model vdw 2.208 2.520 nonbonded pdb=" OG SER B 786 " pdb=" OD1 ASP B 788 " model vdw 2.236 2.440 nonbonded pdb=" O ILE A 434 " pdb=" ND2 ASN A 438 " model vdw 2.240 2.520 ... (remaining 201051 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 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 422 or (resid 423 and (name N or na \ me CA or name C or name O or name CB )) or resid 424 through 461 or resid 464 th \ rough 506 or (resid 507 and (name N or name CA or name C or name O or name CB )) \ or resid 508 through 511 or (resid 512 and (name N or name CA or name C or name \ O or name CB )) or resid 513 through 529 or (resid 530 and (name N or name CA o \ r name C or name O or name CB )) or resid 531 through 533 or (resid 534 and (nam \ e N or name CA or name C or name O or name CB )) or resid 535 through 563 or (re \ sid 564 and (name N or name CA or name C or name O or name CB )) or resid 565 th \ rough 661 or (resid 662 and (name N or name CA or name C or name O or name CB )) \ or resid 663 or resid 669 through 700 or (resid 701 and (name N or name CA or n \ ame C or name O or name CB )) or resid 702 or (resid 703 and (name N or name CA \ or name C or name O or name CB )) or resid 704 through 822 or (resid 823 and (na \ me N or name CA or name C or name O or name CB )) or resid 824 through 831 or (r \ esid 832 through 833 and (name N or name CA or name C or name O or name CB )) or \ resid 834 through 844 or (resid 845 and (name N or name CA or name C or name O \ or name CB )) or resid 846 through 1027 or (resid 1028 and (name N or name CA or \ name C or name O or name CB )) or resid 1029 through 1032)) selection = (chain 'B' and (resid 1 through 773 or (resid 774 and (name N or name CA or name \ C or name O or name CB )) or resid 775 through 844 or (resid 845 and (name N or \ name CA or name C or name O or name CB )) or resid 846 through 1031 or (resid 1 \ 032 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 1 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 422 or (resid 423 and (name N or na \ me CA or name C or name O or name CB )) or resid 424 through 461 or resid 464 th \ rough 506 or (resid 507 and (name N or name CA or name C or name O or name CB )) \ or resid 508 through 511 or (resid 512 and (name N or name CA or name C or name \ O or name CB )) or resid 513 through 529 or (resid 530 and (name N or name CA o \ r name C or name O or name CB )) or resid 531 through 533 or (resid 534 and (nam \ e N or name CA or name C or name O or name CB )) or resid 535 through 563 or (re \ sid 564 and (name N or name CA or name C or name O or name CB )) or resid 565 th \ rough 661 or (resid 662 and (name N or name CA or name C or name O or name CB )) \ or resid 663 or resid 669 through 700 or (resid 701 and (name N or name CA or n \ ame C or name O or name CB )) or resid 702 or (resid 703 and (name N or name CA \ or name C or name O or name CB )) or resid 704 through 773 or (resid 774 and (na \ me N or name CA or name C or name O or name CB )) or resid 775 through 822 or (r \ esid 823 and (name N or name CA or name C or name O or name CB )) or resid 824 t \ hrough 831 or (resid 832 through 833 and (name N or name CA or name C or name O \ or name CB )) or resid 834 through 1027 or (resid 1028 and (name N or name CA or \ name C or name O or name CB )) or resid 1029 through 1031 or (resid 1032 and (n \ ame N or name CA or name C or name O or name CB )))) } 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: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 10.150 Check model and map are aligned: 0.380 Set scattering table: 0.210 Process input model: 64.690 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.100 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 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 0.094 24340 Z= 0.244 Angle : 0.709 11.528 33075 Z= 0.402 Chirality : 0.170 5.350 3951 Planarity : 0.004 0.059 4182 Dihedral : 15.011 147.501 8788 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.88 % Favored : 98.08 % Rotamer: Outliers : 0.77 % Allowed : 21.65 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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: 0.87 (0.15), residues: 3079 helix: 1.38 (0.12), residues: 1716 sheet: -0.12 (0.23), residues: 468 loop : -0.46 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 853 HIS 0.014 0.001 HIS B 995 PHE 0.024 0.001 PHE A 538 TYR 0.023 0.001 TYR A 869 ARG 0.012 0.000 ARG B 994 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 500 time to evaluate : 2.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 36 TYR cc_start: 0.8608 (m-80) cc_final: 0.8365 (m-10) REVERT: B 347 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8194 (mt-10) REVERT: B 380 THR cc_start: 0.9095 (m) cc_final: 0.8875 (p) REVERT: B 514 ASN cc_start: 0.8761 (t0) cc_final: 0.8465 (m-40) REVERT: B 537 ARG cc_start: 0.6658 (ttt90) cc_final: 0.6305 (ttp-110) REVERT: B 548 PHE cc_start: 0.8681 (m-80) cc_final: 0.8389 (m-80) REVERT: B 887 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8469 (mm-30) REVERT: B 965 ARG cc_start: 0.7794 (tpt170) cc_final: 0.7128 (mmm160) REVERT: B 1021 TYR cc_start: 0.8313 (t80) cc_final: 0.8091 (t80) REVERT: A 370 MET cc_start: 0.8654 (mmt) cc_final: 0.8119 (mmm) REVERT: A 467 GLU cc_start: 0.8972 (tp30) cc_final: 0.8516 (tp30) REVERT: A 488 LEU cc_start: 0.9397 (mt) cc_final: 0.9174 (mt) REVERT: A 736 MET cc_start: 0.9067 (mmm) cc_final: 0.8770 (tpt) REVERT: C 30 ASN cc_start: 0.8748 (m110) cc_final: 0.8510 (m-40) REVERT: C 168 ARG cc_start: 0.8371 (ttm-80) cc_final: 0.8086 (mtt-85) REVERT: C 185 MET cc_start: 0.9363 (tpp) cc_final: 0.9123 (mmt) REVERT: C 211 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.6508 (mp10) REVERT: C 696 MET cc_start: 0.8111 (ttm) cc_final: 0.7782 (ttm) REVERT: C 888 ARG cc_start: 0.7030 (ttm170) cc_final: 0.5892 (tpm170) REVERT: C 891 MET cc_start: 0.8943 (mmm) cc_final: 0.8681 (tpt) outliers start: 20 outliers final: 9 residues processed: 509 average time/residue: 0.3033 time to fit residues: 253.7794 Evaluate side-chains 437 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 427 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 PHE Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 363 PHE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 1014 PHE Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain C residue 758 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 241 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 179 optimal weight: 10.0000 chunk 279 optimal weight: 0.1980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN B 885 GLN A 95 ASN ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24340 Z= 0.209 Angle : 0.723 27.432 33075 Z= 0.330 Chirality : 0.072 2.495 3951 Planarity : 0.004 0.050 4182 Dihedral : 6.521 147.216 3325 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.95 % Allowed : 20.96 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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: 0.95 (0.15), residues: 3079 helix: 1.45 (0.12), residues: 1731 sheet: -0.13 (0.22), residues: 471 loop : -0.45 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 631 HIS 0.008 0.001 HIS B 995 PHE 0.027 0.001 PHE B 966 TYR 0.017 0.001 TYR A 36 ARG 0.005 0.000 ARG C 994 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 451 time to evaluate : 2.842 Fit side-chains revert: symmetry clash REVERT: B 185 MET cc_start: 0.9004 (tpp) cc_final: 0.8756 (mmt) REVERT: B 347 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8285 (mt-10) REVERT: B 380 THR cc_start: 0.9006 (m) cc_final: 0.8765 (p) REVERT: B 384 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9226 (mm) REVERT: B 399 LEU cc_start: 0.9552 (mt) cc_final: 0.9352 (mt) REVERT: B 517 PHE cc_start: 0.8138 (t80) cc_final: 0.7845 (t80) REVERT: B 537 ARG cc_start: 0.6711 (ttt90) cc_final: 0.6290 (ttp-110) REVERT: B 696 MET cc_start: 0.9058 (tmm) cc_final: 0.8646 (tmm) REVERT: B 853 TRP cc_start: 0.8481 (m-90) cc_final: 0.8235 (m-90) REVERT: B 887 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8509 (mm-30) REVERT: B 940 ILE cc_start: 0.9247 (mm) cc_final: 0.8772 (mm) REVERT: B 965 ARG cc_start: 0.7781 (tpt170) cc_final: 0.7368 (mmm160) REVERT: A 311 MET cc_start: 0.9126 (mmm) cc_final: 0.8402 (mmm) REVERT: A 370 MET cc_start: 0.8617 (mmt) cc_final: 0.8142 (mmm) REVERT: A 478 ILE cc_start: 0.9481 (mp) cc_final: 0.9228 (mt) REVERT: A 488 LEU cc_start: 0.9421 (mt) cc_final: 0.9163 (mt) REVERT: A 545 MET cc_start: 0.8805 (ttp) cc_final: 0.8502 (tmm) REVERT: A 736 MET cc_start: 0.9117 (mmm) cc_final: 0.8388 (tpp) REVERT: C 106 ASP cc_start: 0.8544 (m-30) cc_final: 0.8338 (m-30) REVERT: C 164 ASP cc_start: 0.7964 (t0) cc_final: 0.7692 (t0) REVERT: C 211 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.6577 (mp10) REVERT: C 358 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8919 (tp) REVERT: C 737 GLN cc_start: 0.8631 (tp-100) cc_final: 0.8399 (tp-100) REVERT: C 761 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.7669 (t0) outliers start: 77 outliers final: 43 residues processed: 496 average time/residue: 0.3011 time to fit residues: 247.5322 Evaluate side-chains 459 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 412 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 847 ASP Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 901 PHE Chi-restraints excluded: chain B residue 904 PHE Chi-restraints excluded: chain B residue 1014 PHE Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 1014 PHE Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 676 MET Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 761 ASN Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain C residue 910 VAL Chi-restraints excluded: chain C residue 987 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 232 optimal weight: 2.9990 chunk 190 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 280 optimal weight: 0.9990 chunk 302 optimal weight: 1.9990 chunk 249 optimal weight: 0.7980 chunk 277 optimal weight: 0.0170 chunk 95 optimal weight: 9.9990 chunk 224 optimal weight: 4.9990 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 GLN A 45 GLN ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24340 Z= 0.196 Angle : 0.700 25.964 33075 Z= 0.316 Chirality : 0.071 2.377 3951 Planarity : 0.004 0.047 4182 Dihedral : 6.227 142.503 3313 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.41 % Allowed : 20.57 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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: 1.00 (0.15), residues: 3079 helix: 1.49 (0.12), residues: 1732 sheet: -0.16 (0.23), residues: 475 loop : -0.41 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 631 HIS 0.008 0.001 HIS B 995 PHE 0.020 0.001 PHE B 976 TYR 0.017 0.001 TYR B 858 ARG 0.005 0.000 ARG C 994 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 445 time to evaluate : 3.159 Fit side-chains revert: symmetry clash REVERT: B 347 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8334 (mt-10) REVERT: B 380 THR cc_start: 0.8970 (m) cc_final: 0.8728 (p) REVERT: B 384 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9200 (mm) REVERT: B 470 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8418 (ttp80) REVERT: B 537 ARG cc_start: 0.6745 (ttt90) cc_final: 0.6287 (ttp-110) REVERT: B 696 MET cc_start: 0.8954 (tmm) cc_final: 0.8532 (tmm) REVERT: B 887 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8514 (mm-30) REVERT: B 891 MET cc_start: 0.8592 (tpp) cc_final: 0.8358 (mmm) REVERT: B 940 ILE cc_start: 0.9163 (mm) cc_final: 0.8885 (mm) REVERT: B 965 ARG cc_start: 0.7704 (tpt170) cc_final: 0.7338 (mmm160) REVERT: A 370 MET cc_start: 0.8636 (mmt) cc_final: 0.8108 (mmm) REVERT: A 488 LEU cc_start: 0.9420 (mt) cc_final: 0.9169 (mt) REVERT: A 545 MET cc_start: 0.8955 (ttp) cc_final: 0.8645 (tmm) REVERT: A 736 MET cc_start: 0.9041 (mmm) cc_final: 0.8722 (tpt) REVERT: A 941 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8216 (tm-30) REVERT: C 106 ASP cc_start: 0.8594 (m-30) cc_final: 0.8325 (m-30) REVERT: C 164 ASP cc_start: 0.8024 (t0) cc_final: 0.7662 (t0) REVERT: C 211 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.6687 (mp10) REVERT: C 237 MET cc_start: 0.7933 (ttp) cc_final: 0.7677 (ttp) REVERT: C 311 MET cc_start: 0.8997 (mmm) cc_final: 0.7290 (mmm) REVERT: C 358 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8937 (tp) REVERT: C 370 MET cc_start: 0.8050 (tmm) cc_final: 0.7821 (tmm) REVERT: C 407 VAL cc_start: 0.9372 (m) cc_final: 0.9108 (p) REVERT: C 509 PHE cc_start: 0.8583 (t80) cc_final: 0.8266 (p90) REVERT: C 737 GLN cc_start: 0.8707 (tp-100) cc_final: 0.8309 (tp-100) REVERT: C 761 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.7738 (t0) outliers start: 89 outliers final: 55 residues processed: 495 average time/residue: 0.2994 time to fit residues: 246.2956 Evaluate side-chains 479 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 419 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 311 MET Chi-restraints excluded: chain B residue 333 PHE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 470 ARG Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 821 GLN Chi-restraints excluded: chain B residue 847 ASP Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 901 PHE Chi-restraints excluded: chain B residue 904 PHE Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1014 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 363 PHE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1014 PHE Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 452 CYS Chi-restraints excluded: chain C residue 519 TRP Chi-restraints excluded: chain C residue 676 MET Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain C residue 761 ASN Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain C residue 910 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 4.9990 chunk 210 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 chunk 281 optimal weight: 1.9990 chunk 297 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 266 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 GLN ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 56 GLN ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 ASN C 737 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24340 Z= 0.275 Angle : 0.718 25.639 33075 Z= 0.327 Chirality : 0.071 2.376 3951 Planarity : 0.004 0.045 4182 Dihedral : 6.217 143.105 3311 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.02 % Allowed : 21.34 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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: 1.03 (0.15), residues: 3079 helix: 1.53 (0.12), residues: 1732 sheet: -0.09 (0.23), residues: 464 loop : -0.47 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 853 HIS 0.003 0.001 HIS B 422 PHE 0.029 0.001 PHE B 976 TYR 0.024 0.001 TYR A 649 ARG 0.006 0.000 ARG B 965 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 435 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 185 MET cc_start: 0.9055 (tpp) cc_final: 0.8755 (mmt) REVERT: B 347 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8288 (mt-10) REVERT: B 380 THR cc_start: 0.8952 (m) cc_final: 0.8721 (p) REVERT: B 384 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9187 (mm) REVERT: B 430 LYS cc_start: 0.9322 (tttm) cc_final: 0.9111 (tptp) REVERT: B 470 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8458 (ttp80) REVERT: B 537 ARG cc_start: 0.6713 (ttt90) cc_final: 0.6261 (ttp-110) REVERT: B 676 MET cc_start: 0.8174 (tpp) cc_final: 0.7495 (tpp) REVERT: B 696 MET cc_start: 0.9004 (tmm) cc_final: 0.8584 (tmm) REVERT: B 853 TRP cc_start: 0.8448 (m-90) cc_final: 0.8164 (m-90) REVERT: B 887 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8536 (mm-30) REVERT: B 891 MET cc_start: 0.8666 (tpp) cc_final: 0.8400 (mmm) REVERT: B 937 ILE cc_start: 0.8661 (mt) cc_final: 0.8440 (mt) REVERT: B 940 ILE cc_start: 0.9182 (mm) cc_final: 0.8886 (mm) REVERT: B 1015 PHE cc_start: 0.8777 (m-80) cc_final: 0.8575 (m-80) REVERT: A 76 MET cc_start: 0.9211 (ttp) cc_final: 0.8607 (tmm) REVERT: A 88 MET cc_start: 0.9207 (tmm) cc_final: 0.8741 (tmm) REVERT: A 124 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8309 (pttm) REVERT: A 370 MET cc_start: 0.8673 (mmt) cc_final: 0.8146 (mmm) REVERT: A 417 ILE cc_start: 0.9449 (OUTLIER) cc_final: 0.9241 (mp) REVERT: A 478 ILE cc_start: 0.9563 (mm) cc_final: 0.9178 (mt) REVERT: A 488 LEU cc_start: 0.9445 (mt) cc_final: 0.9199 (mt) REVERT: A 545 MET cc_start: 0.8963 (ttp) cc_final: 0.8644 (tmm) REVERT: A 568 VAL cc_start: 0.9605 (OUTLIER) cc_final: 0.9342 (p) REVERT: C 96 ILE cc_start: 0.9288 (mt) cc_final: 0.9035 (tp) REVERT: C 106 ASP cc_start: 0.8630 (m-30) cc_final: 0.8319 (m-30) REVERT: C 211 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.6814 (mp10) REVERT: C 311 MET cc_start: 0.8993 (mmm) cc_final: 0.7345 (mmm) REVERT: C 358 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9062 (tp) REVERT: C 370 MET cc_start: 0.8079 (tmm) cc_final: 0.7851 (tmm) REVERT: C 407 VAL cc_start: 0.9392 (m) cc_final: 0.9167 (p) REVERT: C 441 SER cc_start: 0.8912 (p) cc_final: 0.8606 (m) REVERT: C 509 PHE cc_start: 0.8630 (t80) cc_final: 0.8346 (p90) REVERT: C 737 GLN cc_start: 0.8837 (tp40) cc_final: 0.8439 (tp-100) REVERT: C 761 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.7786 (t0) REVERT: C 819 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9073 (tp) outliers start: 105 outliers final: 73 residues processed: 497 average time/residue: 0.3033 time to fit residues: 250.5565 Evaluate side-chains 489 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 407 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 311 MET Chi-restraints excluded: chain B residue 333 PHE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 470 ARG Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 821 GLN Chi-restraints excluded: chain B residue 847 ASP Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 901 PHE Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 1014 PHE Chi-restraints excluded: chain B residue 1025 ASN Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 363 PHE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 452 CYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 676 MET Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain C residue 761 ASN Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain C residue 910 VAL Chi-restraints excluded: chain C residue 944 MET Chi-restraints excluded: chain C residue 987 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 221 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 254 optimal weight: 0.9980 chunk 205 optimal weight: 0.0980 chunk 0 optimal weight: 8.9990 chunk 152 optimal weight: 0.0270 chunk 267 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 GLN ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 45 GLN ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24340 Z= 0.176 Angle : 0.706 25.720 33075 Z= 0.316 Chirality : 0.071 2.380 3951 Planarity : 0.004 0.045 4182 Dihedral : 6.095 147.139 3308 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.41 % Allowed : 22.11 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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: 3079 helix: 1.56 (0.12), residues: 1730 sheet: 0.02 (0.23), residues: 459 loop : -0.47 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 853 HIS 0.002 0.000 HIS C 995 PHE 0.029 0.001 PHE B 455 TYR 0.018 0.001 TYR C 886 ARG 0.005 0.000 ARG C 994 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 453 time to evaluate : 3.013 Fit side-chains revert: symmetry clash REVERT: B 36 TYR cc_start: 0.8641 (m-80) cc_final: 0.8436 (m-80) REVERT: B 185 MET cc_start: 0.9042 (tpp) cc_final: 0.8829 (mmt) REVERT: B 347 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8311 (mt-10) REVERT: B 380 THR cc_start: 0.8950 (m) cc_final: 0.8704 (p) REVERT: B 384 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9181 (mm) REVERT: B 430 LYS cc_start: 0.9308 (tttm) cc_final: 0.9080 (tptp) REVERT: B 470 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.8467 (ttp80) REVERT: B 537 ARG cc_start: 0.6597 (ttt90) cc_final: 0.6155 (ttp-110) REVERT: B 696 MET cc_start: 0.9000 (tmm) cc_final: 0.8591 (tmm) REVERT: B 887 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8514 (mm-30) REVERT: B 937 ILE cc_start: 0.8508 (mt) cc_final: 0.8301 (mt) REVERT: B 1015 PHE cc_start: 0.8753 (m-80) cc_final: 0.8529 (m-80) REVERT: A 30 ASN cc_start: 0.8510 (t0) cc_final: 0.7846 (t0) REVERT: A 88 MET cc_start: 0.9239 (tmm) cc_final: 0.8825 (tmm) REVERT: A 124 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8317 (pttp) REVERT: A 370 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8113 (mmm) REVERT: A 417 ILE cc_start: 0.9437 (OUTLIER) cc_final: 0.9232 (mp) REVERT: A 478 ILE cc_start: 0.9472 (mm) cc_final: 0.9204 (mt) REVERT: A 545 MET cc_start: 0.8957 (ttp) cc_final: 0.8515 (tmm) REVERT: A 736 MET cc_start: 0.9097 (tpp) cc_final: 0.8829 (tpt) REVERT: A 941 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8170 (tm-30) REVERT: C 96 ILE cc_start: 0.9270 (mt) cc_final: 0.8992 (tp) REVERT: C 106 ASP cc_start: 0.8617 (m-30) cc_final: 0.8289 (m-30) REVERT: C 164 ASP cc_start: 0.8019 (t0) cc_final: 0.7739 (t0) REVERT: C 185 MET cc_start: 0.9262 (tpp) cc_final: 0.8985 (mmt) REVERT: C 211 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.6643 (mp10) REVERT: C 311 MET cc_start: 0.8971 (mmm) cc_final: 0.7333 (mmm) REVERT: C 358 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8995 (tp) REVERT: C 370 MET cc_start: 0.8035 (tmm) cc_final: 0.7736 (tmm) REVERT: C 460 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.7407 (t80) REVERT: C 509 PHE cc_start: 0.8604 (t80) cc_final: 0.8333 (p90) REVERT: C 737 GLN cc_start: 0.8777 (tp40) cc_final: 0.8309 (tp-100) REVERT: C 761 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.7753 (t0) REVERT: C 819 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9040 (tp) outliers start: 89 outliers final: 56 residues processed: 506 average time/residue: 0.3254 time to fit residues: 273.6843 Evaluate side-chains 482 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 416 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 333 PHE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 ARG Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 821 GLN Chi-restraints excluded: chain B residue 847 ASP Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 901 PHE Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 1014 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 363 PHE Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1014 PHE Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 452 CYS Chi-restraints excluded: chain C residue 460 PHE Chi-restraints excluded: chain C residue 676 MET Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain C residue 761 ASN Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 944 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 10.0000 chunk 268 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 298 optimal weight: 0.8980 chunk 247 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 GLN B 245 GLN ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 GLN ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24340 Z= 0.193 Angle : 0.705 25.580 33075 Z= 0.316 Chirality : 0.071 2.379 3951 Planarity : 0.004 0.045 4182 Dihedral : 6.079 149.940 3308 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.14 % Allowed : 22.76 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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: 1.13 (0.15), residues: 3079 helix: 1.58 (0.12), residues: 1726 sheet: 0.07 (0.23), residues: 458 loop : -0.38 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 853 HIS 0.002 0.000 HIS C 995 PHE 0.021 0.001 PHE B 455 TYR 0.017 0.001 TYR A 649 ARG 0.004 0.000 ARG C 994 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 438 time to evaluate : 2.382 Fit side-chains revert: symmetry clash REVERT: B 380 THR cc_start: 0.8951 (m) cc_final: 0.8715 (p) REVERT: B 384 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9194 (mm) REVERT: B 537 ARG cc_start: 0.6529 (ttt90) cc_final: 0.6080 (ttp-110) REVERT: B 696 MET cc_start: 0.9026 (tmm) cc_final: 0.8618 (tmm) REVERT: B 887 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8537 (mm-30) REVERT: B 937 ILE cc_start: 0.8509 (mt) cc_final: 0.8262 (mt) REVERT: B 940 ILE cc_start: 0.9186 (mm) cc_final: 0.8805 (mm) REVERT: B 1015 PHE cc_start: 0.8752 (m-80) cc_final: 0.8525 (m-80) REVERT: A 26 ILE cc_start: 0.9264 (mm) cc_final: 0.9055 (mm) REVERT: A 30 ASN cc_start: 0.8533 (t0) cc_final: 0.7854 (t0) REVERT: A 88 MET cc_start: 0.9211 (tmm) cc_final: 0.8830 (tmm) REVERT: A 124 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8217 (pttp) REVERT: A 370 MET cc_start: 0.8613 (mmt) cc_final: 0.8084 (mmm) REVERT: A 478 ILE cc_start: 0.9472 (mm) cc_final: 0.9194 (mt) REVERT: A 545 MET cc_start: 0.8960 (ttp) cc_final: 0.8503 (tmm) REVERT: A 736 MET cc_start: 0.9158 (tpp) cc_final: 0.8860 (tpt) REVERT: A 941 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8171 (tm-30) REVERT: C 96 ILE cc_start: 0.9252 (mt) cc_final: 0.8967 (tp) REVERT: C 106 ASP cc_start: 0.8628 (m-30) cc_final: 0.8307 (m-30) REVERT: C 211 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.6649 (mp10) REVERT: C 237 MET cc_start: 0.7892 (ttp) cc_final: 0.7591 (ttp) REVERT: C 311 MET cc_start: 0.8976 (mmm) cc_final: 0.7358 (mmm) REVERT: C 358 LEU cc_start: 0.9297 (tp) cc_final: 0.8992 (tp) REVERT: C 370 MET cc_start: 0.8049 (tmm) cc_final: 0.7765 (tmm) REVERT: C 460 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7462 (t80) REVERT: C 474 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8713 (mt) REVERT: C 509 PHE cc_start: 0.8620 (t80) cc_final: 0.8323 (p90) REVERT: C 737 GLN cc_start: 0.8781 (tp40) cc_final: 0.8343 (tp-100) REVERT: C 819 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9027 (tp) outliers start: 82 outliers final: 64 residues processed: 487 average time/residue: 0.2951 time to fit residues: 240.0618 Evaluate side-chains 478 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 408 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 333 PHE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 821 GLN Chi-restraints excluded: chain B residue 847 ASP Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 901 PHE Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 996 SER Chi-restraints excluded: chain B residue 1014 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 363 PHE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 452 CYS Chi-restraints excluded: chain C residue 460 PHE Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 676 MET Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 944 MET Chi-restraints excluded: chain C residue 987 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 169 optimal weight: 8.9990 chunk 217 optimal weight: 0.9990 chunk 168 optimal weight: 0.0870 chunk 250 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 chunk 296 optimal weight: 8.9990 chunk 185 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 24340 Z= 0.191 Angle : 0.714 25.674 33075 Z= 0.321 Chirality : 0.071 2.380 3951 Planarity : 0.004 0.060 4182 Dihedral : 6.076 153.060 3308 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.41 % Allowed : 23.14 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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: 1.15 (0.15), residues: 3079 helix: 1.59 (0.12), residues: 1719 sheet: 0.19 (0.24), residues: 450 loop : -0.43 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 853 HIS 0.002 0.000 HIS C 995 PHE 0.026 0.001 PHE B 966 TYR 0.018 0.001 TYR C 886 ARG 0.010 0.000 ARG C 703 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 430 time to evaluate : 2.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 185 MET cc_start: 0.9033 (mmt) cc_final: 0.8679 (tpp) REVERT: B 380 THR cc_start: 0.8951 (m) cc_final: 0.8702 (p) REVERT: B 384 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9175 (mm) REVERT: B 537 ARG cc_start: 0.6504 (ttt90) cc_final: 0.6040 (ttp-110) REVERT: B 631 TRP cc_start: 0.8614 (m-90) cc_final: 0.8234 (m-90) REVERT: B 676 MET cc_start: 0.8404 (tpp) cc_final: 0.7603 (tpp) REVERT: B 696 MET cc_start: 0.9024 (tmm) cc_final: 0.8647 (tmm) REVERT: B 887 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8670 (mm-30) REVERT: B 891 MET cc_start: 0.8608 (mmm) cc_final: 0.8407 (tpt) REVERT: B 937 ILE cc_start: 0.8502 (mt) cc_final: 0.8297 (mt) REVERT: B 940 ILE cc_start: 0.9223 (mm) cc_final: 0.8890 (mm) REVERT: B 1015 PHE cc_start: 0.8764 (m-80) cc_final: 0.8519 (m-80) REVERT: A 26 ILE cc_start: 0.9257 (mm) cc_final: 0.9049 (mm) REVERT: A 30 ASN cc_start: 0.8543 (t0) cc_final: 0.7838 (t0) REVERT: A 88 MET cc_start: 0.9209 (tmm) cc_final: 0.8831 (tmm) REVERT: A 124 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8234 (pttp) REVERT: A 370 MET cc_start: 0.8599 (mmt) cc_final: 0.8330 (mmm) REVERT: A 478 ILE cc_start: 0.9467 (mm) cc_final: 0.9207 (mt) REVERT: A 545 MET cc_start: 0.8982 (ttp) cc_final: 0.8520 (tmm) REVERT: A 652 ASP cc_start: 0.7036 (t0) cc_final: 0.6783 (t0) REVERT: C 96 ILE cc_start: 0.9256 (mt) cc_final: 0.8947 (tp) REVERT: C 164 ASP cc_start: 0.8077 (t0) cc_final: 0.7828 (t0) REVERT: C 211 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.6638 (mp10) REVERT: C 358 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9008 (tp) REVERT: C 370 MET cc_start: 0.7997 (tmm) cc_final: 0.7705 (tmm) REVERT: C 437 MET cc_start: 0.9245 (mmm) cc_final: 0.9006 (mmm) REVERT: C 460 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7466 (t80) REVERT: C 467 GLU cc_start: 0.9151 (tp30) cc_final: 0.8677 (tm-30) REVERT: C 474 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8566 (mt) REVERT: C 509 PHE cc_start: 0.8624 (t80) cc_final: 0.8313 (p90) REVERT: C 631 TRP cc_start: 0.8667 (m-10) cc_final: 0.8127 (m-10) REVERT: C 696 MET cc_start: 0.8063 (ttm) cc_final: 0.7742 (ttm) REVERT: C 737 GLN cc_start: 0.8780 (tp40) cc_final: 0.8353 (tp-100) REVERT: C 761 ASN cc_start: 0.8360 (OUTLIER) cc_final: 0.7825 (t0) REVERT: C 819 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9029 (tp) outliers start: 89 outliers final: 69 residues processed: 485 average time/residue: 0.2999 time to fit residues: 244.1132 Evaluate side-chains 490 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 413 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 311 MET Chi-restraints excluded: chain B residue 333 PHE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 821 GLN Chi-restraints excluded: chain B residue 847 ASP Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 901 PHE Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 996 SER Chi-restraints excluded: chain B residue 1014 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 363 PHE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1014 PHE Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 452 CYS Chi-restraints excluded: chain C residue 460 PHE Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 676 MET Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain C residue 761 ASN Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 944 MET Chi-restraints excluded: chain C residue 987 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 188 optimal weight: 10.0000 chunk 202 optimal weight: 0.7980 chunk 146 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 233 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 ASN ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 GLN A 859 GLN C 708 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24340 Z= 0.223 Angle : 0.720 25.657 33075 Z= 0.323 Chirality : 0.071 2.377 3951 Planarity : 0.004 0.045 4182 Dihedral : 6.080 155.810 3308 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.45 % Allowed : 23.49 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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: 1.16 (0.15), residues: 3079 helix: 1.62 (0.12), residues: 1718 sheet: 0.16 (0.24), residues: 446 loop : -0.44 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 853 HIS 0.002 0.000 HIS B 422 PHE 0.026 0.001 PHE B 966 TYR 0.019 0.001 TYR A 508 ARG 0.007 0.000 ARG C 703 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 428 time to evaluate : 3.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 185 MET cc_start: 0.9083 (mmt) cc_final: 0.8678 (tpp) REVERT: B 380 THR cc_start: 0.8949 (m) cc_final: 0.8727 (p) REVERT: B 384 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9201 (mm) REVERT: B 676 MET cc_start: 0.8311 (tpp) cc_final: 0.7602 (tpp) REVERT: B 696 MET cc_start: 0.9058 (tmm) cc_final: 0.8672 (tmm) REVERT: B 887 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8665 (mm-30) REVERT: B 937 ILE cc_start: 0.8533 (mt) cc_final: 0.8321 (mt) REVERT: B 940 ILE cc_start: 0.9247 (mm) cc_final: 0.8917 (mm) REVERT: B 1015 PHE cc_start: 0.8798 (m-80) cc_final: 0.8562 (m-80) REVERT: A 26 ILE cc_start: 0.9268 (mm) cc_final: 0.9066 (mm) REVERT: A 30 ASN cc_start: 0.8533 (t0) cc_final: 0.7838 (t0) REVERT: A 88 MET cc_start: 0.9209 (tmm) cc_final: 0.8818 (tmm) REVERT: A 147 SER cc_start: 0.9110 (OUTLIER) cc_final: 0.8780 (p) REVERT: A 370 MET cc_start: 0.8600 (mmt) cc_final: 0.8351 (mmm) REVERT: A 478 ILE cc_start: 0.9467 (mm) cc_final: 0.9198 (mt) REVERT: A 545 MET cc_start: 0.8988 (ttp) cc_final: 0.8587 (tmm) REVERT: C 96 ILE cc_start: 0.9259 (mt) cc_final: 0.8954 (tp) REVERT: C 164 ASP cc_start: 0.8061 (t0) cc_final: 0.7831 (t0) REVERT: C 211 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.6782 (mp10) REVERT: C 358 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9021 (tp) REVERT: C 370 MET cc_start: 0.7999 (tmm) cc_final: 0.7707 (tmm) REVERT: C 437 MET cc_start: 0.9275 (mmm) cc_final: 0.9017 (mmm) REVERT: C 467 GLU cc_start: 0.9159 (tp30) cc_final: 0.8674 (tm-30) REVERT: C 474 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8554 (mt) REVERT: C 509 PHE cc_start: 0.8695 (t80) cc_final: 0.8329 (p90) REVERT: C 631 TRP cc_start: 0.8699 (m-10) cc_final: 0.8161 (m-10) REVERT: C 696 MET cc_start: 0.8085 (ttm) cc_final: 0.7757 (ttm) REVERT: C 737 GLN cc_start: 0.8837 (tp40) cc_final: 0.8413 (tp-100) REVERT: C 761 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.7828 (t0) REVERT: C 819 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9041 (tp) REVERT: C 891 MET cc_start: 0.9238 (tpt) cc_final: 0.8936 (tpp) outliers start: 90 outliers final: 72 residues processed: 482 average time/residue: 0.3026 time to fit residues: 245.2447 Evaluate side-chains 489 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 410 time to evaluate : 3.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 311 MET Chi-restraints excluded: chain B residue 333 PHE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 821 GLN Chi-restraints excluded: chain B residue 847 ASP Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 901 PHE Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 996 SER Chi-restraints excluded: chain B residue 1014 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 363 PHE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 452 CYS Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 676 MET Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain C residue 761 ASN Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 944 MET Chi-restraints excluded: chain C residue 987 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 4.9990 chunk 284 optimal weight: 3.9990 chunk 259 optimal weight: 4.9990 chunk 276 optimal weight: 2.9990 chunk 166 optimal weight: 0.0980 chunk 120 optimal weight: 0.8980 chunk 217 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 249 optimal weight: 0.9990 chunk 261 optimal weight: 0.4980 chunk 275 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 GLN A 885 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24340 Z= 0.182 Angle : 0.731 25.827 33075 Z= 0.324 Chirality : 0.071 2.380 3951 Planarity : 0.004 0.045 4182 Dihedral : 6.076 159.396 3308 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.26 % Allowed : 23.95 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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: 1.17 (0.15), residues: 3079 helix: 1.61 (0.12), residues: 1714 sheet: 0.25 (0.24), residues: 450 loop : -0.45 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 853 HIS 0.002 0.000 HIS B 422 PHE 0.028 0.001 PHE B 966 TYR 0.022 0.001 TYR C 36 ARG 0.008 0.000 ARG C 703 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 433 time to evaluate : 2.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 185 MET cc_start: 0.9077 (mmt) cc_final: 0.8643 (tpp) REVERT: B 380 THR cc_start: 0.8949 (m) cc_final: 0.8703 (p) REVERT: B 676 MET cc_start: 0.8310 (tpp) cc_final: 0.7648 (tpp) REVERT: B 696 MET cc_start: 0.9047 (tmm) cc_final: 0.8673 (tmm) REVERT: B 937 ILE cc_start: 0.8537 (mt) cc_final: 0.8305 (mt) REVERT: B 940 ILE cc_start: 0.9240 (mm) cc_final: 0.9011 (mt) REVERT: A 26 ILE cc_start: 0.9245 (mm) cc_final: 0.9038 (mm) REVERT: A 30 ASN cc_start: 0.8535 (t0) cc_final: 0.7815 (t0) REVERT: A 88 MET cc_start: 0.9207 (tmm) cc_final: 0.8834 (tmm) REVERT: A 147 SER cc_start: 0.9099 (OUTLIER) cc_final: 0.8777 (p) REVERT: A 365 SER cc_start: 0.9494 (m) cc_final: 0.9245 (p) REVERT: A 370 MET cc_start: 0.8636 (mmt) cc_final: 0.8360 (mmm) REVERT: A 478 ILE cc_start: 0.9457 (mm) cc_final: 0.9187 (mt) REVERT: A 545 MET cc_start: 0.8973 (ttp) cc_final: 0.8523 (tmm) REVERT: C 96 ILE cc_start: 0.9243 (mt) cc_final: 0.8922 (tp) REVERT: C 106 ASP cc_start: 0.8614 (m-30) cc_final: 0.8277 (m-30) REVERT: C 164 ASP cc_start: 0.8095 (t0) cc_final: 0.7863 (t0) REVERT: C 211 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.6776 (mp10) REVERT: C 358 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9013 (tp) REVERT: C 370 MET cc_start: 0.7969 (tmm) cc_final: 0.7670 (tmm) REVERT: C 437 MET cc_start: 0.9256 (mmm) cc_final: 0.8999 (mmm) REVERT: C 460 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7462 (t80) REVERT: C 467 GLU cc_start: 0.9136 (tp30) cc_final: 0.8658 (tm-30) REVERT: C 474 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8511 (mt) REVERT: C 509 PHE cc_start: 0.8659 (t80) cc_final: 0.8286 (p90) REVERT: C 631 TRP cc_start: 0.8683 (m-10) cc_final: 0.8116 (m-10) REVERT: C 696 MET cc_start: 0.8074 (ttm) cc_final: 0.7735 (ttm) REVERT: C 737 GLN cc_start: 0.8792 (tp40) cc_final: 0.8360 (tp-100) REVERT: C 761 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.7822 (t0) REVERT: C 819 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9071 (tp) REVERT: C 891 MET cc_start: 0.9319 (tpt) cc_final: 0.9077 (tpp) outliers start: 85 outliers final: 69 residues processed: 481 average time/residue: 0.2949 time to fit residues: 240.3141 Evaluate side-chains 485 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 409 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 333 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 821 GLN Chi-restraints excluded: chain B residue 847 ASP Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 901 PHE Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 1014 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 363 PHE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 452 CYS Chi-restraints excluded: chain C residue 460 PHE Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 676 MET Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain C residue 761 ASN Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 944 MET Chi-restraints excluded: chain C residue 987 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 2.9990 chunk 292 optimal weight: 8.9990 chunk 178 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 203 optimal weight: 0.0980 chunk 306 optimal weight: 2.9990 chunk 282 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 188 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 GLN A 859 GLN A 885 GLN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24340 Z= 0.243 Angle : 0.743 25.705 33075 Z= 0.335 Chirality : 0.071 2.376 3951 Planarity : 0.004 0.046 4182 Dihedral : 6.111 160.962 3308 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.07 % Allowed : 24.33 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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: 1.16 (0.15), residues: 3079 helix: 1.63 (0.13), residues: 1712 sheet: 0.20 (0.24), residues: 448 loop : -0.47 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 853 HIS 0.002 0.000 HIS B 422 PHE 0.034 0.001 PHE A 538 TYR 0.029 0.001 TYR C 36 ARG 0.008 0.000 ARG C 703 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 416 time to evaluate : 2.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 185 MET cc_start: 0.9120 (mmt) cc_final: 0.8652 (tpp) REVERT: B 631 TRP cc_start: 0.8738 (m-90) cc_final: 0.8351 (m-90) REVERT: B 696 MET cc_start: 0.9065 (tmm) cc_final: 0.8678 (tmm) REVERT: B 887 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8637 (mm-30) REVERT: B 937 ILE cc_start: 0.8607 (mt) cc_final: 0.8335 (mt) REVERT: B 1015 PHE cc_start: 0.8956 (m-80) cc_final: 0.8693 (m-80) REVERT: A 26 ILE cc_start: 0.9261 (mm) cc_final: 0.9059 (mm) REVERT: A 30 ASN cc_start: 0.8580 (t0) cc_final: 0.7842 (t0) REVERT: A 88 MET cc_start: 0.9210 (tmm) cc_final: 0.8810 (tmm) REVERT: A 147 SER cc_start: 0.9125 (OUTLIER) cc_final: 0.8819 (p) REVERT: A 370 MET cc_start: 0.8634 (mmt) cc_final: 0.8414 (mmm) REVERT: A 478 ILE cc_start: 0.9458 (mm) cc_final: 0.9184 (mt) REVERT: A 545 MET cc_start: 0.9003 (ttp) cc_final: 0.8590 (tmm) REVERT: A 944 MET cc_start: 0.8311 (mtt) cc_final: 0.7960 (mtp) REVERT: C 96 ILE cc_start: 0.9250 (mt) cc_final: 0.8940 (tp) REVERT: C 106 ASP cc_start: 0.8643 (m-30) cc_final: 0.8302 (m-30) REVERT: C 211 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.6827 (mp10) REVERT: C 311 MET cc_start: 0.8934 (mmm) cc_final: 0.7333 (mmm) REVERT: C 358 LEU cc_start: 0.9346 (tp) cc_final: 0.9049 (tp) REVERT: C 370 MET cc_start: 0.7882 (tmm) cc_final: 0.7631 (tmm) REVERT: C 437 MET cc_start: 0.9291 (mmm) cc_final: 0.8859 (mmm) REVERT: C 467 GLU cc_start: 0.9160 (tp30) cc_final: 0.8655 (tm-30) REVERT: C 474 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8531 (mt) REVERT: C 509 PHE cc_start: 0.8730 (t80) cc_final: 0.8337 (p90) REVERT: C 631 TRP cc_start: 0.8705 (m-10) cc_final: 0.8124 (m-10) REVERT: C 696 MET cc_start: 0.8086 (ttm) cc_final: 0.7761 (ttm) REVERT: C 737 GLN cc_start: 0.8873 (tp40) cc_final: 0.8451 (tp-100) REVERT: C 761 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.7817 (t0) REVERT: C 819 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9077 (tp) REVERT: C 891 MET cc_start: 0.9353 (tpt) cc_final: 0.9079 (tpp) outliers start: 80 outliers final: 70 residues processed: 464 average time/residue: 0.2987 time to fit residues: 235.6239 Evaluate side-chains 482 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 407 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 333 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 821 GLN Chi-restraints excluded: chain B residue 847 ASP Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 901 PHE Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 1014 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 363 PHE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1014 PHE Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 277 ASN Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 452 CYS Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 676 MET Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain C residue 761 ASN Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain C residue 893 LEU Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 944 MET Chi-restraints excluded: chain C residue 987 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 1.9990 chunk 260 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 225 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 244 optimal weight: 3.9990 chunk 102 optimal weight: 0.4980 chunk 251 optimal weight: 0.0970 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 GLN ** C 108 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 = 0.3377 r_free = 0.3377 target = 0.091575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.075035 restraints weight = 60067.012| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.02 r_work: 0.2954 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24340 Z= 0.181 Angle : 0.742 25.848 33075 Z= 0.330 Chirality : 0.071 2.380 3951 Planarity : 0.004 0.045 4182 Dihedral : 6.093 163.366 3308 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.99 % Allowed : 24.33 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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: 1.17 (0.15), residues: 3079 helix: 1.60 (0.13), residues: 1714 sheet: 0.28 (0.24), residues: 451 loop : -0.45 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 853 HIS 0.001 0.000 HIS C 995 PHE 0.029 0.001 PHE A 538 TYR 0.027 0.001 TYR C 36 ARG 0.007 0.000 ARG C 703 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5506.22 seconds wall clock time: 100 minutes 51.47 seconds (6051.47 seconds total)