Starting phenix.real_space_refine on Sat Feb 24 23:16:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p1i_17350/02_2024/8p1i_17350_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p1i_17350/02_2024/8p1i_17350.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p1i_17350/02_2024/8p1i_17350_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p1i_17350/02_2024/8p1i_17350_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p1i_17350/02_2024/8p1i_17350_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p1i_17350/02_2024/8p1i_17350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p1i_17350/02_2024/8p1i_17350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p1i_17350/02_2024/8p1i_17350_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p1i_17350/02_2024/8p1i_17350_trim_updated.pdb" } resolution = 2.97 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= 0.004 sd= 0.134 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: 7 Type Number sf(0) Gaussians P 3 5.49 5 S 132 5.16 5 Cl 1 4.86 5 C 15157 2.51 5 N 3854 2.21 5 O 4361 1.98 5 H 23762 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 202": "OD1" <-> "OD2" Residue "B ASP 202": "OD1" <-> "OD2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "B PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 528": "OD1" <-> "OD2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 917": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 810": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 947": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 961": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 47270 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 15689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 15689 Classifications: {'peptide': 1024} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 976} Chain breaks: 1 Chain: "B" Number of atoms: 15730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 15730 Classifications: {'peptide': 1026} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 978} Chain breaks: 1 Chain: "C" Number of atoms: 15711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 15711 Classifications: {'peptide': 1026} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 978} Chain breaks: 1 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'WQW': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'WR6': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'PG8': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.59, per 1000 atoms: 0.44 Number of scatterers: 47270 At special positions: 0 Unit cell: (115.506, 123.876, 143.127, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 132 16.00 P 3 15.00 O 4361 8.00 N 3854 7.00 C 15157 6.00 H 23762 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 38.94 Conformation dependent library (CDL) restraints added in 4.9 seconds 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5600 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 27 sheets defined 54.4% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.09 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 9 through 29 Processing helix chain 'A' and resid 54 through 60 Processing helix chain 'A' and resid 62 through 68 removed outlier: 3.755A pdb=" N ASN A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 117 removed outlier: 3.838A pdb=" N LEU A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Proline residue: A 116 - end of helix Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 151 through 161 Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 299 through 312 removed outlier: 3.705A pdb=" N LYS A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 330 through 359 Processing helix chain 'A' and resid 362 through 386 removed outlier: 4.715A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 392 through 405 removed outlier: 3.612A pdb=" N ILE A 402 " --> pdb=" O MET A 398 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 422 removed outlier: 3.685A pdb=" N VAL A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 458 removed outlier: 5.447A pdb=" N GLY A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Proline residue: A 455 - end of helix removed outlier: 4.065A pdb=" N PHE A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 495 removed outlier: 3.986A pdb=" N ILE A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 511 through 536 Processing helix chain 'A' and resid 540 through 557 removed outlier: 3.630A pdb=" N TYR A 544 " --> pdb=" O TYR A 540 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 600 Processing helix chain 'A' and resid 633 through 635 No H-bonds generated for 'chain 'A' and resid 633 through 635' Processing helix chain 'A' and resid 643 through 656 removed outlier: 4.509A pdb=" N GLN A 656 " --> pdb=" O GLY A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 707 removed outlier: 3.965A pdb=" N GLN A 707 " --> pdb=" O GLY A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 737 Processing helix chain 'A' and resid 742 through 754 Processing helix chain 'A' and resid 776 through 778 No H-bonds generated for 'chain 'A' and resid 776 through 778' Processing helix chain 'A' and resid 782 through 787 removed outlier: 4.048A pdb=" N GLY A 786 " --> pdb=" O GLU A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 802 No H-bonds generated for 'chain 'A' and resid 800 through 802' Processing helix chain 'A' and resid 838 through 849 removed outlier: 3.572A pdb=" N GLY A 848 " --> pdb=" O GLU A 844 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS A 849 " --> pdb=" O GLU A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 867 removed outlier: 3.811A pdb=" N GLN A 864 " --> pdb=" O GLY A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 891 Processing helix chain 'A' and resid 896 through 918 removed outlier: 3.846A pdb=" N MET A 901 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU A 902 " --> pdb=" O SER A 899 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 903 " --> pdb=" O VAL A 900 " (cutoff:3.500A) Proline residue: A 905 - end of helix removed outlier: 3.563A pdb=" N VAL A 908 " --> pdb=" O PRO A 905 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A 909 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 917 " --> pdb=" O ALA A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 952 removed outlier: 3.696A pdb=" N LEU A 931 " --> pdb=" O GLN A 927 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU A 951 " --> pdb=" O PHE A 947 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET A 952 " --> pdb=" O ALA A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 967 No H-bonds generated for 'chain 'A' and resid 964 through 967' Processing helix chain 'A' and resid 972 through 989 removed outlier: 4.036A pdb=" N MET A 986 " --> pdb=" O ILE A 982 " (cutoff:3.500A) Proline residue: A 987 - end of helix Processing helix chain 'A' and resid 996 through 1015 removed outlier: 3.760A pdb=" N GLY A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1031 Proline residue: A1022 - end of helix Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 9 through 29 Processing helix chain 'B' and resid 54 through 60 Processing helix chain 'B' and resid 62 through 68 removed outlier: 3.716A pdb=" N ASN B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 113 Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 151 through 168 removed outlier: 4.369A pdb=" N LYS B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ASP B 164 " --> pdb=" O ALA B 160 " (cutoff:3.500A) Proline residue: B 165 - end of helix Processing helix chain 'B' and resid 190 through 195 Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.695A pdb=" N ALA B 209 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 248 Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'B' and resid 299 through 312 Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 330 through 359 Processing helix chain 'B' and resid 362 through 385 removed outlier: 3.773A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 392 through 423 removed outlier: 4.629A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 435 Processing helix chain 'B' and resid 439 through 458 Proline residue: B 455 - end of helix removed outlier: 4.031A pdb=" N PHE B 458 " --> pdb=" O ILE B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 485 removed outlier: 3.602A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 496 Processing helix chain 'B' and resid 510 through 535 removed outlier: 3.643A pdb=" N ARG B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 556 removed outlier: 3.898A pdb=" N VAL B 542 " --> pdb=" O GLY B 538 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 600 Processing helix chain 'B' and resid 633 through 635 No H-bonds generated for 'chain 'B' and resid 633 through 635' Processing helix chain 'B' and resid 639 through 641 No H-bonds generated for 'chain 'B' and resid 639 through 641' Processing helix chain 'B' and resid 643 through 656 removed outlier: 4.607A pdb=" N GLN B 656 " --> pdb=" O GLY B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 707 removed outlier: 4.014A pdb=" N GLN B 707 " --> pdb=" O GLY B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 737 Processing helix chain 'B' and resid 742 through 753 Processing helix chain 'B' and resid 776 through 778 No H-bonds generated for 'chain 'B' and resid 776 through 778' Processing helix chain 'B' and resid 782 through 787 removed outlier: 3.748A pdb=" N GLY B 786 " --> pdb=" O GLU B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 802 No H-bonds generated for 'chain 'B' and resid 800 through 802' Processing helix chain 'B' and resid 836 through 848 Processing helix chain 'B' and resid 861 through 869 Processing helix chain 'B' and resid 872 through 891 removed outlier: 3.977A pdb=" N TYR B 876 " --> pdb=" O ALA B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 918 removed outlier: 3.658A pdb=" N MET B 901 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LEU B 902 " --> pdb=" O SER B 899 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL B 903 " --> pdb=" O VAL B 900 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 904 " --> pdb=" O MET B 901 " (cutoff:3.500A) Proline residue: B 905 - end of helix removed outlier: 3.620A pdb=" N VAL B 908 " --> pdb=" O PRO B 905 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 909 " --> pdb=" O LEU B 906 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG B 918 " --> pdb=" O ALA B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 954 Processing helix chain 'B' and resid 959 through 990 removed outlier: 4.754A pdb=" N ARG B 972 " --> pdb=" O ARG B 968 " (cutoff:3.500A) Proline residue: B 973 - end of helix Proline residue: B 987 - end of helix Processing helix chain 'B' and resid 996 through 1031 removed outlier: 4.133A pdb=" N GLY B1005 " --> pdb=" O ALA B1001 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B1006 " --> pdb=" O VAL B1002 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE B1018 " --> pdb=" O THR B1014 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE B1019 " --> pdb=" O ILE B1015 " (cutoff:3.500A) Proline residue: B1022 - end of helix Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 9 through 29 removed outlier: 3.661A pdb=" N LEU C 28 " --> pdb=" O GLY C 24 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 60 Processing helix chain 'C' and resid 62 through 68 removed outlier: 3.682A pdb=" N ASN C 68 " --> pdb=" O VAL C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 117 removed outlier: 3.590A pdb=" N LEU C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) Proline residue: C 116 - end of helix Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 151 through 161 Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 200 through 210 Processing helix chain 'C' and resid 243 through 248 Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 299 through 316 Proline residue: C 315 - end of helix Processing helix chain 'C' and resid 330 through 359 Processing helix chain 'C' and resid 362 through 385 Proline residue: C 368 - end of helix removed outlier: 4.170A pdb=" N ALA C 371 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 392 through 401 Processing helix chain 'C' and resid 407 through 423 Processing helix chain 'C' and resid 427 through 451 removed outlier: 5.749A pdb=" N GLY C 440 " --> pdb=" O GLY C 436 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ALA C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 443 " --> pdb=" O GLN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 458 Processing helix chain 'C' and resid 461 through 496 removed outlier: 3.826A pdb=" N GLN C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Proline residue: C 490 - end of helix Processing helix chain 'C' and resid 511 through 535 removed outlier: 3.631A pdb=" N ARG C 535 " --> pdb=" O GLY C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 557 removed outlier: 3.548A pdb=" N LEU C 541 " --> pdb=" O GLY C 538 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL C 542 " --> pdb=" O ARG C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 599 Processing helix chain 'C' and resid 633 through 635 No H-bonds generated for 'chain 'C' and resid 633 through 635' Processing helix chain 'C' and resid 639 through 641 No H-bonds generated for 'chain 'C' and resid 639 through 641' Processing helix chain 'C' and resid 643 through 656 removed outlier: 4.354A pdb=" N GLN C 656 " --> pdb=" O GLY C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 707 removed outlier: 3.967A pdb=" N GLN C 707 " --> pdb=" O GLY C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 737 Processing helix chain 'C' and resid 742 through 753 Processing helix chain 'C' and resid 776 through 778 No H-bonds generated for 'chain 'C' and resid 776 through 778' Processing helix chain 'C' and resid 782 through 787 Processing helix chain 'C' and resid 800 through 802 No H-bonds generated for 'chain 'C' and resid 800 through 802' Processing helix chain 'C' and resid 836 through 848 Processing helix chain 'C' and resid 861 through 891 Proline residue: C 873 - end of helix Processing helix chain 'C' and resid 896 through 901 Processing helix chain 'C' and resid 904 through 918 removed outlier: 4.041A pdb=" N GLY C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 954 removed outlier: 3.828A pdb=" N ILE C 944 " --> pdb=" O ASN C 940 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 984 removed outlier: 5.103A pdb=" N ARG C 972 " --> pdb=" O ARG C 968 " (cutoff:3.500A) Proline residue: C 973 - end of helix Processing helix chain 'C' and resid 986 through 989 No H-bonds generated for 'chain 'C' and resid 986 through 989' Processing helix chain 'C' and resid 997 through 1015 removed outlier: 4.268A pdb=" N GLY C1005 " --> pdb=" O ALA C1001 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL C1006 " --> pdb=" O VAL C1002 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1031 Proline residue: C1022 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 128 through 130 removed outlier: 3.837A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 77 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 321 through 324 removed outlier: 3.695A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 268 through 272 Processing sheet with id= D, first strand: chain 'A' and resid 278 through 281 removed outlier: 6.919A pdb=" N SER A 629 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL A 608 " --> pdb=" O PHE A 627 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE A 627 " --> pdb=" O VAL A 608 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ALA A 610 " --> pdb=" O ILE A 625 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE A 625 " --> pdb=" O ALA A 610 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ASN A 612 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N THR A 623 " --> pdb=" O ASN A 612 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 681 through 684 Processing sheet with id= F, first strand: chain 'A' and resid 722 through 730 Processing sheet with id= G, first strand: chain 'A' and resid 760 through 763 Processing sheet with id= H, first strand: chain 'A' and resid 789 through 791 Processing sheet with id= I, first strand: chain 'A' and resid 250 through 253 removed outlier: 7.022A pdb=" N VAL A 260 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 128 through 131 removed outlier: 3.869A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 321 through 324 removed outlier: 3.578A pdb=" N LYS B 322 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY B 288 " --> pdb=" O PHE B 178 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 266 through 272 Processing sheet with id= M, first strand: chain 'B' and resid 278 through 281 removed outlier: 6.808A pdb=" N SER B 629 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL B 608 " --> pdb=" O PHE B 627 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE B 627 " --> pdb=" O VAL B 608 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA B 610 " --> pdb=" O ILE B 625 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE B 625 " --> pdb=" O ALA B 610 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 679 through 682 removed outlier: 3.555A pdb=" N GLY B 828 " --> pdb=" O PHE B 679 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 722 through 730 Processing sheet with id= P, first strand: chain 'B' and resid 760 through 762 Processing sheet with id= Q, first strand: chain 'B' and resid 789 through 791 Processing sheet with id= R, first strand: chain 'B' and resid 250 through 253 removed outlier: 6.846A pdb=" N VAL B 260 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 127 through 131 removed outlier: 4.034A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 321 through 324 Processing sheet with id= U, first strand: chain 'C' and resid 266 through 272 Processing sheet with id= V, first strand: chain 'C' and resid 278 through 281 removed outlier: 6.834A pdb=" N SER C 629 " --> pdb=" O GLU C 606 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL C 608 " --> pdb=" O PHE C 627 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE C 627 " --> pdb=" O VAL C 608 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ALA C 610 " --> pdb=" O ILE C 625 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE C 625 " --> pdb=" O ALA C 610 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ASN C 612 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N THR C 623 " --> pdb=" O ASN C 612 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 679 through 684 removed outlier: 3.566A pdb=" N GLY C 828 " --> pdb=" O PHE C 679 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 722 through 730 Processing sheet with id= Y, first strand: chain 'C' and resid 760 through 763 Processing sheet with id= Z, first strand: chain 'C' and resid 789 through 791 Processing sheet with id= AA, first strand: chain 'C' and resid 250 through 253 removed outlier: 6.854A pdb=" N VAL C 260 " --> pdb=" O LEU C 251 " (cutoff:3.500A) 1284 hydrogen bonds defined for protein. 3663 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 21.96 Time building geometry restraints manager: 39.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 23756 1.02 - 1.22: 12 1.22 - 1.41: 9554 1.41 - 1.61: 14146 1.61 - 1.81: 261 Bond restraints: 47729 Sorted by residual: bond pdb=" C13 WQW A1101 " pdb=" N4 WQW A1101 " ideal model delta sigma weight residual 1.451 1.365 0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" CA VAL A 671 " pdb=" CB VAL A 671 " ideal model delta sigma weight residual 1.540 1.589 -0.049 1.36e-02 5.41e+03 1.31e+01 bond pdb=" C5 WQW A1101 " pdb=" N2 WQW A1101 " ideal model delta sigma weight residual 1.452 1.389 0.063 2.00e-02 2.50e+03 9.95e+00 bond pdb=" C12 WQW A1101 " pdb="CL1 WQW A1101 " ideal model delta sigma weight residual 1.785 1.726 0.059 2.00e-02 2.50e+03 8.65e+00 bond pdb=" CA GLU A 672 " pdb=" C GLU A 672 " ideal model delta sigma weight residual 1.520 1.481 0.039 1.37e-02 5.33e+03 8.25e+00 ... (remaining 47724 not shown) Histogram of bond angle deviations from ideal: 73.35 - 85.49: 3 85.49 - 97.63: 0 97.63 - 109.77: 35377 109.77 - 121.91: 43466 121.91 - 134.05: 7607 Bond angle restraints: 86453 Sorted by residual: angle pdb=" C LYS B1034 " pdb=" CA LYS B1034 " pdb=" HA LYS B1034 " ideal model delta sigma weight residual 109.00 73.35 35.65 3.00e+00 1.11e-01 1.41e+02 angle pdb=" N LYS B1034 " pdb=" CA LYS B1034 " pdb=" HA LYS B1034 " ideal model delta sigma weight residual 110.00 74.76 35.24 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CB LYS B1034 " pdb=" CA LYS B1034 " pdb=" HA LYS B1034 " ideal model delta sigma weight residual 109.00 79.91 29.09 3.00e+00 1.11e-01 9.40e+01 angle pdb=" C13 WQW A1101 " pdb=" N4 WQW A1101 " pdb=" C14 WQW A1101 " ideal model delta sigma weight residual 109.47 125.30 -15.83 3.00e+00 1.11e-01 2.79e+01 angle pdb=" C11 WQW A1101 " pdb=" C12 WQW A1101 " pdb="CL1 WQW A1101 " ideal model delta sigma weight residual 103.55 117.99 -14.44 3.00e+00 1.11e-01 2.32e+01 ... (remaining 86448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.14: 21742 33.14 - 66.28: 719 66.28 - 99.42: 19 99.42 - 132.56: 3 132.56 - 165.71: 2 Dihedral angle restraints: 22485 sinusoidal: 12356 harmonic: 10129 Sorted by residual: dihedral pdb=" CA VAL A 671 " pdb=" C VAL A 671 " pdb=" N GLU A 672 " pdb=" CA GLU A 672 " ideal model delta harmonic sigma weight residual 180.00 154.64 25.36 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" C47 WR6 B1101 " pdb=" O46 WR6 B1101 " pdb=" P43 WR6 B1101 " pdb=" O42 WR6 B1101 " ideal model delta sinusoidal sigma weight residual -147.80 17.91 -165.71 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C23 WR6 B1101 " pdb=" C26 WR6 B1101 " pdb=" O25 WR6 B1101 " pdb=" C27 WR6 B1101 " ideal model delta sinusoidal sigma weight residual 96.06 -58.01 154.07 1 3.00e+01 1.11e-03 2.03e+01 ... (remaining 22482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3601 0.092 - 0.184: 196 0.184 - 0.275: 0 0.275 - 0.367: 0 0.367 - 0.459: 1 Chirality restraints: 3798 Sorted by residual: chirality pdb=" CA LYS B1034 " pdb=" N LYS B1034 " pdb=" C LYS B1034 " pdb=" CB LYS B1034 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" CA VAL A 671 " pdb=" N VAL A 671 " pdb=" C VAL A 671 " pdb=" CB VAL A 671 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CA ILE C 186 " pdb=" N ILE C 186 " pdb=" C ILE C 186 " pdb=" CB ILE C 186 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 3795 not shown) Planarity restraints: 7079 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET C 69 " 0.025 2.00e-02 2.50e+03 4.65e-02 2.16e+01 pdb=" N ASN C 70 " -0.080 2.00e-02 2.50e+03 pdb=" CA ASN C 70 " 0.020 2.00e-02 2.50e+03 pdb=" H ASN C 70 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 671 " -0.023 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" N GLU A 672 " 0.079 2.00e-02 2.50e+03 pdb=" CA GLU A 672 " -0.020 2.00e-02 2.50e+03 pdb=" H GLU A 672 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 960 " -0.023 2.00e-02 2.50e+03 4.19e-02 1.76e+01 pdb=" N GLU A 961 " 0.072 2.00e-02 2.50e+03 pdb=" CA GLU A 961 " -0.019 2.00e-02 2.50e+03 pdb=" H GLU A 961 " -0.031 2.00e-02 2.50e+03 ... (remaining 7076 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1697 2.17 - 2.78: 94057 2.78 - 3.38: 135783 3.38 - 3.99: 177838 3.99 - 4.60: 281804 Nonbonded interactions: 691179 Sorted by model distance: nonbonded pdb=" O VAL A 711 " pdb=" H ALA A 831 " model vdw 1.560 1.850 nonbonded pdb=" HH TYR A 757 " pdb=" OD1 ASP A 760 " model vdw 1.576 1.850 nonbonded pdb=" O ASN C 361 " pdb=" HG1 THR C 365 " model vdw 1.577 1.850 nonbonded pdb=" H GLY A 792 " pdb=" O GLN A 796 " model vdw 1.607 1.850 nonbonded pdb="HH21 ARG B 307 " pdb=" OD2 ASP B 328 " model vdw 1.607 1.850 ... (remaining 691174 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 1031 or (resid 1032 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ )) or (resid 1033 and (name N or name CA or name C or name O or \ name CB or name OG )))) selection = (chain 'B' and (resid 1 through 499 or resid 509 through 1031 or (resid 1032 and \ (name N or name CA or name C or name O or name CB or name CG or name CD1 or nam \ e CD2 or name CE1 or name CE2 or name CZ )) or (resid 1033 and (name N or name C \ A or name C or name O or name CB or name OG )))) selection = (chain 'C' and (resid 1 through 499 or resid 509 through 1033)) } 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: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.690 Extract box with map and model: 14.190 Check model and map are aligned: 0.730 Set scattering table: 0.450 Process input model: 151.140 Find NCS groups from input model: 2.620 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 183.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 : 0.005 0.086 23967 Z= 0.295 Angle : 0.568 15.834 32532 Z= 0.277 Chirality : 0.041 0.459 3798 Planarity : 0.003 0.047 4152 Dihedral : 14.045 165.706 8705 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.24 (0.15), residues: 3064 helix: 1.98 (0.13), residues: 1639 sheet: -0.54 (0.27), residues: 355 loop : -0.47 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 894 HIS 0.003 0.001 HIS A 338 PHE 0.028 0.001 PHE A 761 TYR 0.023 0.002 TYR B 49 ARG 0.002 0.000 ARG B 918 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 345 time to evaluate : 4.081 Fit side-chains revert: symmetry clash REVERT: A 917 PHE cc_start: 0.7112 (m-80) cc_final: 0.6630 (t80) REVERT: B 29 LYS cc_start: 0.7213 (mttt) cc_final: 0.5769 (pptt) REVERT: B 269 GLU cc_start: 0.8221 (pt0) cc_final: 0.7961 (pt0) REVERT: B 309 GLU cc_start: 0.7468 (tp30) cc_final: 0.7192 (mm-30) REVERT: B 574 MET cc_start: 0.7442 (ptt) cc_final: 0.7088 (ptm) REVERT: B 1015 ILE cc_start: 0.8589 (mm) cc_final: 0.8338 (mt) REVERT: C 29 LYS cc_start: 0.8206 (mmmt) cc_final: 0.7132 (pptt) REVERT: C 267 LYS cc_start: 0.7652 (tttp) cc_final: 0.7391 (tttp) REVERT: C 312 LYS cc_start: 0.7101 (mttt) cc_final: 0.6764 (tmtt) REVERT: C 528 ASP cc_start: 0.7507 (t70) cc_final: 0.7229 (t0) REVERT: C 780 MET cc_start: 0.8860 (mmt) cc_final: 0.7911 (mmt) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 2.8517 time to fit residues: 1141.3411 Evaluate side-chains 278 residues out of total 2500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 3.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.7980 chunk 231 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 239 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 277 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 922 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.0622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23967 Z= 0.254 Angle : 0.523 10.626 32532 Z= 0.268 Chirality : 0.041 0.457 3798 Planarity : 0.004 0.038 4152 Dihedral : 8.014 171.773 3369 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.84 % Allowed : 7.12 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.19 (0.15), residues: 3064 helix: 1.94 (0.13), residues: 1651 sheet: -0.70 (0.26), residues: 371 loop : -0.47 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 553 HIS 0.003 0.001 HIS A 525 PHE 0.027 0.001 PHE C 616 TYR 0.014 0.001 TYR B 49 ARG 0.002 0.000 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 292 time to evaluate : 3.663 Fit side-chains REVERT: A 29 LYS cc_start: 0.7394 (mmmt) cc_final: 0.5573 (pptt) REVERT: A 307 ARG cc_start: 0.7113 (mtt-85) cc_final: 0.6435 (mtm110) REVERT: A 672 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: A 917 PHE cc_start: 0.7240 (m-80) cc_final: 0.6715 (t80) REVERT: B 29 LYS cc_start: 0.7167 (mttt) cc_final: 0.5718 (pptt) REVERT: B 248 ASN cc_start: 0.8052 (t160) cc_final: 0.7789 (t0) REVERT: B 269 GLU cc_start: 0.8259 (pt0) cc_final: 0.7975 (pt0) REVERT: B 309 GLU cc_start: 0.7511 (tp30) cc_final: 0.7275 (mm-30) REVERT: B 574 MET cc_start: 0.7344 (ptt) cc_final: 0.7044 (ptm) REVERT: B 644 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.6315 (mp0) REVERT: B 1015 ILE cc_start: 0.8573 (mm) cc_final: 0.8321 (mt) REVERT: C 3 ASN cc_start: 0.8055 (OUTLIER) cc_final: 0.7840 (m110) REVERT: C 29 LYS cc_start: 0.8202 (mmmt) cc_final: 0.7153 (pptt) REVERT: C 48 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.6614 (tmm) REVERT: C 151 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.6885 (mt0) REVERT: C 267 LYS cc_start: 0.7579 (tttp) cc_final: 0.7314 (tttp) REVERT: C 312 LYS cc_start: 0.7207 (mttt) cc_final: 0.6804 (tmtt) REVERT: C 528 ASP cc_start: 0.7466 (t70) cc_final: 0.7209 (t0) REVERT: C 780 MET cc_start: 0.8867 (mmt) cc_final: 0.8117 (mmt) REVERT: C 840 MET cc_start: 0.8118 (mtp) cc_final: 0.7812 (mtm) outliers start: 21 outliers final: 7 residues processed: 302 average time/residue: 2.7506 time to fit residues: 969.0154 Evaluate side-chains 293 residues out of total 2500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 281 time to evaluate : 3.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 965 GLU Chi-restraints excluded: chain C residue 992 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 231 optimal weight: 0.1980 chunk 189 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 278 optimal weight: 5.9990 chunk 300 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 276 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 223 optimal weight: 0.5980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 922 ASN C 144 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23967 Z= 0.207 Angle : 0.489 10.664 32532 Z= 0.248 Chirality : 0.040 0.458 3798 Planarity : 0.003 0.036 4152 Dihedral : 7.695 178.661 3369 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.88 % Allowed : 8.40 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.30 (0.16), residues: 3064 helix: 2.05 (0.13), residues: 1654 sheet: -0.71 (0.26), residues: 379 loop : -0.42 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 553 HIS 0.004 0.001 HIS A 525 PHE 0.014 0.001 PHE C 571 TYR 0.013 0.001 TYR B 49 ARG 0.002 0.000 ARG C 619 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 291 time to evaluate : 3.587 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7416 (mmmt) cc_final: 0.5563 (pptt) REVERT: A 69 MET cc_start: 0.8826 (mmt) cc_final: 0.8098 (mmt) REVERT: A 836 THR cc_start: 0.7899 (m) cc_final: 0.7603 (p) REVERT: A 917 PHE cc_start: 0.7252 (m-80) cc_final: 0.6734 (t80) REVERT: B 29 LYS cc_start: 0.7159 (mttt) cc_final: 0.5721 (pptt) REVERT: B 248 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7791 (t0) REVERT: B 269 GLU cc_start: 0.8279 (pt0) cc_final: 0.7992 (pt0) REVERT: B 309 GLU cc_start: 0.7521 (tp30) cc_final: 0.7306 (mm-30) REVERT: B 566 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7518 (mt-10) REVERT: B 574 MET cc_start: 0.7318 (ptt) cc_final: 0.6991 (ptm) REVERT: B 644 GLU cc_start: 0.6415 (OUTLIER) cc_final: 0.6136 (mp0) REVERT: B 1015 ILE cc_start: 0.8588 (mm) cc_final: 0.8334 (mt) REVERT: C 29 LYS cc_start: 0.8196 (mmmt) cc_final: 0.7127 (pptt) REVERT: C 151 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.6839 (mt0) REVERT: C 267 LYS cc_start: 0.7587 (tttp) cc_final: 0.7297 (tttp) REVERT: C 312 LYS cc_start: 0.7347 (mttt) cc_final: 0.6825 (tmtt) REVERT: C 528 ASP cc_start: 0.7424 (t70) cc_final: 0.7180 (t0) REVERT: C 780 MET cc_start: 0.8835 (mmt) cc_final: 0.8192 (mmt) REVERT: C 840 MET cc_start: 0.8085 (mtp) cc_final: 0.7821 (mtm) outliers start: 22 outliers final: 11 residues processed: 302 average time/residue: 2.7306 time to fit residues: 962.8555 Evaluate side-chains 297 residues out of total 2500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 282 time to evaluate : 3.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 965 GLU Chi-restraints excluded: chain C residue 992 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 4.9990 chunk 209 optimal weight: 0.8980 chunk 144 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 264 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 922 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23967 Z= 0.241 Angle : 0.495 10.649 32532 Z= 0.251 Chirality : 0.041 0.458 3798 Planarity : 0.004 0.035 4152 Dihedral : 7.515 172.216 3369 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.04 % Allowed : 9.44 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.27 (0.16), residues: 3064 helix: 2.02 (0.13), residues: 1654 sheet: -0.71 (0.26), residues: 385 loop : -0.42 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 553 HIS 0.003 0.001 HIS A 525 PHE 0.015 0.001 PHE C 571 TYR 0.014 0.001 TYR B 653 ARG 0.002 0.000 ARG C 619 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 285 time to evaluate : 3.722 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7468 (mmmt) cc_final: 0.5610 (pptt) REVERT: A 69 MET cc_start: 0.8806 (mmt) cc_final: 0.8147 (mmt) REVERT: A 836 THR cc_start: 0.8037 (m) cc_final: 0.7755 (p) REVERT: B 29 LYS cc_start: 0.7180 (mttt) cc_final: 0.5743 (pptt) REVERT: B 248 ASN cc_start: 0.8075 (OUTLIER) cc_final: 0.7797 (t0) REVERT: B 269 GLU cc_start: 0.8285 (pt0) cc_final: 0.8014 (pt0) REVERT: B 309 GLU cc_start: 0.7521 (tp30) cc_final: 0.7297 (mm-30) REVERT: B 423 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7124 (mt-10) REVERT: B 566 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7471 (mt-10) REVERT: B 574 MET cc_start: 0.7273 (ptt) cc_final: 0.6958 (ptm) REVERT: B 644 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.6169 (mp0) REVERT: B 1015 ILE cc_start: 0.8578 (mm) cc_final: 0.8320 (mt) REVERT: C 29 LYS cc_start: 0.8193 (mmmt) cc_final: 0.7140 (pptt) REVERT: C 151 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.6843 (mt0) REVERT: C 267 LYS cc_start: 0.7605 (tttp) cc_final: 0.7377 (tttp) REVERT: C 312 LYS cc_start: 0.7358 (mttt) cc_final: 0.6797 (tmtt) REVERT: C 528 ASP cc_start: 0.7445 (t70) cc_final: 0.7191 (t0) REVERT: C 780 MET cc_start: 0.8783 (mmt) cc_final: 0.8264 (mmt) REVERT: C 840 MET cc_start: 0.8081 (mtp) cc_final: 0.7785 (mtm) outliers start: 26 outliers final: 15 residues processed: 295 average time/residue: 2.7619 time to fit residues: 953.3136 Evaluate side-chains 300 residues out of total 2500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 280 time to evaluate : 3.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 242 ASN Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 965 GLU Chi-restraints excluded: chain C residue 992 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 252 optimal weight: 2.9990 chunk 204 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 265 optimal weight: 0.0470 chunk 74 optimal weight: 4.9990 overall best weight: 1.5082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23967 Z= 0.218 Angle : 0.485 10.661 32532 Z= 0.246 Chirality : 0.040 0.458 3798 Planarity : 0.004 0.036 4152 Dihedral : 7.338 163.953 3369 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.08 % Allowed : 10.24 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.33 (0.16), residues: 3064 helix: 2.07 (0.13), residues: 1653 sheet: -0.74 (0.25), residues: 410 loop : -0.35 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 553 HIS 0.003 0.001 HIS A 525 PHE 0.014 0.001 PHE C 571 TYR 0.018 0.001 TYR B 653 ARG 0.004 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 289 time to evaluate : 3.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7430 (mmmt) cc_final: 0.5535 (pptt) REVERT: A 69 MET cc_start: 0.8806 (mmt) cc_final: 0.8204 (mmt) REVERT: A 836 THR cc_start: 0.8036 (m) cc_final: 0.7767 (p) REVERT: B 29 LYS cc_start: 0.7165 (mttt) cc_final: 0.5735 (pptt) REVERT: B 248 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7838 (t0) REVERT: B 269 GLU cc_start: 0.8273 (pt0) cc_final: 0.8008 (pt0) REVERT: B 309 GLU cc_start: 0.7528 (tp30) cc_final: 0.7305 (mm-30) REVERT: B 566 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7468 (mt-10) REVERT: B 574 MET cc_start: 0.7249 (ptt) cc_final: 0.6927 (ptm) REVERT: B 644 GLU cc_start: 0.6465 (OUTLIER) cc_final: 0.6149 (mp0) REVERT: B 1015 ILE cc_start: 0.8517 (mm) cc_final: 0.8255 (mt) REVERT: C 29 LYS cc_start: 0.8195 (mmmt) cc_final: 0.7147 (pptt) REVERT: C 48 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.6797 (tmm) REVERT: C 151 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.6849 (mt0) REVERT: C 267 LYS cc_start: 0.7599 (tttp) cc_final: 0.7361 (tttp) REVERT: C 312 LYS cc_start: 0.7360 (mttt) cc_final: 0.6777 (tmtt) REVERT: C 528 ASP cc_start: 0.7417 (t70) cc_final: 0.7163 (t0) REVERT: C 780 MET cc_start: 0.8765 (mmt) cc_final: 0.8289 (mmt) REVERT: C 840 MET cc_start: 0.8056 (mtp) cc_final: 0.7745 (mtm) outliers start: 27 outliers final: 13 residues processed: 302 average time/residue: 2.7656 time to fit residues: 986.2008 Evaluate side-chains 301 residues out of total 2500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 283 time to evaluate : 3.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 242 ASN Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 992 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 3.9990 chunk 266 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 23967 Z= 0.323 Angle : 0.517 10.631 32532 Z= 0.264 Chirality : 0.042 0.457 3798 Planarity : 0.004 0.047 4152 Dihedral : 7.327 160.272 3369 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.12 % Allowed : 10.76 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 3064 helix: 1.92 (0.13), residues: 1653 sheet: -0.81 (0.25), residues: 410 loop : -0.43 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 894 HIS 0.004 0.001 HIS A 525 PHE 0.019 0.001 PHE A 11 TYR 0.018 0.001 TYR B 49 ARG 0.008 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 285 time to evaluate : 3.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7654 (mmmt) cc_final: 0.5745 (pptt) REVERT: A 69 MET cc_start: 0.8781 (mmt) cc_final: 0.8189 (mmt) REVERT: A 836 THR cc_start: 0.8123 (m) cc_final: 0.7868 (p) REVERT: B 29 LYS cc_start: 0.7212 (mttt) cc_final: 0.5767 (pptt) REVERT: B 248 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7841 (t0) REVERT: B 269 GLU cc_start: 0.8267 (pt0) cc_final: 0.8051 (pt0) REVERT: B 309 GLU cc_start: 0.7523 (tp30) cc_final: 0.7316 (mm-30) REVERT: B 566 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7493 (mt-10) REVERT: B 574 MET cc_start: 0.7283 (ptt) cc_final: 0.6964 (ptm) REVERT: B 644 GLU cc_start: 0.6470 (OUTLIER) cc_final: 0.6159 (mp0) REVERT: B 1015 ILE cc_start: 0.8511 (mm) cc_final: 0.8249 (mt) REVERT: C 3 ASN cc_start: 0.8122 (OUTLIER) cc_final: 0.7892 (m110) REVERT: C 29 LYS cc_start: 0.8206 (mmmt) cc_final: 0.7143 (pptt) REVERT: C 48 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.6741 (tmm) REVERT: C 151 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.6947 (mt0) REVERT: C 267 LYS cc_start: 0.7585 (tttp) cc_final: 0.7363 (tttp) REVERT: C 312 LYS cc_start: 0.7350 (mttt) cc_final: 0.6775 (tmtt) REVERT: C 528 ASP cc_start: 0.7454 (t70) cc_final: 0.7199 (t0) REVERT: C 780 MET cc_start: 0.8737 (mmt) cc_final: 0.8298 (mmt) REVERT: C 840 MET cc_start: 0.8070 (mtp) cc_final: 0.7775 (mtm) outliers start: 28 outliers final: 12 residues processed: 297 average time/residue: 2.8188 time to fit residues: 974.9071 Evaluate side-chains 298 residues out of total 2500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 280 time to evaluate : 3.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 992 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 168 optimal weight: 0.4980 chunk 216 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 249 optimal weight: 0.0870 chunk 165 optimal weight: 0.8980 chunk 294 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 23967 Z= 0.145 Angle : 0.462 10.668 32532 Z= 0.233 Chirality : 0.040 0.458 3798 Planarity : 0.003 0.056 4152 Dihedral : 6.994 149.654 3369 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.80 % Allowed : 11.28 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.50 (0.16), residues: 3064 helix: 2.19 (0.13), residues: 1660 sheet: -0.68 (0.25), residues: 418 loop : -0.25 (0.21), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 753 HIS 0.002 0.000 HIS A 525 PHE 0.014 0.001 PHE A 380 TYR 0.012 0.001 TYR B 653 ARG 0.007 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 286 time to evaluate : 3.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7354 (mmmt) cc_final: 0.5486 (pptt) REVERT: A 69 MET cc_start: 0.8773 (mmt) cc_final: 0.8295 (mmt) REVERT: A 79 SER cc_start: 0.8582 (p) cc_final: 0.8200 (t) REVERT: A 836 THR cc_start: 0.8033 (m) cc_final: 0.7792 (p) REVERT: A 931 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7895 (mt) REVERT: B 29 LYS cc_start: 0.7100 (mttt) cc_final: 0.5683 (pptt) REVERT: B 248 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.7873 (t0) REVERT: B 269 GLU cc_start: 0.8270 (pt0) cc_final: 0.8003 (pt0) REVERT: B 309 GLU cc_start: 0.7551 (tp30) cc_final: 0.7289 (mm-30) REVERT: B 566 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7488 (mt-10) REVERT: B 574 MET cc_start: 0.7210 (ptt) cc_final: 0.6883 (ptm) REVERT: B 644 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.6070 (mp0) REVERT: B 1015 ILE cc_start: 0.8479 (mm) cc_final: 0.8226 (mt) REVERT: C 29 LYS cc_start: 0.8192 (mmmt) cc_final: 0.7113 (pptt) REVERT: C 267 LYS cc_start: 0.7480 (tttp) cc_final: 0.7193 (tttp) REVERT: C 312 LYS cc_start: 0.7303 (mttt) cc_final: 0.6757 (tmtt) REVERT: C 528 ASP cc_start: 0.7371 (t70) cc_final: 0.7127 (t0) REVERT: C 727 LYS cc_start: 0.8159 (mttm) cc_final: 0.7832 (mttt) REVERT: C 780 MET cc_start: 0.8733 (mmt) cc_final: 0.8410 (mmt) REVERT: C 840 MET cc_start: 0.8047 (mtp) cc_final: 0.7706 (mtm) outliers start: 20 outliers final: 7 residues processed: 296 average time/residue: 2.7773 time to fit residues: 968.8608 Evaluate side-chains 285 residues out of total 2500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 274 time to evaluate : 3.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 182 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 231 optimal weight: 4.9990 chunk 268 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 23967 Z= 0.358 Angle : 0.526 10.605 32532 Z= 0.269 Chirality : 0.042 0.457 3798 Planarity : 0.004 0.053 4152 Dihedral : 7.209 149.225 3369 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.92 % Allowed : 11.48 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.18 (0.16), residues: 3064 helix: 1.94 (0.13), residues: 1656 sheet: -0.82 (0.25), residues: 410 loop : -0.42 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 894 HIS 0.004 0.001 HIS A 525 PHE 0.022 0.001 PHE A 11 TYR 0.020 0.002 TYR B 653 ARG 0.008 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 282 time to evaluate : 3.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7656 (mmmt) cc_final: 0.5771 (pptt) REVERT: A 69 MET cc_start: 0.8757 (mmt) cc_final: 0.8207 (mmt) REVERT: A 836 THR cc_start: 0.8108 (m) cc_final: 0.7878 (p) REVERT: A 931 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7997 (mt) REVERT: B 29 LYS cc_start: 0.7201 (mttt) cc_final: 0.5768 (pptt) REVERT: B 248 ASN cc_start: 0.8100 (OUTLIER) cc_final: 0.7845 (t0) REVERT: B 269 GLU cc_start: 0.8274 (pt0) cc_final: 0.8050 (pt0) REVERT: B 309 GLU cc_start: 0.7572 (tp30) cc_final: 0.7326 (mm-30) REVERT: B 566 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7568 (mt-10) REVERT: B 574 MET cc_start: 0.7274 (ptt) cc_final: 0.6955 (ptm) REVERT: B 644 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.6170 (mp0) REVERT: B 1015 ILE cc_start: 0.8499 (mm) cc_final: 0.8234 (mt) REVERT: C 29 LYS cc_start: 0.8204 (mmmt) cc_final: 0.7125 (pptt) REVERT: C 151 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.6954 (mt0) REVERT: C 267 LYS cc_start: 0.7549 (tttp) cc_final: 0.7257 (tttp) REVERT: C 312 LYS cc_start: 0.7302 (mttt) cc_final: 0.6753 (tmtt) REVERT: C 528 ASP cc_start: 0.7456 (t70) cc_final: 0.7189 (t0) REVERT: C 780 MET cc_start: 0.8694 (mmt) cc_final: 0.8280 (mmt) REVERT: C 840 MET cc_start: 0.8065 (mtp) cc_final: 0.7735 (mtm) outliers start: 23 outliers final: 9 residues processed: 292 average time/residue: 2.8799 time to fit residues: 980.2099 Evaluate side-chains 295 residues out of total 2500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 281 time to evaluate : 3.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 783 GLU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 448 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 chunk 274 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 259 optimal weight: 0.9980 chunk 273 optimal weight: 0.7980 chunk 180 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23967 Z= 0.187 Angle : 0.479 10.632 32532 Z= 0.242 Chirality : 0.040 0.457 3798 Planarity : 0.004 0.061 4152 Dihedral : 6.994 141.769 3369 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.60 % Allowed : 12.12 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.36 (0.16), residues: 3064 helix: 2.10 (0.13), residues: 1655 sheet: -0.76 (0.25), residues: 412 loop : -0.35 (0.20), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 753 HIS 0.002 0.000 HIS A 525 PHE 0.016 0.001 PHE C 11 TYR 0.018 0.001 TYR B 653 ARG 0.008 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 280 time to evaluate : 3.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7467 (mmmt) cc_final: 0.5581 (pptt) REVERT: A 69 MET cc_start: 0.8748 (mmt) cc_final: 0.8291 (mmt) REVERT: A 79 SER cc_start: 0.8517 (p) cc_final: 0.8171 (t) REVERT: A 836 THR cc_start: 0.8077 (m) cc_final: 0.7851 (p) REVERT: B 29 LYS cc_start: 0.7153 (mttt) cc_final: 0.5709 (pptt) REVERT: B 248 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.7852 (t0) REVERT: B 269 GLU cc_start: 0.8268 (pt0) cc_final: 0.8050 (pt0) REVERT: B 309 GLU cc_start: 0.7554 (tp30) cc_final: 0.7306 (mm-30) REVERT: B 566 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7486 (mt-10) REVERT: B 574 MET cc_start: 0.7237 (ptt) cc_final: 0.6911 (ptm) REVERT: B 644 GLU cc_start: 0.6437 (OUTLIER) cc_final: 0.6116 (mp0) REVERT: C 29 LYS cc_start: 0.8194 (mmmt) cc_final: 0.7119 (pptt) REVERT: C 267 LYS cc_start: 0.7531 (tttp) cc_final: 0.7226 (tttp) REVERT: C 312 LYS cc_start: 0.7298 (mttt) cc_final: 0.6734 (tmtt) REVERT: C 528 ASP cc_start: 0.7404 (t70) cc_final: 0.7142 (t0) REVERT: C 780 MET cc_start: 0.8699 (mmt) cc_final: 0.8317 (mmt) REVERT: C 840 MET cc_start: 0.8041 (mtp) cc_final: 0.7694 (mtm) outliers start: 15 outliers final: 7 residues processed: 287 average time/residue: 2.7780 time to fit residues: 939.7807 Evaluate side-chains 282 residues out of total 2500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 272 time to evaluate : 4.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 448 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 0.6980 chunk 177 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 304 optimal weight: 2.9990 chunk 280 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23967 Z= 0.198 Angle : 0.479 10.689 32532 Z= 0.241 Chirality : 0.040 0.458 3798 Planarity : 0.004 0.060 4152 Dihedral : 6.852 140.326 3369 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.56 % Allowed : 12.36 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.43 (0.16), residues: 3064 helix: 2.15 (0.13), residues: 1657 sheet: -0.71 (0.25), residues: 421 loop : -0.32 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 553 HIS 0.002 0.000 HIS A 525 PHE 0.017 0.001 PHE B 627 TYR 0.020 0.001 TYR B 653 ARG 0.006 0.000 ARG C 619 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 277 time to evaluate : 4.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7471 (mmmt) cc_final: 0.5592 (pptt) REVERT: A 69 MET cc_start: 0.8741 (mmt) cc_final: 0.8265 (mmt) REVERT: A 79 SER cc_start: 0.8512 (p) cc_final: 0.8176 (t) REVERT: A 824 LEU cc_start: 0.7990 (mt) cc_final: 0.7787 (mt) REVERT: A 836 THR cc_start: 0.8060 (m) cc_final: 0.7850 (p) REVERT: B 29 LYS cc_start: 0.7104 (mttt) cc_final: 0.5700 (pptt) REVERT: B 248 ASN cc_start: 0.8108 (OUTLIER) cc_final: 0.7853 (t0) REVERT: B 269 GLU cc_start: 0.8272 (pt0) cc_final: 0.8047 (pt0) REVERT: B 309 GLU cc_start: 0.7561 (tp30) cc_final: 0.7315 (mm-30) REVERT: B 566 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7491 (mt-10) REVERT: B 574 MET cc_start: 0.7252 (ptt) cc_final: 0.6914 (ptm) REVERT: B 644 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.6157 (mp0) REVERT: C 29 LYS cc_start: 0.8199 (mmmt) cc_final: 0.7129 (pptt) REVERT: C 267 LYS cc_start: 0.7505 (tttp) cc_final: 0.7203 (tttp) REVERT: C 312 LYS cc_start: 0.7278 (mttt) cc_final: 0.6732 (tmtt) REVERT: C 528 ASP cc_start: 0.7395 (t70) cc_final: 0.7122 (t0) REVERT: C 539 ARG cc_start: 0.8080 (ptp-170) cc_final: 0.7834 (ttm170) REVERT: C 780 MET cc_start: 0.8683 (mmt) cc_final: 0.8393 (mmt) REVERT: C 840 MET cc_start: 0.8038 (mtp) cc_final: 0.7693 (mtm) outliers start: 14 outliers final: 9 residues processed: 286 average time/residue: 2.7526 time to fit residues: 923.5710 Evaluate side-chains 287 residues out of total 2500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 275 time to evaluate : 3.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 241 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 243 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 249 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.111751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.093510 restraints weight = 81026.682| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.01 r_work: 0.2950 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 23967 Z= 0.249 Angle : 0.641 59.195 32532 Z= 0.369 Chirality : 0.041 0.457 3798 Planarity : 0.004 0.060 4152 Dihedral : 6.854 140.199 3369 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.52 % Allowed : 12.56 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.41 (0.16), residues: 3064 helix: 2.13 (0.13), residues: 1657 sheet: -0.71 (0.25), residues: 421 loop : -0.32 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 553 HIS 0.002 0.001 HIS A 525 PHE 0.015 0.001 PHE C 11 TYR 0.018 0.001 TYR B 653 ARG 0.004 0.000 ARG C 619 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15332.40 seconds wall clock time: 269 minutes 56.03 seconds (16196.03 seconds total)