Starting phenix.real_space_refine on Mon Feb 19 02:56:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffs_29055/02_2024/8ffs_29055_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffs_29055/02_2024/8ffs_29055.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffs_29055/02_2024/8ffs_29055_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffs_29055/02_2024/8ffs_29055_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffs_29055/02_2024/8ffs_29055_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffs_29055/02_2024/8ffs_29055.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffs_29055/02_2024/8ffs_29055.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffs_29055/02_2024/8ffs_29055_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffs_29055/02_2024/8ffs_29055_updated.pdb" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 15162 2.51 5 N 3876 2.21 5 O 4372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 23542 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 7836 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 985} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 7836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 7836 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 985} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 7819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 7819 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 985} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ERY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.96, per 1000 atoms: 0.55 Number of scatterers: 23542 At special positions: 0 Unit cell: (118.77, 116.63, 145.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 4372 8.00 N 3876 7.00 C 15162 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.04 Conformation dependent library (CDL) restraints added in 4.4 seconds 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5634 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 106 helices and 25 sheets defined 55.2% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.14 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 9 through 28 Processing helix chain 'A' and resid 54 through 67 removed outlier: 5.266A pdb=" N GLN A 63 " --> pdb=" O ASN A 59 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N VAL A 64 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 117 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 167 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 247 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 316 Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 330 through 359 Processing helix chain 'A' and resid 362 through 385 removed outlier: 3.500A pdb=" N LEU A 366 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 3.768A 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 422 removed outlier: 4.571A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 458 removed outlier: 5.454A pdb=" N GLY A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Proline residue: A 455 - end of helix removed outlier: 4.017A pdb=" N PHE A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 496 removed outlier: 4.735A 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 510 through 535 removed outlier: 3.606A pdb=" N ARG A 517 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 531 " --> pdb=" O THR A 527 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG A 535 " --> pdb=" O GLY A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 557 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: 4.215A pdb=" N GLN A 656 " --> pdb=" O GLY A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 673 No H-bonds generated for 'chain 'A' and resid 671 through 673' Processing helix chain 'A' and resid 691 through 706 Processing helix chain 'A' and resid 732 through 737 Processing helix chain 'A' and resid 742 through 753 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 Processing helix chain 'A' and resid 836 through 848 Processing helix chain 'A' and resid 861 through 867 Processing helix chain 'A' and resid 871 through 891 Processing helix chain 'A' and resid 896 through 918 removed outlier: 3.769A pdb=" N VAL A 900 " --> pdb=" O ILE A 896 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL A 903 " --> pdb=" O SER A 899 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL A 904 " --> pdb=" O VAL A 900 " (cutoff:3.500A) Proline residue: A 905 - end of helix removed outlier: 4.477A pdb=" N GLY A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 953 Processing helix chain 'A' and resid 959 through 990 removed outlier: 4.730A pdb=" N ARG A 972 " --> pdb=" O ARG A 968 " (cutoff:3.500A) Proline residue: A 973 - end of helix Proline residue: A 987 - end of helix Processing helix chain 'A' and resid 996 through 1031 removed outlier: 3.935A pdb=" N GLY A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A1018 " --> pdb=" O THR A1014 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE A1019 " --> pdb=" O ILE A1015 " (cutoff:3.500A) Proline residue: A1022 - end of helix Processing helix chain 'B' and resid 2 through 7 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 69 removed outlier: 3.508A pdb=" N ASN B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 117 Proline residue: B 116 - end of helix Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 151 through 161 Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 190 through 195 Processing helix chain 'B' and resid 200 through 210 Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 299 through 316 Proline residue: B 315 - end of helix Processing helix chain 'B' and resid 330 through 359 Processing helix chain 'B' and resid 362 through 385 removed outlier: 3.549A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix removed outlier: 3.618A pdb=" N ALA B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 392 through 423 removed outlier: 4.185A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASP B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 458 removed outlier: 5.610A pdb=" N GLY B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL B 443 " --> pdb=" O GLN B 439 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) Proline residue: B 455 - end of helix removed outlier: 4.202A pdb=" N PHE B 458 " --> pdb=" O ILE B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 495 removed outlier: 3.528A pdb=" N ALA B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Proline residue: B 490 - end of helix Processing helix chain 'B' and resid 510 through 557 removed outlier: 6.518A pdb=" N GLY B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ARG B 539 " --> pdb=" O ARG B 535 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR B 540 " --> pdb=" O SER B 536 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL B 542 " --> pdb=" O GLY B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 599 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 643 through 656 removed outlier: 4.436A pdb=" N GLN B 656 " --> pdb=" O GLY B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 707 removed outlier: 3.739A pdb=" N GLN B 707 " --> pdb=" O GLY B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 738 Processing helix chain 'B' and resid 742 through 754 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 785 Processing helix chain 'B' and resid 800 through 803 No H-bonds generated for 'chain 'B' and resid 800 through 803' Processing helix chain 'B' and resid 836 through 849 removed outlier: 3.650A pdb=" N LYS B 849 " --> pdb=" O GLU B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 891 Proline residue: B 873 - end of helix Processing helix chain 'B' and resid 895 through 918 removed outlier: 4.064A pdb=" N VAL B 903 " --> pdb=" O SER B 899 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL B 904 " --> pdb=" O VAL B 900 " (cutoff:3.500A) Proline residue: B 905 - end of helix removed outlier: 3.642A pdb=" N GLY B 910 " --> pdb=" O LEU B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 953 removed outlier: 4.295A pdb=" N PHE B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 969 Processing helix chain 'B' and resid 971 through 989 Proline residue: B 987 - end of helix Processing helix chain 'B' and resid 996 through 1015 removed outlier: 4.101A pdb=" N GLY B1005 " --> pdb=" O ALA B1001 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL B1006 " --> pdb=" O VAL B1002 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY B1008 " --> pdb=" O THR B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1031 Proline residue: B1022 - end of helix Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 9 through 29 Processing helix chain 'C' and resid 54 through 68 removed outlier: 5.598A pdb=" N GLN C 63 " --> pdb=" O ASN C 59 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N VAL C 64 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN C 68 " --> pdb=" O VAL C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 117 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 168 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 247 Processing helix chain 'C' and resid 262 through 265 Processing helix chain 'C' and resid 299 through 316 Proline residue: C 315 - end of helix Processing helix chain 'C' and resid 330 through 358 Processing helix chain 'C' and resid 362 through 386 removed outlier: 3.878A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 392 through 423 removed outlier: 4.289A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 458 removed outlier: 5.298A pdb=" N GLY C 440 " --> pdb=" O GLY C 436 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) Proline residue: C 455 - end of helix removed outlier: 3.977A pdb=" N PHE C 458 " --> pdb=" O ILE C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 496 removed outlier: 3.822A pdb=" N ALA C 465 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR C 467 " --> pdb=" O GLY C 464 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LEU C 488 " --> pdb=" O ALA C 485 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N THR C 489 " --> pdb=" O LEU C 486 " (cutoff:3.500A) Proline residue: C 490 - end of helix removed outlier: 3.514A pdb=" N ALA C 494 " --> pdb=" O ALA C 491 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N MET C 496 " --> pdb=" O CYS C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 535 removed outlier: 3.661A pdb=" N ARG C 535 " --> pdb=" O GLY C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 557 removed outlier: 3.514A pdb=" N VAL C 556 " --> pdb=" O ALA C 552 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG C 557 " --> pdb=" O TRP C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 599 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 657 Processing helix chain 'C' and resid 691 through 708 removed outlier: 3.618A pdb=" N HIS C 708 " --> pdb=" O MET C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 738 Processing helix chain 'C' and resid 742 through 754 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 849 removed outlier: 3.714A pdb=" N LYS C 849 " --> pdb=" O GLU C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 867 Processing helix chain 'C' and resid 872 through 891 Processing helix chain 'C' and resid 896 through 918 removed outlier: 3.995A pdb=" N VAL C 900 " --> pdb=" O ILE C 896 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL C 903 " --> pdb=" O SER C 899 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL C 904 " --> pdb=" O VAL C 900 " (cutoff:3.500A) Proline residue: C 905 - end of helix removed outlier: 3.774A pdb=" N GLY C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 953 Processing helix chain 'C' and resid 959 through 990 removed outlier: 4.895A pdb=" N ARG C 972 " --> pdb=" O ARG C 968 " (cutoff:3.500A) Proline residue: C 973 - end of helix Proline residue: C 987 - end of helix Processing helix chain 'C' and resid 996 through 1031 removed outlier: 3.909A pdb=" N GLY C1005 " --> pdb=" O ALA C1001 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE C1018 " --> pdb=" O THR C1014 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE C1019 " --> pdb=" O ILE C1015 " (cutoff:3.500A) Proline residue: C1022 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 128 through 131 removed outlier: 4.102A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 321 through 328 removed outlier: 7.073A pdb=" N VAL A 139 " --> pdb=" O PRO A 326 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 266 through 272 removed outlier: 8.294A pdb=" N VAL A 767 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N MET A 184 " --> pdb=" O VAL A 767 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LYS A 769 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILE A 186 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TYR A 771 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N MET A 188 " --> pdb=" O TYR A 771 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N MET A 773 " --> pdb=" O MET A 188 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN A 759 " --> pdb=" O VAL A 770 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE A 772 " --> pdb=" O TYR A 757 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N TYR A 757 " --> pdb=" O ILE A 772 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 278 through 281 removed outlier: 6.907A pdb=" N SER A 629 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL A 608 " --> pdb=" O PHE A 627 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N PHE A 627 " --> pdb=" O VAL A 608 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA A 610 " --> pdb=" O ILE A 625 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE A 625 " --> pdb=" O ALA A 610 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ASN A 612 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N THR A 623 " --> pdb=" O ASN A 612 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL A 628 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 823 through 828 removed outlier: 3.508A pdb=" N GLY A 828 " --> pdb=" O PHE A 679 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 723 through 730 Processing sheet with id= G, first strand: chain 'A' and resid 789 through 791 Processing sheet with id= H, first strand: chain 'A' and resid 250 through 253 removed outlier: 6.656A pdb=" N VAL A 260 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 128 through 131 removed outlier: 4.270A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 321 through 324 removed outlier: 7.018A pdb=" N ILE B 291 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL B 139 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU B 289 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLY B 141 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SER B 287 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE B 143 " --> pdb=" O PRO B 285 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N SER B 629 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL B 608 " --> pdb=" O PHE B 627 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE B 627 " --> pdb=" O VAL B 608 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA B 610 " --> pdb=" O ILE B 625 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE B 625 " --> pdb=" O ALA B 610 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ASN B 612 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR B 623 " --> pdb=" O ASN B 612 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 266 through 272 removed outlier: 3.519A pdb=" N TRP B 187 " --> pdb=" O LYS B 267 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N TYR B 182 " --> pdb=" O VAL B 767 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LYS B 769 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN B 759 " --> pdb=" O VAL B 770 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE B 772 " --> pdb=" O TYR B 757 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N TYR B 757 " --> pdb=" O ILE B 772 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 823 through 828 removed outlier: 3.519A pdb=" N GLY B 828 " --> pdb=" O PHE B 679 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 723 through 730 Processing sheet with id= N, first strand: chain 'B' and resid 789 through 791 Processing sheet with id= O, first strand: chain 'B' and resid 172 through 177 removed outlier: 6.537A pdb=" N LYS B 292 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL B 175 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLY B 290 " --> pdb=" O VAL B 175 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 250 through 253 removed outlier: 6.795A pdb=" N VAL B 260 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 128 through 130 removed outlier: 4.148A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 321 through 324 removed outlier: 4.819A pdb=" N ASN C 144 " --> pdb=" O PRO C 285 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER C 629 " --> pdb=" O GLU C 606 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL C 608 " --> pdb=" O PHE C 627 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE C 627 " --> pdb=" O VAL C 608 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA C 610 " --> pdb=" O ILE C 625 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE C 625 " --> pdb=" O ALA C 610 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ASN C 612 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N THR C 623 " --> pdb=" O ASN C 612 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 266 through 272 Processing sheet with id= T, first strand: chain 'C' and resid 823 through 829 removed outlier: 4.388A pdb=" N ASP C 680 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 722 through 730 Processing sheet with id= V, first strand: chain 'C' and resid 760 through 763 Processing sheet with id= W, first strand: chain 'C' and resid 789 through 791 Processing sheet with id= X, first strand: chain 'C' and resid 172 through 177 removed outlier: 6.611A pdb=" N LYS C 292 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL C 175 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY C 290 " --> pdb=" O VAL C 175 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 250 through 253 removed outlier: 6.919A pdb=" N VAL C 260 " --> pdb=" O LEU C 251 " (cutoff:3.500A) 1379 hydrogen bonds defined for protein. 3990 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: 10.35 Time building geometry restraints manager: 10.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7580 1.34 - 1.45: 3112 1.45 - 1.57: 13058 1.57 - 1.69: 0 1.69 - 1.80: 258 Bond restraints: 24008 Sorted by residual: bond pdb=" C14 ERY A1101 " pdb=" O4 ERY A1101 " ideal model delta sigma weight residual 1.512 1.426 0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C22 ERY A1101 " pdb=" O9 ERY A1101 " ideal model delta sigma weight residual 1.489 1.425 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C14 ERY A1101 " pdb=" O3 ERY A1101 " ideal model delta sigma weight residual 1.364 1.424 -0.060 2.00e-02 2.50e+03 8.90e+00 bond pdb=" C16 ERY A1101 " pdb=" C19 ERY A1101 " ideal model delta sigma weight residual 1.581 1.523 0.058 2.00e-02 2.50e+03 8.38e+00 bond pdb=" C1 ERY A1101 " pdb=" C2 ERY A1101 " ideal model delta sigma weight residual 1.558 1.500 0.058 2.00e-02 2.50e+03 8.27e+00 ... (remaining 24003 not shown) Histogram of bond angle deviations from ideal: 99.43 - 106.34: 700 106.34 - 113.26: 13389 113.26 - 120.17: 8193 120.17 - 127.08: 10125 127.08 - 133.99: 221 Bond angle restraints: 32628 Sorted by residual: angle pdb=" N LEU A 137 " pdb=" CA LEU A 137 " pdb=" C LEU A 137 " ideal model delta sigma weight residual 111.14 106.57 4.57 1.08e+00 8.57e-01 1.79e+01 angle pdb=" O ILE A 454 " pdb=" C ILE A 454 " pdb=" N PRO A 455 " ideal model delta sigma weight residual 120.07 122.94 -2.87 7.10e-01 1.98e+00 1.63e+01 angle pdb=" N VAL C 643 " pdb=" CA VAL C 643 " pdb=" C VAL C 643 " ideal model delta sigma weight residual 110.23 114.14 -3.91 1.04e+00 9.25e-01 1.42e+01 angle pdb=" C2 ERY A1101 " pdb=" C1 ERY A1101 " pdb=" O2 ERY A1101 " ideal model delta sigma weight residual 109.39 120.11 -10.72 3.00e+00 1.11e-01 1.28e+01 angle pdb=" C10 ERY A1101 " pdb=" C9 ERY A1101 " pdb=" C8 ERY A1101 " ideal model delta sigma weight residual 109.61 119.84 -10.23 3.00e+00 1.11e-01 1.16e+01 ... (remaining 32623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.00: 14023 28.00 - 56.00: 248 56.00 - 84.01: 11 84.01 - 112.01: 2 112.01 - 140.01: 2 Dihedral angle restraints: 14286 sinusoidal: 5475 harmonic: 8811 Sorted by residual: dihedral pdb=" C4 ERY A1101 " pdb=" C5 ERY A1101 " pdb=" C6 ERY A1101 " pdb=" C7 ERY A1101 " ideal model delta sinusoidal sigma weight residual 32.57 -107.44 140.01 1 3.00e+01 1.11e-03 1.88e+01 dihedral pdb=" C1 ERY A1101 " pdb=" C2 ERY A1101 " pdb=" C3 ERY A1101 " pdb=" C4 ERY A1101 " ideal model delta sinusoidal sigma weight residual -127.86 -6.76 -121.10 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" C16 ERY A1101 " pdb=" C17 ERY A1101 " pdb=" C18 ERY A1101 " pdb=" O4 ERY A1101 " ideal model delta sinusoidal sigma weight residual -53.00 56.83 -109.83 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 14283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.070: 3827 1.070 - 2.141: 0 2.141 - 3.211: 0 3.211 - 4.281: 0 4.281 - 5.352: 4 Chirality restraints: 3831 Sorted by residual: chirality pdb=" C16 ERY A1101 " pdb=" C15 ERY A1101 " pdb=" C17 ERY A1101 " pdb=" C19 ERY A1101 " both_signs ideal model delta sigma weight residual False 2.68 -2.67 5.35 2.00e-01 2.50e+01 7.16e+02 chirality pdb=" C6 ERY A1101 " pdb=" C32 ERY A1101 " pdb=" C5 ERY A1101 " pdb=" C7 ERY A1101 " both_signs ideal model delta sigma weight residual False -2.75 2.58 -5.34 2.00e-01 2.50e+01 7.12e+02 chirality pdb=" C12 ERY A1101 " pdb=" C11 ERY A1101 " pdb=" C13 ERY A1101 " pdb=" C35 ERY A1101 " both_signs ideal model delta sigma weight residual False -2.75 2.59 -5.34 2.00e-01 2.50e+01 7.12e+02 ... (remaining 3828 not shown) Planarity restraints: 4175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 58 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C GLN C 58 " -0.031 2.00e-02 2.50e+03 pdb=" O GLN C 58 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN C 59 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 58 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C GLN A 58 " 0.029 2.00e-02 2.50e+03 pdb=" O GLN A 58 " -0.011 2.00e-02 2.50e+03 pdb=" N ASN A 59 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 199 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO A 200 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 200 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 200 " -0.022 5.00e-02 4.00e+02 ... (remaining 4172 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3368 2.74 - 3.28: 24327 3.28 - 3.82: 40731 3.82 - 4.36: 48426 4.36 - 4.90: 84303 Nonbonded interactions: 201155 Sorted by model distance: nonbonded pdb=" OD1 ASP A 408 " pdb=" NZ LYS A 939 " model vdw 2.203 2.520 nonbonded pdb=" O ILE A 974 " pdb=" OG SER A 978 " model vdw 2.203 2.440 nonbonded pdb=" OH TYR B 526 " pdb=" O ILE B1018 " model vdw 2.206 2.440 nonbonded pdb=" OE2 GLU A 66 " pdb=" OG SER A 80 " model vdw 2.214 2.440 nonbonded pdb=" O PHE A 800 " pdb=" OG SER A 804 " model vdw 2.228 2.440 ... (remaining 201150 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 345 or (resid 346 through 347 and (name N or nam \ e CA or name C or name O or name CB )) or resid 348 through 497 or (resid 498 an \ d (name N or name CA or name C or name O or name CB )) or resid 499 through 500 \ or (resid 501 through 502 and (name N or name CA or name C or name O or name CB \ )) or resid 503 through 504 or (resid 505 and (name N or name CA or name C or na \ me O or name CB )) or resid 506 through 1033)) selection = (chain 'B' and (resid 1 through 345 or (resid 346 through 347 and (name N or nam \ e CA or name C or name O or name CB )) or resid 348 through 497 or (resid 498 an \ d (name N or name CA or name C or name O or name CB )) or resid 499 through 500 \ or (resid 501 through 502 and (name N or name CA or name C or name O or name CB \ )) or resid 503 through 504 or (resid 505 and (name N or name CA or name C or na \ me O or name CB )) or resid 506 through 1033)) selection = chain 'C' } 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: 2.640 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: 0.030 Extract box with map and model: 10.480 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 66.610 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.110 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:12.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 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 : 0.007 0.086 24008 Z= 0.433 Angle : 0.621 10.722 32628 Z= 0.350 Chirality : 0.173 5.352 3831 Planarity : 0.003 0.040 4175 Dihedral : 10.699 140.009 8652 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.43 % Allowed : 5.03 % Favored : 92.54 % 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: 1.82 (0.15), residues: 3093 helix: 2.29 (0.12), residues: 1688 sheet: -0.61 (0.25), residues: 427 loop : 0.24 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 788 HIS 0.005 0.001 HIS A 708 PHE 0.016 0.001 PHE A 681 TYR 0.017 0.001 TYR A 540 ARG 0.005 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 541 time to evaluate : 2.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.9179 (mtm) cc_final: 0.8920 (mtp) REVERT: A 28 LEU cc_start: 0.8930 (mp) cc_final: 0.8696 (mp) REVERT: A 170 SER cc_start: 0.9312 (t) cc_final: 0.9099 (p) REVERT: A 301 ASP cc_start: 0.8938 (m-30) cc_final: 0.8731 (m-30) REVERT: A 313 MET cc_start: 0.8726 (mtm) cc_final: 0.8349 (mtp) REVERT: A 314 GLU cc_start: 0.8435 (tp30) cc_final: 0.8100 (mt-10) REVERT: A 322 LYS cc_start: 0.8798 (tttt) cc_final: 0.8486 (mtpp) REVERT: A 342 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8140 (tttp) REVERT: A 478 MET cc_start: 0.8608 (tmm) cc_final: 0.8222 (tmm) REVERT: A 557 ARG cc_start: 0.8108 (tpp80) cc_final: 0.7868 (ttm110) REVERT: A 644 GLU cc_start: 0.8323 (tp30) cc_final: 0.7969 (tp30) REVERT: A 667 LEU cc_start: 0.8981 (mt) cc_final: 0.8774 (pp) REVERT: A 796 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8040 (mp10) REVERT: A 800 PHE cc_start: 0.9282 (OUTLIER) cc_final: 0.8479 (t80) REVERT: A 825 GLU cc_start: 0.8306 (tt0) cc_final: 0.8020 (tt0) REVERT: B 20 MET cc_start: 0.9140 (mtm) cc_final: 0.8919 (mtp) REVERT: B 67 GLN cc_start: 0.8698 (tt0) cc_final: 0.8265 (tm-30) REVERT: B 99 ASP cc_start: 0.8947 (t0) cc_final: 0.8506 (t0) REVERT: B 120 GLN cc_start: 0.8386 (mt0) cc_final: 0.7919 (mm110) REVERT: B 121 GLU cc_start: 0.8690 (mm-30) cc_final: 0.7973 (tp30) REVERT: B 124 GLN cc_start: 0.8984 (mm110) cc_final: 0.8552 (mm110) REVERT: B 407 ASP cc_start: 0.8632 (m-30) cc_final: 0.8311 (m-30) REVERT: B 439 GLN cc_start: 0.8709 (tt0) cc_final: 0.7741 (tm-30) REVERT: B 692 GLU cc_start: 0.8371 (tp30) cc_final: 0.7729 (tp30) REVERT: B 965 GLU cc_start: 0.7908 (tp30) cc_final: 0.7419 (tp30) REVERT: B 1031 ARG cc_start: 0.7991 (ttm-80) cc_final: 0.7561 (mtm180) REVERT: C 29 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8038 (pttp) REVERT: C 44 SER cc_start: 0.9189 (m) cc_final: 0.8667 (t) REVERT: C 76 MET cc_start: 0.8971 (mtt) cc_final: 0.8723 (mtm) REVERT: C 322 LYS cc_start: 0.8713 (ttpt) cc_final: 0.8502 (tttp) REVERT: C 342 LYS cc_start: 0.8083 (mmtt) cc_final: 0.7787 (mttm) REVERT: C 354 VAL cc_start: 0.8975 (t) cc_final: 0.8770 (p) REVERT: C 360 GLN cc_start: 0.8410 (mt0) cc_final: 0.8052 (mt0) REVERT: C 362 PHE cc_start: 0.8152 (t80) cc_final: 0.7776 (OUTLIER) REVERT: C 407 ASP cc_start: 0.8882 (t0) cc_final: 0.8447 (t0) REVERT: C 459 PHE cc_start: 0.8946 (m-80) cc_final: 0.8262 (m-10) REVERT: C 518 MET cc_start: 0.8254 (tmm) cc_final: 0.8035 (tmt) REVERT: C 533 ILE cc_start: 0.8773 (pt) cc_final: 0.8568 (pp) REVERT: C 553 TRP cc_start: 0.8656 (t60) cc_final: 0.8453 (t60) REVERT: C 656 GLN cc_start: 0.8896 (tt0) cc_final: 0.8615 (tm-30) REVERT: C 663 PHE cc_start: 0.8070 (m-80) cc_final: 0.7851 (m-80) REVERT: C 796 GLN cc_start: 0.8360 (mm-40) cc_final: 0.7657 (mp10) REVERT: C 857 ASP cc_start: 0.8601 (t0) cc_final: 0.8354 (t0) REVERT: C 864 GLN cc_start: 0.8960 (tt0) cc_final: 0.8510 (tm-30) REVERT: C 865 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8375 (mm-30) REVERT: C 917 PHE cc_start: 0.7957 (m-10) cc_final: 0.7731 (m-10) REVERT: C 946 GLU cc_start: 0.8528 (tp30) cc_final: 0.7977 (tp30) REVERT: C 950 ASP cc_start: 0.7860 (t0) cc_final: 0.7440 (t0) REVERT: C 1015 ILE cc_start: 0.8776 (mm) cc_final: 0.8557 (mt) outliers start: 61 outliers final: 14 residues processed: 583 average time/residue: 1.3236 time to fit residues: 884.3639 Evaluate side-chains 389 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 374 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 LYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 903 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 3.9990 chunk 234 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 125 optimal weight: 0.5980 chunk 242 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 280 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN A 181 GLN A 213 GLN A 231 ASN A 259 GLN A 284 GLN A 338 HIS A 525 HIS A 587 GLN A 656 GLN B 109 ASN B 123 GLN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN B 197 GLN B 360 GLN B 516 ASN B 576 GLN B 583 GLN B 700 GLN B 725 GLN B 796 GLN C 58 GLN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 124 GLN C 237 GLN C 242 ASN C 284 GLN C 338 HIS C 360 GLN ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 GLN C 635 GLN C 656 GLN C 686 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24008 Z= 0.236 Angle : 0.710 28.736 32628 Z= 0.319 Chirality : 0.070 2.119 3831 Planarity : 0.004 0.037 4175 Dihedral : 6.799 122.050 3336 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.11 % Allowed : 11.81 % Favored : 84.08 % 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: 2.06 (0.15), residues: 3093 helix: 2.47 (0.12), residues: 1686 sheet: -0.50 (0.25), residues: 422 loop : 0.38 (0.21), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 788 HIS 0.003 0.001 HIS A 708 PHE 0.017 0.001 PHE C 555 TYR 0.016 0.001 TYR B 182 ARG 0.003 0.000 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 410 time to evaluate : 2.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6630 (OUTLIER) cc_final: 0.6372 (ttt) REVERT: A 20 MET cc_start: 0.9213 (mtm) cc_final: 0.8954 (mtp) REVERT: A 28 LEU cc_start: 0.8930 (mp) cc_final: 0.8671 (mp) REVERT: A 108 GLN cc_start: 0.8342 (tp40) cc_final: 0.7908 (tp-100) REVERT: A 138 MET cc_start: 0.8529 (ptp) cc_final: 0.8284 (ptp) REVERT: A 309 GLU cc_start: 0.8669 (tp30) cc_final: 0.8443 (tp30) REVERT: A 313 MET cc_start: 0.8726 (mtm) cc_final: 0.8341 (mtp) REVERT: A 314 GLU cc_start: 0.8372 (tp30) cc_final: 0.8051 (mt-10) REVERT: A 322 LYS cc_start: 0.8516 (tttt) cc_final: 0.8315 (mtpp) REVERT: A 342 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8175 (tttp) REVERT: A 407 ASP cc_start: 0.8846 (t0) cc_final: 0.8568 (t0) REVERT: A 478 MET cc_start: 0.8523 (tmm) cc_final: 0.8263 (tmm) REVERT: A 483 LEU cc_start: 0.8715 (tm) cc_final: 0.8510 (mm) REVERT: A 566 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7227 (mm-30) REVERT: A 796 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8063 (mp10) REVERT: A 800 PHE cc_start: 0.9334 (OUTLIER) cc_final: 0.8292 (t80) REVERT: A 918 ARG cc_start: 0.9003 (mmm-85) cc_final: 0.8643 (ttt90) REVERT: A 986 MET cc_start: 0.7597 (ttp) cc_final: 0.7330 (ttp) REVERT: B 20 MET cc_start: 0.9081 (mtm) cc_final: 0.8821 (mtp) REVERT: B 67 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8304 (tm-30) REVERT: B 99 ASP cc_start: 0.8876 (t0) cc_final: 0.8443 (t0) REVERT: B 120 GLN cc_start: 0.8251 (mt0) cc_final: 0.7889 (mm110) REVERT: B 124 GLN cc_start: 0.8979 (mm110) cc_final: 0.8515 (mm110) REVERT: B 268 ILE cc_start: 0.9569 (OUTLIER) cc_final: 0.9314 (mm) REVERT: B 309 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8079 (mp0) REVERT: B 407 ASP cc_start: 0.8517 (m-30) cc_final: 0.8253 (m-30) REVERT: B 439 GLN cc_start: 0.8408 (tt0) cc_final: 0.7374 (tm-30) REVERT: B 670 ILE cc_start: 0.8669 (mp) cc_final: 0.8376 (tt) REVERT: B 692 GLU cc_start: 0.8247 (tp30) cc_final: 0.7425 (tp30) REVERT: B 923 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.8018 (p0) REVERT: B 946 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7246 (tm-30) REVERT: B 965 GLU cc_start: 0.7974 (tp30) cc_final: 0.7579 (tp30) REVERT: B 976 MET cc_start: 0.8896 (ttm) cc_final: 0.8681 (mtm) REVERT: B 1031 ARG cc_start: 0.8042 (ttm-80) cc_final: 0.7836 (tmt170) REVERT: C 29 LYS cc_start: 0.8250 (mtpp) cc_final: 0.7855 (pttp) REVERT: C 48 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7969 (tmm) REVERT: C 76 MET cc_start: 0.8805 (mtt) cc_final: 0.8596 (mtm) REVERT: C 176 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8040 (tt0) REVERT: C 342 LYS cc_start: 0.8006 (mmtt) cc_final: 0.7769 (mttp) REVERT: C 407 ASP cc_start: 0.8832 (t0) cc_final: 0.8205 (t0) REVERT: C 459 PHE cc_start: 0.8820 (m-80) cc_final: 0.8158 (m-10) REVERT: C 518 MET cc_start: 0.8411 (tmm) cc_final: 0.8175 (tmt) REVERT: C 651 MET cc_start: 0.8827 (tpp) cc_final: 0.8586 (mmm) REVERT: C 656 GLN cc_start: 0.8882 (tt0) cc_final: 0.8470 (tm-30) REVERT: C 663 PHE cc_start: 0.7930 (m-80) cc_final: 0.7645 (m-80) REVERT: C 796 GLN cc_start: 0.8354 (mm-40) cc_final: 0.7781 (mp10) REVERT: C 857 ASP cc_start: 0.8485 (t0) cc_final: 0.8282 (t0) REVERT: C 921 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8486 (m) REVERT: C 939 LYS cc_start: 0.8619 (ttpt) cc_final: 0.8365 (ttmm) REVERT: C 946 GLU cc_start: 0.8463 (tp30) cc_final: 0.7913 (tp30) REVERT: C 950 ASP cc_start: 0.7733 (t0) cc_final: 0.7235 (t0) outliers start: 103 outliers final: 38 residues processed: 469 average time/residue: 1.2485 time to fit residues: 680.8365 Evaluate side-chains 403 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 356 time to evaluate : 2.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 342 LYS Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 923 ASP Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 226 LYS Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 321 MET Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 921 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 233 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 281 optimal weight: 0.8980 chunk 303 optimal weight: 0.8980 chunk 250 optimal weight: 1.9990 chunk 278 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN A 871 GLN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN C 237 GLN C 338 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24008 Z= 0.227 Angle : 0.686 28.383 32628 Z= 0.304 Chirality : 0.071 2.181 3831 Planarity : 0.004 0.039 4175 Dihedral : 6.600 124.637 3333 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.87 % Allowed : 13.00 % Favored : 83.13 % 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: 2.01 (0.15), residues: 3093 helix: 2.41 (0.12), residues: 1685 sheet: -0.46 (0.25), residues: 408 loop : 0.35 (0.21), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 553 HIS 0.004 0.001 HIS A 708 PHE 0.027 0.001 PHE C 362 TYR 0.017 0.001 TYR B 182 ARG 0.008 0.000 ARG C 517 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 379 time to evaluate : 2.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6499 (OUTLIER) cc_final: 0.6272 (ttt) REVERT: A 20 MET cc_start: 0.9218 (mtm) cc_final: 0.8967 (mtp) REVERT: A 28 LEU cc_start: 0.8956 (mp) cc_final: 0.8704 (mp) REVERT: A 138 MET cc_start: 0.8345 (ptp) cc_final: 0.8015 (ptp) REVERT: A 301 ASP cc_start: 0.8984 (m-30) cc_final: 0.8767 (m-30) REVERT: A 309 GLU cc_start: 0.8670 (tp30) cc_final: 0.8457 (tp30) REVERT: A 313 MET cc_start: 0.8712 (mtm) cc_final: 0.8335 (mtp) REVERT: A 314 GLU cc_start: 0.8412 (tp30) cc_final: 0.8015 (mt-10) REVERT: A 322 LYS cc_start: 0.8534 (tttt) cc_final: 0.8286 (mtpp) REVERT: A 342 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8125 (tttp) REVERT: A 407 ASP cc_start: 0.8848 (t0) cc_final: 0.8572 (t0) REVERT: A 478 MET cc_start: 0.8592 (tmm) cc_final: 0.8272 (tmm) REVERT: A 796 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8026 (mp10) REVERT: A 800 PHE cc_start: 0.9344 (OUTLIER) cc_final: 0.8288 (t80) REVERT: A 865 GLU cc_start: 0.8821 (tt0) cc_final: 0.8614 (tt0) REVERT: A 871 GLN cc_start: 0.8071 (mt0) cc_final: 0.7664 (mt0) REVERT: A 918 ARG cc_start: 0.9004 (mmm-85) cc_final: 0.8648 (ttt90) REVERT: A 986 MET cc_start: 0.7527 (ttp) cc_final: 0.7276 (ttp) REVERT: B 20 MET cc_start: 0.9117 (mtm) cc_final: 0.8811 (mtp) REVERT: B 67 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8296 (tm-30) REVERT: B 99 ASP cc_start: 0.8871 (t0) cc_final: 0.8455 (t0) REVERT: B 268 ILE cc_start: 0.9567 (OUTLIER) cc_final: 0.9317 (mm) REVERT: B 407 ASP cc_start: 0.8484 (m-30) cc_final: 0.8079 (m-30) REVERT: B 417 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: B 439 GLN cc_start: 0.8385 (tt0) cc_final: 0.7336 (tm-30) REVERT: B 539 ARG cc_start: 0.7988 (mtp-110) cc_final: 0.7587 (ptp90) REVERT: B 557 ARG cc_start: 0.8118 (mpt180) cc_final: 0.7692 (ttm-80) REVERT: B 692 GLU cc_start: 0.8216 (tp30) cc_final: 0.7392 (tp30) REVERT: B 946 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7317 (tm-30) REVERT: B 965 GLU cc_start: 0.7977 (tp30) cc_final: 0.7609 (tp30) REVERT: B 1031 ARG cc_start: 0.8018 (ttm-80) cc_final: 0.7782 (tmt170) REVERT: C 29 LYS cc_start: 0.8257 (mtpp) cc_final: 0.7791 (pttp) REVERT: C 44 SER cc_start: 0.8900 (m) cc_final: 0.8591 (t) REVERT: C 76 MET cc_start: 0.8802 (mtt) cc_final: 0.8585 (mtm) REVERT: C 120 GLN cc_start: 0.8352 (tp-100) cc_final: 0.7851 (tp-100) REVERT: C 342 LYS cc_start: 0.8000 (mmtt) cc_final: 0.7756 (mttp) REVERT: C 366 LEU cc_start: 0.8838 (tp) cc_final: 0.8526 (mt) REVERT: C 370 ILE cc_start: 0.9155 (mt) cc_final: 0.8870 (mp) REVERT: C 407 ASP cc_start: 0.8799 (t0) cc_final: 0.8196 (t0) REVERT: C 459 PHE cc_start: 0.8845 (m-80) cc_final: 0.8143 (m-10) REVERT: C 651 MET cc_start: 0.8836 (tpp) cc_final: 0.8597 (mmm) REVERT: C 656 GLN cc_start: 0.8943 (tt0) cc_final: 0.8565 (tm-30) REVERT: C 663 PHE cc_start: 0.7937 (m-80) cc_final: 0.7652 (m-80) REVERT: C 796 GLN cc_start: 0.8343 (mm-40) cc_final: 0.7807 (mp10) REVERT: C 921 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.7782 (t) REVERT: C 946 GLU cc_start: 0.8460 (tp30) cc_final: 0.7916 (tp30) outliers start: 97 outliers final: 41 residues processed: 438 average time/residue: 1.2433 time to fit residues: 633.3353 Evaluate side-chains 402 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 354 time to evaluate : 3.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 342 LYS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 680 ASP Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 921 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 3.9990 chunk 211 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 134 optimal weight: 0.5980 chunk 188 optimal weight: 0.6980 chunk 282 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 267 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 176 GLN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN C 338 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24008 Z= 0.187 Angle : 0.673 28.756 32628 Z= 0.296 Chirality : 0.070 2.130 3831 Planarity : 0.003 0.039 4175 Dihedral : 6.417 125.459 3330 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.83 % Allowed : 13.72 % Favored : 82.45 % 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: 2.03 (0.15), residues: 3093 helix: 2.43 (0.12), residues: 1683 sheet: -0.39 (0.25), residues: 406 loop : 0.33 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 788 HIS 0.004 0.000 HIS A 708 PHE 0.025 0.001 PHE C 362 TYR 0.016 0.001 TYR B 182 ARG 0.006 0.000 ARG C 517 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 384 time to evaluate : 2.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6568 (OUTLIER) cc_final: 0.6326 (ttt) REVERT: A 20 MET cc_start: 0.9222 (mtm) cc_final: 0.8974 (mtp) REVERT: A 28 LEU cc_start: 0.8961 (mp) cc_final: 0.8703 (mp) REVERT: A 108 GLN cc_start: 0.8815 (tp40) cc_final: 0.8106 (tp-100) REVERT: A 149 MET cc_start: 0.8533 (mtm) cc_final: 0.8167 (ptm) REVERT: A 301 ASP cc_start: 0.8985 (m-30) cc_final: 0.8772 (m-30) REVERT: A 309 GLU cc_start: 0.8664 (tp30) cc_final: 0.8444 (tp30) REVERT: A 313 MET cc_start: 0.8730 (mtm) cc_final: 0.8345 (mtp) REVERT: A 314 GLU cc_start: 0.8410 (tp30) cc_final: 0.8006 (mt-10) REVERT: A 322 LYS cc_start: 0.8538 (tttt) cc_final: 0.8265 (mtpp) REVERT: A 341 VAL cc_start: 0.9239 (t) cc_final: 0.8984 (m) REVERT: A 342 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8108 (tttp) REVERT: A 407 ASP cc_start: 0.8857 (t0) cc_final: 0.8608 (t0) REVERT: A 439 GLN cc_start: 0.7263 (pt0) cc_final: 0.7059 (pt0) REVERT: A 478 MET cc_start: 0.8574 (tmm) cc_final: 0.8255 (tmm) REVERT: A 557 ARG cc_start: 0.8319 (ttm-80) cc_final: 0.7882 (ttm-80) REVERT: A 796 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8032 (mp10) REVERT: A 800 PHE cc_start: 0.9320 (OUTLIER) cc_final: 0.8291 (t80) REVERT: A 871 GLN cc_start: 0.8164 (mt0) cc_final: 0.7810 (mt0) REVERT: A 918 ARG cc_start: 0.9016 (mmm-85) cc_final: 0.8597 (ttt90) REVERT: B 20 MET cc_start: 0.9102 (mtm) cc_final: 0.8780 (mtp) REVERT: B 67 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8280 (tm-30) REVERT: B 99 ASP cc_start: 0.8872 (t0) cc_final: 0.8453 (t0) REVERT: B 268 ILE cc_start: 0.9557 (OUTLIER) cc_final: 0.9310 (mm) REVERT: B 309 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: B 417 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8070 (mt-10) REVERT: B 439 GLN cc_start: 0.8322 (tt0) cc_final: 0.7258 (tm-30) REVERT: B 539 ARG cc_start: 0.7958 (mtp-110) cc_final: 0.7640 (ptp90) REVERT: B 557 ARG cc_start: 0.8118 (mpt180) cc_final: 0.7669 (ttm-80) REVERT: B 692 GLU cc_start: 0.8190 (tp30) cc_final: 0.7371 (tp30) REVERT: B 946 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7389 (tm-30) REVERT: B 950 ASP cc_start: 0.8140 (m-30) cc_final: 0.7784 (m-30) REVERT: C 21 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8836 (mp) REVERT: C 29 LYS cc_start: 0.8217 (mtpp) cc_final: 0.7780 (pttp) REVERT: C 44 SER cc_start: 0.8907 (m) cc_final: 0.8594 (t) REVERT: C 89 THR cc_start: 0.8984 (m) cc_final: 0.8701 (p) REVERT: C 111 LEU cc_start: 0.9197 (tp) cc_final: 0.8977 (tm) REVERT: C 120 GLN cc_start: 0.8345 (tp-100) cc_final: 0.7859 (tp-100) REVERT: C 342 LYS cc_start: 0.7957 (mmtt) cc_final: 0.7727 (mttp) REVERT: C 362 PHE cc_start: 0.7863 (t80) cc_final: 0.7550 (t80) REVERT: C 366 LEU cc_start: 0.8881 (tp) cc_final: 0.8569 (mt) REVERT: C 370 ILE cc_start: 0.9159 (mt) cc_final: 0.8923 (mp) REVERT: C 407 ASP cc_start: 0.8793 (t0) cc_final: 0.8222 (t0) REVERT: C 459 PHE cc_start: 0.8866 (m-80) cc_final: 0.8208 (m-10) REVERT: C 574 MET cc_start: 0.8374 (ptm) cc_final: 0.8100 (ptm) REVERT: C 576 GLN cc_start: 0.8283 (tp-100) cc_final: 0.7833 (tp40) REVERT: C 651 MET cc_start: 0.8838 (tpp) cc_final: 0.8627 (mmm) REVERT: C 656 GLN cc_start: 0.8904 (tt0) cc_final: 0.8525 (tm-30) REVERT: C 663 PHE cc_start: 0.7933 (m-80) cc_final: 0.7667 (m-80) REVERT: C 773 MET cc_start: 0.9175 (ttt) cc_final: 0.8955 (ttt) REVERT: C 796 GLN cc_start: 0.8405 (mm-40) cc_final: 0.7872 (mp10) REVERT: C 921 THR cc_start: 0.8616 (OUTLIER) cc_final: 0.7750 (t) REVERT: C 946 GLU cc_start: 0.8460 (tp30) cc_final: 0.7925 (tp30) REVERT: C 950 ASP cc_start: 0.7679 (t0) cc_final: 0.7220 (t0) REVERT: C 954 LYS cc_start: 0.8934 (tttt) cc_final: 0.8360 (mttt) outliers start: 96 outliers final: 42 residues processed: 443 average time/residue: 1.2355 time to fit residues: 637.1724 Evaluate side-chains 407 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 356 time to evaluate : 2.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 342 LYS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 727 LYS Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 949 LYS Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 321 MET Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 680 ASP Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 921 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 222 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 254 optimal weight: 0.8980 chunk 206 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 268 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN A 248 ASN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN C 254 ASN C 338 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24008 Z= 0.189 Angle : 0.677 28.697 32628 Z= 0.296 Chirality : 0.070 2.112 3831 Planarity : 0.003 0.040 4175 Dihedral : 6.267 126.078 3327 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.11 % Allowed : 13.84 % Favored : 82.05 % 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: 2.04 (0.15), residues: 3093 helix: 2.43 (0.13), residues: 1686 sheet: -0.39 (0.25), residues: 406 loop : 0.33 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 553 HIS 0.004 0.000 HIS A 708 PHE 0.021 0.001 PHE C 362 TYR 0.016 0.001 TYR B 182 ARG 0.009 0.000 ARG C 517 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 388 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6520 (OUTLIER) cc_final: 0.6297 (ttt) REVERT: A 20 MET cc_start: 0.9227 (mtm) cc_final: 0.9006 (mtp) REVERT: A 28 LEU cc_start: 0.8926 (mp) cc_final: 0.8640 (mp) REVERT: A 108 GLN cc_start: 0.8872 (tp40) cc_final: 0.8200 (tp-100) REVERT: A 149 MET cc_start: 0.8494 (mtm) cc_final: 0.8202 (ptm) REVERT: A 301 ASP cc_start: 0.8961 (m-30) cc_final: 0.8575 (m-30) REVERT: A 309 GLU cc_start: 0.8664 (tp30) cc_final: 0.8449 (tp30) REVERT: A 313 MET cc_start: 0.8706 (mtm) cc_final: 0.8323 (mtp) REVERT: A 314 GLU cc_start: 0.8373 (tp30) cc_final: 0.7971 (mt-10) REVERT: A 322 LYS cc_start: 0.8483 (tttt) cc_final: 0.8191 (mtpp) REVERT: A 342 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8202 (tttp) REVERT: A 478 MET cc_start: 0.8533 (tmm) cc_final: 0.8236 (tmm) REVERT: A 539 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.7161 (ttt90) REVERT: A 557 ARG cc_start: 0.8287 (ttm-80) cc_final: 0.7788 (ttm-80) REVERT: A 796 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8058 (mp10) REVERT: A 800 PHE cc_start: 0.9316 (OUTLIER) cc_final: 0.8293 (t80) REVERT: A 829 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7369 (tt0) REVERT: A 866 ARG cc_start: 0.8295 (ttm-80) cc_final: 0.8049 (ttm-80) REVERT: A 871 GLN cc_start: 0.8168 (mt0) cc_final: 0.7788 (mt0) REVERT: A 918 ARG cc_start: 0.9039 (mmm-85) cc_final: 0.8679 (ttt90) REVERT: A 1010 MET cc_start: 0.8498 (tpt) cc_final: 0.8226 (tpp) REVERT: B 20 MET cc_start: 0.9103 (mtm) cc_final: 0.8822 (mtp) REVERT: B 44 SER cc_start: 0.9169 (t) cc_final: 0.8736 (p) REVERT: B 67 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8313 (tm-30) REVERT: B 99 ASP cc_start: 0.8865 (t0) cc_final: 0.8455 (t0) REVERT: B 124 GLN cc_start: 0.8996 (mm110) cc_final: 0.8621 (mp10) REVERT: B 162 MET cc_start: 0.9391 (mtp) cc_final: 0.9074 (mtm) REVERT: B 255 GLN cc_start: 0.8588 (pm20) cc_final: 0.8305 (pm20) REVERT: B 268 ILE cc_start: 0.9554 (OUTLIER) cc_final: 0.9306 (mm) REVERT: B 309 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7883 (mp0) REVERT: B 414 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7758 (tm-30) REVERT: B 417 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8071 (mt-10) REVERT: B 439 GLN cc_start: 0.8296 (tt0) cc_final: 0.7230 (tm-30) REVERT: B 539 ARG cc_start: 0.7960 (mtp-110) cc_final: 0.7558 (ptp90) REVERT: B 557 ARG cc_start: 0.8127 (mpt180) cc_final: 0.7672 (ttm-80) REVERT: B 692 GLU cc_start: 0.8193 (tp30) cc_final: 0.7388 (tp30) REVERT: B 946 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7365 (tm-30) REVERT: B 947 PHE cc_start: 0.8860 (t80) cc_final: 0.7982 (t80) REVERT: B 950 ASP cc_start: 0.8184 (m-30) cc_final: 0.7708 (m-30) REVERT: B 965 GLU cc_start: 0.8075 (tp30) cc_final: 0.7761 (tp30) REVERT: C 21 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8802 (mp) REVERT: C 29 LYS cc_start: 0.8196 (mtpp) cc_final: 0.7792 (pttp) REVERT: C 44 SER cc_start: 0.8890 (m) cc_final: 0.8596 (t) REVERT: C 89 THR cc_start: 0.8947 (m) cc_final: 0.8688 (p) REVERT: C 111 LEU cc_start: 0.9198 (tp) cc_final: 0.8982 (tm) REVERT: C 120 GLN cc_start: 0.8357 (tp-100) cc_final: 0.7877 (tp-100) REVERT: C 342 LYS cc_start: 0.7993 (mmtt) cc_final: 0.7757 (mttp) REVERT: C 370 ILE cc_start: 0.9137 (mt) cc_final: 0.8898 (mp) REVERT: C 407 ASP cc_start: 0.8772 (t0) cc_final: 0.8219 (t0) REVERT: C 459 PHE cc_start: 0.8898 (m-80) cc_final: 0.8232 (m-10) REVERT: C 574 MET cc_start: 0.8319 (ptm) cc_final: 0.8065 (ptm) REVERT: C 576 GLN cc_start: 0.8272 (tp-100) cc_final: 0.7841 (tp-100) REVERT: C 651 MET cc_start: 0.8750 (tpp) cc_final: 0.8541 (mmm) REVERT: C 656 GLN cc_start: 0.8935 (tt0) cc_final: 0.8488 (tm-30) REVERT: C 663 PHE cc_start: 0.7922 (m-80) cc_final: 0.7708 (m-80) REVERT: C 773 MET cc_start: 0.9188 (ttt) cc_final: 0.8946 (ttt) REVERT: C 796 GLN cc_start: 0.8424 (mm-40) cc_final: 0.7916 (mp10) REVERT: C 843 MET cc_start: 0.8962 (tpp) cc_final: 0.8585 (tpp) REVERT: C 921 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.7742 (t) REVERT: C 946 GLU cc_start: 0.8470 (tp30) cc_final: 0.7901 (tp30) REVERT: C 950 ASP cc_start: 0.7711 (t0) cc_final: 0.7244 (t0) REVERT: C 954 LYS cc_start: 0.8942 (tttt) cc_final: 0.8371 (mttt) outliers start: 103 outliers final: 44 residues processed: 445 average time/residue: 1.2542 time to fit residues: 649.0131 Evaluate side-chains 419 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 364 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 342 LYS Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 880 LEU Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 921 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 3.9990 chunk 268 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 175 optimal weight: 0.0670 chunk 73 optimal weight: 0.5980 chunk 298 optimal weight: 0.7980 chunk 248 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 176 GLN B 144 ASN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN C 338 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24008 Z= 0.168 Angle : 0.679 28.795 32628 Z= 0.294 Chirality : 0.070 2.090 3831 Planarity : 0.003 0.039 4175 Dihedral : 6.140 126.017 3325 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.51 % Allowed : 15.48 % Favored : 81.01 % 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: 2.03 (0.15), residues: 3093 helix: 2.41 (0.13), residues: 1687 sheet: -0.35 (0.25), residues: 403 loop : 0.33 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 788 HIS 0.004 0.000 HIS A 708 PHE 0.014 0.001 PHE A 681 TYR 0.014 0.001 TYR B 182 ARG 0.009 0.000 ARG C 517 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 389 time to evaluate : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6527 (OUTLIER) cc_final: 0.6289 (ttt) REVERT: A 20 MET cc_start: 0.9228 (mtm) cc_final: 0.9006 (mtp) REVERT: A 28 LEU cc_start: 0.8913 (mp) cc_final: 0.8605 (mp) REVERT: A 29 LYS cc_start: 0.8480 (mtpm) cc_final: 0.8151 (pttt) REVERT: A 108 GLN cc_start: 0.8880 (tp40) cc_final: 0.8218 (tp-100) REVERT: A 181 GLN cc_start: 0.8680 (mt0) cc_final: 0.8438 (mt0) REVERT: A 301 ASP cc_start: 0.8971 (m-30) cc_final: 0.8577 (m-30) REVERT: A 309 GLU cc_start: 0.8660 (tp30) cc_final: 0.8445 (tp30) REVERT: A 313 MET cc_start: 0.8695 (mtm) cc_final: 0.8386 (mtp) REVERT: A 314 GLU cc_start: 0.8369 (tp30) cc_final: 0.7932 (mt-10) REVERT: A 322 LYS cc_start: 0.8461 (tttt) cc_final: 0.8168 (mtpp) REVERT: A 341 VAL cc_start: 0.9230 (t) cc_final: 0.9011 (m) REVERT: A 342 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8159 (tttp) REVERT: A 343 THR cc_start: 0.9266 (m) cc_final: 0.8924 (p) REVERT: A 478 MET cc_start: 0.8550 (tmm) cc_final: 0.8253 (tmm) REVERT: A 557 ARG cc_start: 0.8330 (ttm-80) cc_final: 0.7877 (ttm-80) REVERT: A 616 PHE cc_start: 0.7521 (m-80) cc_final: 0.7282 (m-80) REVERT: A 639 GLU cc_start: 0.7738 (tp30) cc_final: 0.7524 (tp30) REVERT: A 796 GLN cc_start: 0.8503 (mm-40) cc_final: 0.8047 (mp10) REVERT: A 800 PHE cc_start: 0.9314 (OUTLIER) cc_final: 0.8295 (t80) REVERT: A 866 ARG cc_start: 0.8318 (ttm-80) cc_final: 0.8044 (ttm-80) REVERT: A 871 GLN cc_start: 0.8172 (mt0) cc_final: 0.7771 (mt0) REVERT: A 918 ARG cc_start: 0.8992 (mmm-85) cc_final: 0.8684 (ttt90) REVERT: A 953 GLU cc_start: 0.7642 (mp0) cc_final: 0.6930 (mp0) REVERT: B 20 MET cc_start: 0.9095 (mtm) cc_final: 0.8791 (mtp) REVERT: B 44 SER cc_start: 0.9151 (t) cc_final: 0.8665 (p) REVERT: B 67 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8278 (tm-30) REVERT: B 99 ASP cc_start: 0.8860 (t0) cc_final: 0.8453 (t0) REVERT: B 120 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8179 (tp40) REVERT: B 124 GLN cc_start: 0.8976 (mm110) cc_final: 0.8631 (mp10) REVERT: B 162 MET cc_start: 0.9360 (mtp) cc_final: 0.9024 (mtm) REVERT: B 255 GLN cc_start: 0.8548 (pm20) cc_final: 0.8279 (pm20) REVERT: B 268 ILE cc_start: 0.9547 (OUTLIER) cc_final: 0.9313 (mm) REVERT: B 309 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: B 417 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8056 (mt-10) REVERT: B 439 GLN cc_start: 0.8240 (tt0) cc_final: 0.7199 (tm-30) REVERT: B 557 ARG cc_start: 0.8130 (mpt180) cc_final: 0.7701 (ttm-80) REVERT: B 692 GLU cc_start: 0.8180 (tp30) cc_final: 0.7376 (tp30) REVERT: B 946 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7264 (tm-30) REVERT: B 947 PHE cc_start: 0.8790 (t80) cc_final: 0.7992 (t80) REVERT: B 1031 ARG cc_start: 0.7867 (tpp80) cc_final: 0.7630 (tmt170) REVERT: C 20 MET cc_start: 0.8372 (mtm) cc_final: 0.8133 (mtm) REVERT: C 21 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8794 (mp) REVERT: C 29 LYS cc_start: 0.8164 (mtpp) cc_final: 0.7784 (pttp) REVERT: C 44 SER cc_start: 0.8822 (m) cc_final: 0.8515 (t) REVERT: C 89 THR cc_start: 0.8924 (m) cc_final: 0.8688 (p) REVERT: C 111 LEU cc_start: 0.9188 (tp) cc_final: 0.8979 (tm) REVERT: C 120 GLN cc_start: 0.8371 (tp-100) cc_final: 0.7901 (tp-100) REVERT: C 342 LYS cc_start: 0.8036 (mmtt) cc_final: 0.7820 (mttp) REVERT: C 362 PHE cc_start: 0.7702 (t80) cc_final: 0.7349 (t80) REVERT: C 366 LEU cc_start: 0.8876 (tp) cc_final: 0.8588 (mt) REVERT: C 370 ILE cc_start: 0.9113 (mt) cc_final: 0.8908 (mp) REVERT: C 407 ASP cc_start: 0.8720 (t0) cc_final: 0.8160 (t0) REVERT: C 450 SER cc_start: 0.9109 (OUTLIER) cc_final: 0.8882 (p) REVERT: C 459 PHE cc_start: 0.8889 (m-80) cc_final: 0.8221 (m-10) REVERT: C 517 ARG cc_start: 0.8095 (mtm110) cc_final: 0.7842 (mtm110) REVERT: C 574 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7964 (ptp) REVERT: C 576 GLN cc_start: 0.8249 (tp-100) cc_final: 0.7832 (tp-100) REVERT: C 651 MET cc_start: 0.8744 (tpp) cc_final: 0.8531 (mmm) REVERT: C 663 PHE cc_start: 0.7893 (m-80) cc_final: 0.7667 (m-80) REVERT: C 796 GLN cc_start: 0.8425 (mm-40) cc_final: 0.7824 (mp10) REVERT: C 939 LYS cc_start: 0.8542 (ttpt) cc_final: 0.8315 (ttmm) REVERT: C 946 GLU cc_start: 0.8467 (tp30) cc_final: 0.7895 (tp30) REVERT: C 950 ASP cc_start: 0.7722 (t0) cc_final: 0.7245 (t0) REVERT: C 954 LYS cc_start: 0.8942 (tttt) cc_final: 0.8371 (mttt) outliers start: 88 outliers final: 44 residues processed: 443 average time/residue: 1.2598 time to fit residues: 648.9893 Evaluate side-chains 422 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 368 time to evaluate : 2.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 342 LYS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 880 LEU Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 904 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 170 optimal weight: 5.9990 chunk 218 optimal weight: 0.4980 chunk 169 optimal weight: 0.9990 chunk 251 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 297 optimal weight: 4.9990 chunk 186 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 137 optimal weight: 0.5980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN C 338 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24008 Z= 0.180 Angle : 0.686 28.724 32628 Z= 0.298 Chirality : 0.070 2.070 3831 Planarity : 0.003 0.038 4175 Dihedral : 6.076 125.995 3325 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.31 % Allowed : 16.27 % Favored : 80.41 % 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: 2.04 (0.15), residues: 3093 helix: 2.38 (0.13), residues: 1694 sheet: -0.26 (0.25), residues: 399 loop : 0.33 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 788 HIS 0.004 0.000 HIS A 708 PHE 0.020 0.001 PHE C 555 TYR 0.014 0.001 TYR B 182 ARG 0.005 0.000 ARG C 517 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 384 time to evaluate : 2.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6344 (OUTLIER) cc_final: 0.6113 (ttt) REVERT: A 20 MET cc_start: 0.9231 (mtm) cc_final: 0.9018 (mtp) REVERT: A 28 LEU cc_start: 0.8902 (mp) cc_final: 0.8596 (mp) REVERT: A 29 LYS cc_start: 0.8456 (mtpm) cc_final: 0.8132 (pttt) REVERT: A 44 SER cc_start: 0.8590 (OUTLIER) cc_final: 0.7953 (t) REVERT: A 108 GLN cc_start: 0.8891 (tp40) cc_final: 0.8239 (tp-100) REVERT: A 130 GLU cc_start: 0.7556 (pm20) cc_final: 0.7355 (pm20) REVERT: A 181 GLN cc_start: 0.8666 (mt0) cc_final: 0.8416 (mt0) REVERT: A 301 ASP cc_start: 0.8970 (m-30) cc_final: 0.8579 (m-30) REVERT: A 309 GLU cc_start: 0.8659 (tp30) cc_final: 0.8442 (tp30) REVERT: A 313 MET cc_start: 0.8686 (mtm) cc_final: 0.8356 (mtp) REVERT: A 314 GLU cc_start: 0.8372 (tp30) cc_final: 0.7932 (mt-10) REVERT: A 322 LYS cc_start: 0.8415 (tttt) cc_final: 0.8095 (mtpp) REVERT: A 341 VAL cc_start: 0.9234 (t) cc_final: 0.9005 (m) REVERT: A 342 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8124 (tttp) REVERT: A 343 THR cc_start: 0.9266 (m) cc_final: 0.8927 (p) REVERT: A 407 ASP cc_start: 0.8913 (t0) cc_final: 0.8662 (t0) REVERT: A 478 MET cc_start: 0.8524 (tmm) cc_final: 0.8215 (tmm) REVERT: A 557 ARG cc_start: 0.8350 (ttm-80) cc_final: 0.7765 (ttm-80) REVERT: A 616 PHE cc_start: 0.7567 (m-80) cc_final: 0.7314 (m-80) REVERT: A 627 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.6849 (t80) REVERT: A 639 GLU cc_start: 0.7756 (tp30) cc_final: 0.7548 (tp30) REVERT: A 682 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8039 (mp0) REVERT: A 796 GLN cc_start: 0.8500 (mm-40) cc_final: 0.8033 (mp10) REVERT: A 800 PHE cc_start: 0.9316 (OUTLIER) cc_final: 0.8296 (t80) REVERT: A 866 ARG cc_start: 0.8309 (ttm-80) cc_final: 0.8028 (ttm-80) REVERT: A 871 GLN cc_start: 0.8178 (mt0) cc_final: 0.7756 (mt0) REVERT: A 918 ARG cc_start: 0.9000 (mmm-85) cc_final: 0.8710 (ttt90) REVERT: A 953 GLU cc_start: 0.7709 (mp0) cc_final: 0.7098 (mp0) REVERT: A 1010 MET cc_start: 0.8485 (tpt) cc_final: 0.8202 (tpp) REVERT: B 20 MET cc_start: 0.9082 (mtm) cc_final: 0.8782 (mtp) REVERT: B 44 SER cc_start: 0.9174 (t) cc_final: 0.8684 (p) REVERT: B 67 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8120 (tm-30) REVERT: B 68 ASN cc_start: 0.9139 (m-40) cc_final: 0.8773 (m-40) REVERT: B 99 ASP cc_start: 0.8862 (t0) cc_final: 0.8449 (t0) REVERT: B 120 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8190 (tp40) REVERT: B 124 GLN cc_start: 0.8933 (mm110) cc_final: 0.8588 (mp10) REVERT: B 162 MET cc_start: 0.9340 (mtp) cc_final: 0.9010 (mtm) REVERT: B 255 GLN cc_start: 0.8564 (pm20) cc_final: 0.8294 (pm20) REVERT: B 268 ILE cc_start: 0.9566 (OUTLIER) cc_final: 0.9300 (mm) REVERT: B 309 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7903 (mp0) REVERT: B 417 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8124 (mt-10) REVERT: B 439 GLN cc_start: 0.8292 (tt0) cc_final: 0.7184 (tm-30) REVERT: B 557 ARG cc_start: 0.8117 (mpt180) cc_final: 0.7704 (ttm-80) REVERT: B 692 GLU cc_start: 0.8185 (tp30) cc_final: 0.7380 (tp30) REVERT: B 946 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7361 (tm-30) REVERT: B 947 PHE cc_start: 0.8752 (t80) cc_final: 0.7958 (t80) REVERT: B 954 LYS cc_start: 0.8751 (mmpt) cc_final: 0.8525 (mmmt) REVERT: B 1031 ARG cc_start: 0.7823 (tpp80) cc_final: 0.7604 (tmt170) REVERT: C 20 MET cc_start: 0.8371 (mtm) cc_final: 0.8153 (mtm) REVERT: C 21 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8798 (mp) REVERT: C 29 LYS cc_start: 0.8170 (mtpp) cc_final: 0.7812 (pttp) REVERT: C 44 SER cc_start: 0.8818 (m) cc_final: 0.8523 (t) REVERT: C 89 THR cc_start: 0.8913 (m) cc_final: 0.8686 (p) REVERT: C 111 LEU cc_start: 0.9189 (tp) cc_final: 0.8979 (tm) REVERT: C 120 GLN cc_start: 0.8375 (tp-100) cc_final: 0.7909 (tp-100) REVERT: C 342 LYS cc_start: 0.8053 (mmtt) cc_final: 0.7852 (mttp) REVERT: C 362 PHE cc_start: 0.7683 (t80) cc_final: 0.7361 (t80) REVERT: C 366 LEU cc_start: 0.8911 (tp) cc_final: 0.8581 (mt) REVERT: C 370 ILE cc_start: 0.9103 (mt) cc_final: 0.8900 (mp) REVERT: C 407 ASP cc_start: 0.8738 (t0) cc_final: 0.8128 (t0) REVERT: C 450 SER cc_start: 0.9006 (OUTLIER) cc_final: 0.8735 (p) REVERT: C 459 PHE cc_start: 0.8906 (m-80) cc_final: 0.8247 (m-10) REVERT: C 574 MET cc_start: 0.8246 (ptm) cc_final: 0.7946 (ptp) REVERT: C 576 GLN cc_start: 0.8248 (tp-100) cc_final: 0.7813 (tp-100) REVERT: C 651 MET cc_start: 0.8759 (tpp) cc_final: 0.8526 (mmm) REVERT: C 663 PHE cc_start: 0.7883 (m-80) cc_final: 0.7666 (m-80) REVERT: C 773 MET cc_start: 0.9201 (ttt) cc_final: 0.8994 (ttt) REVERT: C 796 GLN cc_start: 0.8429 (mm-40) cc_final: 0.7831 (mp10) REVERT: C 921 THR cc_start: 0.8558 (OUTLIER) cc_final: 0.7709 (t) REVERT: C 939 LYS cc_start: 0.8541 (ttpt) cc_final: 0.8308 (ttmm) REVERT: C 946 GLU cc_start: 0.8453 (tp30) cc_final: 0.7857 (tp30) outliers start: 83 outliers final: 42 residues processed: 433 average time/residue: 1.2212 time to fit residues: 615.4168 Evaluate side-chains 419 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 365 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 342 LYS Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 321 MET Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 680 ASP Chi-restraints excluded: chain C residue 880 LEU Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 921 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 177 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 202 optimal weight: 6.9990 chunk 147 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 234 optimal weight: 9.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 176 GLN C 237 GLN C 338 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24008 Z= 0.307 Angle : 0.718 28.600 32628 Z= 0.317 Chirality : 0.070 2.069 3831 Planarity : 0.004 0.038 4175 Dihedral : 6.067 125.555 3323 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.35 % Allowed : 16.63 % Favored : 80.02 % 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: 1.99 (0.15), residues: 3093 helix: 2.34 (0.13), residues: 1689 sheet: -0.30 (0.25), residues: 402 loop : 0.35 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 553 HIS 0.003 0.001 HIS A 708 PHE 0.017 0.001 PHE A 627 TYR 0.015 0.001 TYR B 182 ARG 0.009 0.000 ARG C 517 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 364 time to evaluate : 2.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6422 (OUTLIER) cc_final: 0.6158 (ttt) REVERT: A 20 MET cc_start: 0.9235 (mtm) cc_final: 0.8950 (mtp) REVERT: A 28 LEU cc_start: 0.8908 (mp) cc_final: 0.8615 (mp) REVERT: A 29 LYS cc_start: 0.8520 (mtpm) cc_final: 0.8176 (pttt) REVERT: A 44 SER cc_start: 0.8657 (OUTLIER) cc_final: 0.8034 (t) REVERT: A 108 GLN cc_start: 0.8969 (tp40) cc_final: 0.8309 (tp-100) REVERT: A 130 GLU cc_start: 0.7629 (pm20) cc_final: 0.7401 (pm20) REVERT: A 313 MET cc_start: 0.8715 (mtm) cc_final: 0.8343 (mtp) REVERT: A 314 GLU cc_start: 0.8364 (tp30) cc_final: 0.7966 (mt-10) REVERT: A 322 LYS cc_start: 0.8410 (tttt) cc_final: 0.8186 (mtpp) REVERT: A 341 VAL cc_start: 0.9240 (t) cc_final: 0.8994 (m) REVERT: A 342 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8167 (tttp) REVERT: A 616 PHE cc_start: 0.7611 (m-80) cc_final: 0.7312 (m-80) REVERT: A 627 PHE cc_start: 0.7819 (OUTLIER) cc_final: 0.6906 (t80) REVERT: A 796 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8053 (mp10) REVERT: A 800 PHE cc_start: 0.9373 (OUTLIER) cc_final: 0.8395 (t80) REVERT: A 871 GLN cc_start: 0.8159 (mt0) cc_final: 0.7714 (mt0) REVERT: A 918 ARG cc_start: 0.9024 (mmm-85) cc_final: 0.8669 (ttt90) REVERT: A 953 GLU cc_start: 0.7686 (mp0) cc_final: 0.6932 (mp0) REVERT: B 20 MET cc_start: 0.9106 (mtm) cc_final: 0.8852 (mtp) REVERT: B 67 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8175 (tm-30) REVERT: B 68 ASN cc_start: 0.9160 (m-40) cc_final: 0.8829 (m-40) REVERT: B 99 ASP cc_start: 0.8899 (t0) cc_final: 0.8448 (t0) REVERT: B 255 GLN cc_start: 0.8563 (pm20) cc_final: 0.8293 (pm20) REVERT: B 268 ILE cc_start: 0.9571 (OUTLIER) cc_final: 0.9316 (mm) REVERT: B 309 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7929 (mp0) REVERT: B 417 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8078 (mt-10) REVERT: B 439 GLN cc_start: 0.8413 (tt0) cc_final: 0.7382 (tm-30) REVERT: B 557 ARG cc_start: 0.8117 (mpt180) cc_final: 0.7694 (ttm-80) REVERT: B 692 GLU cc_start: 0.8249 (tp30) cc_final: 0.7545 (tp30) REVERT: B 946 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7401 (tm-30) REVERT: B 947 PHE cc_start: 0.8834 (t80) cc_final: 0.8394 (t80) REVERT: B 954 LYS cc_start: 0.8749 (mmpt) cc_final: 0.8526 (mmmt) REVERT: B 1031 ARG cc_start: 0.7713 (tpp80) cc_final: 0.7476 (tmt170) REVERT: C 20 MET cc_start: 0.8380 (mtm) cc_final: 0.8149 (mtm) REVERT: C 21 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8809 (mp) REVERT: C 29 LYS cc_start: 0.8190 (mtpp) cc_final: 0.7815 (pttp) REVERT: C 44 SER cc_start: 0.8888 (m) cc_final: 0.8550 (t) REVERT: C 89 THR cc_start: 0.8976 (m) cc_final: 0.8696 (p) REVERT: C 120 GLN cc_start: 0.8377 (tp-100) cc_final: 0.7889 (tp-100) REVERT: C 342 LYS cc_start: 0.8063 (mmtt) cc_final: 0.7836 (mttp) REVERT: C 362 PHE cc_start: 0.7698 (t80) cc_final: 0.7395 (t80) REVERT: C 366 LEU cc_start: 0.8939 (tp) cc_final: 0.8584 (mt) REVERT: C 370 ILE cc_start: 0.9156 (mt) cc_final: 0.8947 (mp) REVERT: C 407 ASP cc_start: 0.8729 (t0) cc_final: 0.8163 (t0) REVERT: C 450 SER cc_start: 0.9016 (OUTLIER) cc_final: 0.8745 (p) REVERT: C 459 PHE cc_start: 0.8936 (m-80) cc_final: 0.8270 (m-10) REVERT: C 517 ARG cc_start: 0.7966 (mtm110) cc_final: 0.7664 (mtm110) REVERT: C 576 GLN cc_start: 0.8214 (tp-100) cc_final: 0.7838 (tp-100) REVERT: C 651 MET cc_start: 0.8712 (tpp) cc_final: 0.8484 (mmm) REVERT: C 663 PHE cc_start: 0.7948 (m-80) cc_final: 0.7697 (m-80) REVERT: C 796 GLN cc_start: 0.8374 (mm-40) cc_final: 0.7784 (mp10) REVERT: C 921 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.7722 (t) REVERT: C 939 LYS cc_start: 0.8583 (ttpt) cc_final: 0.8332 (ttmm) REVERT: C 946 GLU cc_start: 0.8499 (tp30) cc_final: 0.7799 (tp30) REVERT: C 950 ASP cc_start: 0.8046 (t0) cc_final: 0.7816 (t0) outliers start: 84 outliers final: 46 residues processed: 414 average time/residue: 1.3581 time to fit residues: 654.2092 Evaluate side-chains 408 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 350 time to evaluate : 2.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 342 LYS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 321 MET Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 680 ASP Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 921 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 0.0670 chunk 285 optimal weight: 0.9990 chunk 260 optimal weight: 0.9990 chunk 277 optimal weight: 7.9990 chunk 167 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 250 optimal weight: 0.9990 chunk 262 optimal weight: 9.9990 chunk 276 optimal weight: 3.9990 overall best weight: 0.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 176 GLN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN C 338 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24008 Z= 0.194 Angle : 0.705 28.592 32628 Z= 0.307 Chirality : 0.069 2.070 3831 Planarity : 0.003 0.048 4175 Dihedral : 6.005 124.876 3323 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.63 % Allowed : 17.71 % Favored : 79.66 % 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: 1.98 (0.15), residues: 3093 helix: 2.31 (0.13), residues: 1692 sheet: -0.25 (0.25), residues: 393 loop : 0.33 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 553 HIS 0.004 0.000 HIS A 708 PHE 0.023 0.001 PHE C 555 TYR 0.014 0.001 TYR B 182 ARG 0.009 0.000 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 371 time to evaluate : 3.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6393 (OUTLIER) cc_final: 0.6153 (ttt) REVERT: A 20 MET cc_start: 0.9234 (mtm) cc_final: 0.8935 (mtp) REVERT: A 28 LEU cc_start: 0.8903 (mp) cc_final: 0.8575 (mp) REVERT: A 29 LYS cc_start: 0.8468 (mtpm) cc_final: 0.8147 (pttt) REVERT: A 44 SER cc_start: 0.8668 (OUTLIER) cc_final: 0.8046 (t) REVERT: A 108 GLN cc_start: 0.8949 (tp40) cc_final: 0.8325 (tp-100) REVERT: A 130 GLU cc_start: 0.7647 (pm20) cc_final: 0.7394 (pm20) REVERT: A 301 ASP cc_start: 0.9033 (m-30) cc_final: 0.8751 (m-30) REVERT: A 309 GLU cc_start: 0.8644 (tp30) cc_final: 0.7976 (tt0) REVERT: A 313 MET cc_start: 0.8695 (mtm) cc_final: 0.8317 (mtp) REVERT: A 314 GLU cc_start: 0.8359 (tp30) cc_final: 0.7960 (mt-10) REVERT: A 322 LYS cc_start: 0.8380 (tttt) cc_final: 0.8159 (mtpp) REVERT: A 341 VAL cc_start: 0.9220 (t) cc_final: 0.8958 (m) REVERT: A 342 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.7968 (tttp) REVERT: A 533 ILE cc_start: 0.9009 (mt) cc_final: 0.8806 (mt) REVERT: A 616 PHE cc_start: 0.7746 (m-80) cc_final: 0.7419 (m-80) REVERT: A 627 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.6872 (t80) REVERT: A 682 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8023 (mp0) REVERT: A 796 GLN cc_start: 0.8508 (mm-40) cc_final: 0.8029 (mp10) REVERT: A 800 PHE cc_start: 0.9356 (OUTLIER) cc_final: 0.8485 (t80) REVERT: A 825 GLU cc_start: 0.8332 (tt0) cc_final: 0.7817 (tt0) REVERT: A 871 GLN cc_start: 0.8140 (mt0) cc_final: 0.7669 (mt0) REVERT: A 918 ARG cc_start: 0.9011 (mmm-85) cc_final: 0.8663 (ttt90) REVERT: A 953 GLU cc_start: 0.7723 (mp0) cc_final: 0.7113 (mp0) REVERT: B 20 MET cc_start: 0.9087 (mtm) cc_final: 0.8820 (mtp) REVERT: B 67 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8137 (tm-30) REVERT: B 68 ASN cc_start: 0.9141 (m-40) cc_final: 0.8774 (m-40) REVERT: B 99 ASP cc_start: 0.8890 (t0) cc_final: 0.8443 (t0) REVERT: B 124 GLN cc_start: 0.8922 (mm110) cc_final: 0.8550 (mp10) REVERT: B 162 MET cc_start: 0.9336 (mtp) cc_final: 0.8969 (mtm) REVERT: B 255 GLN cc_start: 0.8577 (pm20) cc_final: 0.8297 (pm20) REVERT: B 268 ILE cc_start: 0.9569 (OUTLIER) cc_final: 0.9318 (mm) REVERT: B 309 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: B 417 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: B 439 GLN cc_start: 0.8392 (tt0) cc_final: 0.7311 (tm-30) REVERT: B 557 ARG cc_start: 0.8110 (mpt180) cc_final: 0.7692 (ttm-80) REVERT: B 692 GLU cc_start: 0.8198 (tp30) cc_final: 0.7576 (tp30) REVERT: B 879 SER cc_start: 0.8961 (m) cc_final: 0.8738 (p) REVERT: B 946 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7367 (tm-30) REVERT: B 947 PHE cc_start: 0.8821 (t80) cc_final: 0.8369 (t80) REVERT: B 954 LYS cc_start: 0.8761 (mmpt) cc_final: 0.8527 (mmmt) REVERT: C 20 MET cc_start: 0.8368 (mtm) cc_final: 0.8136 (mtm) REVERT: C 21 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8800 (mp) REVERT: C 29 LYS cc_start: 0.8145 (mtpp) cc_final: 0.7835 (pttp) REVERT: C 44 SER cc_start: 0.8844 (m) cc_final: 0.8527 (t) REVERT: C 89 THR cc_start: 0.8932 (m) cc_final: 0.8685 (p) REVERT: C 111 LEU cc_start: 0.9204 (tp) cc_final: 0.8918 (tm) REVERT: C 120 GLN cc_start: 0.8372 (tp-100) cc_final: 0.7933 (tp-100) REVERT: C 342 LYS cc_start: 0.8143 (mmtt) cc_final: 0.7931 (mttp) REVERT: C 362 PHE cc_start: 0.7721 (t80) cc_final: 0.7370 (t80) REVERT: C 366 LEU cc_start: 0.8913 (tp) cc_final: 0.8559 (mt) REVERT: C 370 ILE cc_start: 0.9135 (mt) cc_final: 0.8930 (mp) REVERT: C 407 ASP cc_start: 0.8742 (t0) cc_final: 0.8197 (t0) REVERT: C 450 SER cc_start: 0.9002 (OUTLIER) cc_final: 0.8783 (p) REVERT: C 459 PHE cc_start: 0.8908 (m-80) cc_final: 0.8275 (m-10) REVERT: C 574 MET cc_start: 0.8218 (ptm) cc_final: 0.7901 (ptp) REVERT: C 576 GLN cc_start: 0.8226 (tp-100) cc_final: 0.7787 (tp-100) REVERT: C 651 MET cc_start: 0.8751 (tpp) cc_final: 0.8530 (mmm) REVERT: C 663 PHE cc_start: 0.7888 (m-80) cc_final: 0.7671 (m-80) REVERT: C 773 MET cc_start: 0.9208 (ttt) cc_final: 0.8965 (ttt) REVERT: C 796 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7758 (mp10) REVERT: C 921 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.7704 (t) REVERT: C 946 GLU cc_start: 0.8497 (tp30) cc_final: 0.7814 (tp30) REVERT: C 950 ASP cc_start: 0.8063 (t0) cc_final: 0.7817 (t0) outliers start: 66 outliers final: 42 residues processed: 410 average time/residue: 1.2639 time to fit residues: 602.1177 Evaluate side-chains 414 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 360 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 342 LYS Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 321 MET Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 680 ASP Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 921 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 0.5980 chunk 293 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 139 optimal weight: 0.3980 chunk 204 optimal weight: 0.7980 chunk 307 optimal weight: 0.9980 chunk 283 optimal weight: 2.9990 chunk 245 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 189 optimal weight: 0.7980 chunk 150 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 176 GLN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN C 338 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24008 Z= 0.174 Angle : 0.705 28.486 32628 Z= 0.307 Chirality : 0.069 2.078 3831 Planarity : 0.003 0.047 4175 Dihedral : 5.948 124.401 3323 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.39 % Allowed : 18.27 % Favored : 79.34 % 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: 2.00 (0.15), residues: 3093 helix: 2.32 (0.13), residues: 1686 sheet: -0.22 (0.25), residues: 394 loop : 0.36 (0.20), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 553 HIS 0.004 0.000 HIS A 708 PHE 0.025 0.001 PHE A 614 TYR 0.019 0.001 TYR B 35 ARG 0.012 0.000 ARG C 517 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 385 time to evaluate : 2.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.9234 (mtm) cc_final: 0.9020 (mtp) REVERT: A 28 LEU cc_start: 0.8898 (mp) cc_final: 0.8647 (mp) REVERT: A 29 LYS cc_start: 0.8419 (mtpm) cc_final: 0.8130 (pttt) REVERT: A 44 SER cc_start: 0.8657 (OUTLIER) cc_final: 0.8047 (t) REVERT: A 108 GLN cc_start: 0.8921 (tp40) cc_final: 0.8286 (tp-100) REVERT: A 181 GLN cc_start: 0.8667 (mt0) cc_final: 0.8426 (mt0) REVERT: A 301 ASP cc_start: 0.9031 (m-30) cc_final: 0.8746 (m-30) REVERT: A 309 GLU cc_start: 0.8617 (tp30) cc_final: 0.7930 (tt0) REVERT: A 313 MET cc_start: 0.8678 (mtm) cc_final: 0.8356 (mtp) REVERT: A 314 GLU cc_start: 0.8353 (tp30) cc_final: 0.7969 (mt-10) REVERT: A 322 LYS cc_start: 0.8330 (tttt) cc_final: 0.8107 (mtpp) REVERT: A 341 VAL cc_start: 0.9242 (t) cc_final: 0.8985 (m) REVERT: A 342 LYS cc_start: 0.8590 (ttmp) cc_final: 0.8064 (tttp) REVERT: A 480 LEU cc_start: 0.8800 (mt) cc_final: 0.8566 (tp) REVERT: A 533 ILE cc_start: 0.8963 (mt) cc_final: 0.8751 (mt) REVERT: A 566 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7269 (mm-30) REVERT: A 616 PHE cc_start: 0.7705 (m-80) cc_final: 0.7424 (m-80) REVERT: A 627 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.6876 (t80) REVERT: A 680 ASP cc_start: 0.8350 (t0) cc_final: 0.7856 (t0) REVERT: A 682 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8023 (mp0) REVERT: A 796 GLN cc_start: 0.8504 (mm-40) cc_final: 0.8033 (mp10) REVERT: A 800 PHE cc_start: 0.9317 (OUTLIER) cc_final: 0.8458 (t80) REVERT: A 825 GLU cc_start: 0.8312 (tt0) cc_final: 0.7832 (tt0) REVERT: A 871 GLN cc_start: 0.8155 (mt0) cc_final: 0.7703 (mt0) REVERT: A 918 ARG cc_start: 0.9019 (mmm-85) cc_final: 0.8672 (ttt90) REVERT: A 953 GLU cc_start: 0.7728 (mp0) cc_final: 0.7209 (mp0) REVERT: B 20 MET cc_start: 0.9080 (mtm) cc_final: 0.8810 (mtp) REVERT: B 44 SER cc_start: 0.9203 (t) cc_final: 0.8673 (p) REVERT: B 67 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: B 68 ASN cc_start: 0.9120 (m-40) cc_final: 0.8750 (m-40) REVERT: B 99 ASP cc_start: 0.8876 (t0) cc_final: 0.8463 (t0) REVERT: B 149 MET cc_start: 0.9156 (ptp) cc_final: 0.8733 (ptm) REVERT: B 255 GLN cc_start: 0.8593 (pm20) cc_final: 0.8334 (pm20) REVERT: B 268 ILE cc_start: 0.9561 (OUTLIER) cc_final: 0.9314 (mm) REVERT: B 309 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7849 (mp0) REVERT: B 439 GLN cc_start: 0.8233 (tt0) cc_final: 0.7128 (tm-30) REVERT: B 539 ARG cc_start: 0.7826 (mtp-110) cc_final: 0.7220 (ptm160) REVERT: B 557 ARG cc_start: 0.8134 (mpt180) cc_final: 0.7695 (ttm-80) REVERT: B 692 GLU cc_start: 0.8194 (tp30) cc_final: 0.7578 (tp30) REVERT: B 879 SER cc_start: 0.8949 (m) cc_final: 0.8738 (p) REVERT: B 946 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7322 (tm-30) REVERT: B 947 PHE cc_start: 0.8861 (t80) cc_final: 0.8102 (t80) REVERT: B 954 LYS cc_start: 0.8735 (mmpt) cc_final: 0.8517 (mmmt) REVERT: C 21 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8670 (mp) REVERT: C 29 LYS cc_start: 0.8144 (mtpp) cc_final: 0.7781 (pttp) REVERT: C 44 SER cc_start: 0.8825 (m) cc_final: 0.8506 (t) REVERT: C 89 THR cc_start: 0.8901 (m) cc_final: 0.8553 (p) REVERT: C 111 LEU cc_start: 0.9187 (tp) cc_final: 0.8984 (tm) REVERT: C 120 GLN cc_start: 0.8370 (tp-100) cc_final: 0.7918 (tp-100) REVERT: C 342 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7924 (mttp) REVERT: C 362 PHE cc_start: 0.7687 (t80) cc_final: 0.7275 (t80) REVERT: C 366 LEU cc_start: 0.8968 (tp) cc_final: 0.8605 (mt) REVERT: C 407 ASP cc_start: 0.8736 (t0) cc_final: 0.8177 (t0) REVERT: C 450 SER cc_start: 0.8996 (OUTLIER) cc_final: 0.8732 (p) REVERT: C 459 PHE cc_start: 0.8880 (m-80) cc_final: 0.8226 (m-10) REVERT: C 574 MET cc_start: 0.8181 (ptm) cc_final: 0.7877 (ptp) REVERT: C 576 GLN cc_start: 0.8217 (tp-100) cc_final: 0.7778 (tp-100) REVERT: C 651 MET cc_start: 0.8728 (tpp) cc_final: 0.8490 (mmm) REVERT: C 663 PHE cc_start: 0.7872 (m-80) cc_final: 0.7662 (m-80) REVERT: C 796 GLN cc_start: 0.8419 (mm-40) cc_final: 0.7789 (mp10) REVERT: C 921 THR cc_start: 0.8536 (OUTLIER) cc_final: 0.7686 (t) REVERT: C 939 LYS cc_start: 0.8523 (ttpt) cc_final: 0.8283 (ttmm) REVERT: C 946 GLU cc_start: 0.8478 (tp30) cc_final: 0.7792 (tp30) REVERT: C 950 ASP cc_start: 0.8070 (t0) cc_final: 0.7827 (t0) outliers start: 60 outliers final: 39 residues processed: 421 average time/residue: 1.2696 time to fit residues: 623.7198 Evaluate side-chains 417 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 369 time to evaluate : 2.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 680 ASP Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 921 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 252 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 176 GLN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN C 338 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.078463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.067219 restraints weight = 45548.727| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.25 r_work: 0.2703 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24008 Z= 0.223 Angle : 0.717 28.303 32628 Z= 0.313 Chirality : 0.070 2.083 3831 Planarity : 0.004 0.044 4175 Dihedral : 5.911 124.145 3318 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.03 % Allowed : 18.91 % Favored : 79.06 % 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: 1.99 (0.15), residues: 3093 helix: 2.31 (0.13), residues: 1683 sheet: -0.22 (0.25), residues: 394 loop : 0.38 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 553 HIS 0.003 0.000 HIS A 708 PHE 0.024 0.001 PHE C 555 TYR 0.014 0.001 TYR B 182 ARG 0.019 0.000 ARG C 517 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9731.32 seconds wall clock time: 173 minutes 27.28 seconds (10407.28 seconds total)