Starting phenix.real_space_refine on Thu Feb 15 09:34:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hke_34850/02_2024/8hke_34850.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hke_34850/02_2024/8hke_34850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hke_34850/02_2024/8hke_34850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hke_34850/02_2024/8hke_34850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hke_34850/02_2024/8hke_34850.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hke_34850/02_2024/8hke_34850.pdb" } resolution = 3.71 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= 0.002 sd= 0.059 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 74 5.49 5 S 66 5.16 5 C 7400 2.51 5 N 1983 2.21 5 O 2329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 62": "OE1" <-> "OE2" Residue "B PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B ARG 240": "NH1" <-> "NH2" Residue "B GLU 265": "OE1" <-> "OE2" Residue "B ARG 472": "NH1" <-> "NH2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "A ARG 240": "NH1" <-> "NH2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "A GLU 462": "OE1" <-> "OE2" Residue "A ARG 472": "NH1" <-> "NH2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A GLU 622": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11854 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 5089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5089 Classifications: {'peptide': 647} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 629} Chain breaks: 3 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 8, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "A" Number of atoms: 5189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5189 Classifications: {'peptide': 659} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 640} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 8, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 790 Classifications: {'RNA': 37} Modifications used: {'rna3p_pur': 20, 'rna3p_pyr': 17} Link IDs: {'rna3p': 36} Chain: "D" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 784 Classifications: {'RNA': 37} Modifications used: {'rna3p_pur': 17, 'rna3p_pyr': 20} Link IDs: {'rna3p': 36} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.61, per 1000 atoms: 0.56 Number of scatterers: 11854 At special positions: 0 Unit cell: (116.48, 112.32, 132.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 66 16.00 P 74 15.00 O 2329 8.00 N 1983 7.00 C 7400 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 225 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 731 " distance=2.02 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: 5.64 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 540 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 740 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 744 " pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 540 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 744 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 740 " 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2508 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 11 sheets defined 46.1% alpha, 10.5% beta 24 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 3.76 Creating SS restraints... Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 264 through 272 removed outlier: 4.084A pdb=" N MET B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 323 Processing helix chain 'B' and resid 327 through 332 removed outlier: 4.118A pdb=" N LEU B 331 " --> pdb=" O PRO B 328 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 332 " --> pdb=" O CYS B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 344 removed outlier: 3.658A pdb=" N ILE B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS B 341 " --> pdb=" O ILE B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 433 removed outlier: 3.603A pdb=" N MET B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU B 431 " --> pdb=" O HIS B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 444 through 454 removed outlier: 3.755A pdb=" N HIS B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP B 452 " --> pdb=" O GLU B 448 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR B 454 " --> pdb=" O HIS B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 464 removed outlier: 3.714A pdb=" N CYS B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 485 No H-bonds generated for 'chain 'B' and resid 483 through 485' Processing helix chain 'B' and resid 486 through 502 removed outlier: 4.143A pdb=" N THR B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA B 494 " --> pdb=" O THR B 490 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE B 496 " --> pdb=" O TYR B 492 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE B 501 " --> pdb=" O ILE B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 531 removed outlier: 3.727A pdb=" N THR B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 526 " --> pdb=" O ASP B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 540 removed outlier: 4.411A pdb=" N ALA B 537 " --> pdb=" O SER B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 569 removed outlier: 4.236A pdb=" N MET B 563 " --> pdb=" O CYS B 559 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN B 566 " --> pdb=" O LEU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 577 No H-bonds generated for 'chain 'B' and resid 575 through 577' Processing helix chain 'B' and resid 578 through 596 removed outlier: 3.956A pdb=" N VAL B 584 " --> pdb=" O ASN B 580 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 585 " --> pdb=" O ILE B 581 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 626 removed outlier: 3.644A pdb=" N ILE B 605 " --> pdb=" O TYR B 601 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA B 607 " --> pdb=" O ARG B 603 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N HIS B 610 " --> pdb=" O ILE B 606 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS B 621 " --> pdb=" O ILE B 617 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU B 622 " --> pdb=" O CYS B 618 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER B 624 " --> pdb=" O ALA B 620 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 626 " --> pdb=" O GLU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 652 removed outlier: 3.783A pdb=" N PHE B 639 " --> pdb=" O PHE B 635 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE B 644 " --> pdb=" O SER B 640 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET B 649 " --> pdb=" O ALA B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 684 removed outlier: 4.458A pdb=" N THR B 663 " --> pdb=" O ASN B 659 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR B 677 " --> pdb=" O TYR B 673 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL B 682 " --> pdb=" O GLY B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 709 removed outlier: 3.778A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 713 Processing helix chain 'B' and resid 722 through 727 removed outlier: 3.622A pdb=" N LEU B 727 " --> pdb=" O ALA B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 761 removed outlier: 3.581A pdb=" N TRP B 743 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS B 744 " --> pdb=" O HIS B 740 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 745 " --> pdb=" O ASP B 741 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA B 748 " --> pdb=" O HIS B 744 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE B 755 " --> pdb=" O GLY B 751 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VAL B 758 " --> pdb=" O THR B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 768 removed outlier: 3.860A pdb=" N ASN B 767 " --> pdb=" O ASP B 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 68 removed outlier: 3.713A pdb=" N ILE A 68 " --> pdb=" O GLN A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 Processing helix chain 'A' and resid 128 through 132 removed outlier: 3.982A pdb=" N PHE A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 210 removed outlier: 3.731A pdb=" N ASN A 210 " --> pdb=" O SER A 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 210' Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 314 through 325 removed outlier: 3.696A pdb=" N THR A 318 " --> pdb=" O TYR A 314 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET A 321 " --> pdb=" O PRO A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 341 through 344 Processing helix chain 'A' and resid 426 through 433 Processing helix chain 'A' and resid 438 through 454 Processing helix chain 'A' and resid 458 through 464 Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 486 through 493 removed outlier: 3.683A pdb=" N THR A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 503 removed outlier: 4.193A pdb=" N ILE A 501 " --> pdb=" O ILE A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 540 removed outlier: 3.692A pdb=" N SER A 533 " --> pdb=" O MET A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 569 removed outlier: 4.158A pdb=" N MET A 563 " --> pdb=" O CYS A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 596 removed outlier: 4.199A pdb=" N ILE A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 626 removed outlier: 3.547A pdb=" N SER A 624 " --> pdb=" O ALA A 620 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 625 " --> pdb=" O LYS A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 652 removed outlier: 4.032A pdb=" N MET A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 684 removed outlier: 3.619A pdb=" N ILE A 661 " --> pdb=" O HIS A 657 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ALA A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR A 663 " --> pdb=" O ASN A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 711 Processing helix chain 'A' and resid 720 through 726 Processing helix chain 'A' and resid 739 through 759 removed outlier: 3.609A pdb=" N ALA A 748 " --> pdb=" O HIS A 744 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 35 through 39 removed outlier: 3.531A pdb=" N VAL B 151 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR B 152 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B 154 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU B 93 " --> pdb=" O GLN B 154 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 4.255A pdb=" N ARG B 164 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU B 77 " --> pdb=" O ARG B 164 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 186 through 193 removed outlier: 5.693A pdb=" N THR B 188 " --> pdb=" O PHE B 306 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N PHE B 306 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N SER B 190 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N PHE B 304 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 200 through 204 removed outlier: 3.544A pdb=" N ILE B 200 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN B 227 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B 230 " --> pdb=" O ARG B 251 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 251 " --> pdb=" O THR B 230 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 36 through 39 removed outlier: 3.796A pdb=" N VAL A 58 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 152 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 47 through 51 removed outlier: 3.656A pdb=" N LYS A 49 " --> pdb=" O TYR A 163 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR A 163 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.606A pdb=" N LYS A 73 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA9, first strand: chain 'A' and resid 186 through 187 removed outlier: 3.805A pdb=" N GLN A 213 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 200 through 201 Processing sheet with id=AB2, first strand: chain 'A' and resid 200 through 201 removed outlier: 3.572A pdb=" N ASN A 227 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE A 255 " --> pdb=" O ALA A 226 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1179 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 58 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 4.28 Time building geometry restraints manager: 5.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3281 1.33 - 1.45: 2716 1.45 - 1.57: 6027 1.57 - 1.69: 146 1.69 - 1.81: 98 Bond restraints: 12268 Sorted by residual: bond pdb=" CA TYR B 492 " pdb=" C TYR B 492 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.80e-02 3.09e+03 1.31e+01 bond pdb=" C PRO A 574 " pdb=" N SER A 575 " ideal model delta sigma weight residual 1.331 1.256 0.075 2.07e-02 2.33e+03 1.30e+01 bond pdb=" C GLU A 93 " pdb=" N VAL A 94 " ideal model delta sigma weight residual 1.330 1.300 0.031 1.48e-02 4.57e+03 4.28e+00 bond pdb=" CA VAL A 278 " pdb=" C VAL A 278 " ideal model delta sigma weight residual 1.527 1.509 0.018 8.50e-03 1.38e+04 4.25e+00 bond pdb=" CA SER B 269 " pdb=" C SER B 269 " ideal model delta sigma weight residual 1.523 1.490 0.033 1.80e-02 3.09e+03 3.41e+00 ... (remaining 12263 not shown) Histogram of bond angle deviations from ideal: 90.59 - 99.59: 2 99.59 - 108.60: 1357 108.60 - 117.60: 8148 117.60 - 126.60: 7182 126.60 - 135.61: 297 Bond angle restraints: 16986 Sorted by residual: angle pdb=" C ASN A 234 " pdb=" CA ASN A 234 " pdb=" CB ASN A 234 " ideal model delta sigma weight residual 110.81 135.61 -24.80 1.60e+00 3.91e-01 2.40e+02 angle pdb=" N ALA A 469 " pdb=" CA ALA A 469 " pdb=" C ALA A 469 " ideal model delta sigma weight residual 110.80 90.59 20.21 2.13e+00 2.20e-01 9.01e+01 angle pdb=" C PRO B 553 " pdb=" CA PRO B 553 " pdb=" CB PRO B 553 " ideal model delta sigma weight residual 111.56 125.99 -14.43 1.65e+00 3.67e-01 7.64e+01 angle pdb=" N SER A 66 " pdb=" CA SER A 66 " pdb=" C SER A 66 " ideal model delta sigma weight residual 113.01 122.68 -9.67 1.20e+00 6.94e-01 6.50e+01 angle pdb=" C HIS A 468 " pdb=" CA HIS A 468 " pdb=" CB HIS A 468 " ideal model delta sigma weight residual 111.83 100.42 11.41 1.60e+00 3.91e-01 5.09e+01 ... (remaining 16981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6465 17.99 - 35.98: 637 35.98 - 53.97: 136 53.97 - 71.95: 105 71.95 - 89.94: 27 Dihedral angle restraints: 7370 sinusoidal: 3523 harmonic: 3847 Sorted by residual: dihedral pdb=" C ASN A 234 " pdb=" N ASN A 234 " pdb=" CA ASN A 234 " pdb=" CB ASN A 234 " ideal model delta harmonic sigma weight residual -122.60 -153.92 31.32 0 2.50e+00 1.60e-01 1.57e+02 dihedral pdb=" CB CYS A 470 " pdb=" SG CYS A 470 " pdb=" SG CYS A 731 " pdb=" CB CYS A 731 " ideal model delta sinusoidal sigma weight residual -86.00 -163.25 77.25 1 1.00e+01 1.00e-02 7.48e+01 dihedral pdb=" N ASN A 234 " pdb=" C ASN A 234 " pdb=" CA ASN A 234 " pdb=" CB ASN A 234 " ideal model delta harmonic sigma weight residual 122.80 144.03 -21.23 0 2.50e+00 1.60e-01 7.21e+01 ... (remaining 7367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.234: 2047 0.234 - 0.467: 2 0.467 - 0.701: 2 0.701 - 0.934: 0 0.934 - 1.168: 1 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CA ASN A 234 " pdb=" N ASN A 234 " pdb=" C ASN A 234 " pdb=" CB ASN A 234 " both_signs ideal model delta sigma weight residual False 2.51 1.34 1.17 2.00e-01 2.50e+01 3.41e+01 chirality pdb=" CA PRO B 553 " pdb=" N PRO B 553 " pdb=" C PRO B 553 " pdb=" CB PRO B 553 " both_signs ideal model delta sigma weight residual False 2.72 2.15 0.57 2.00e-01 2.50e+01 8.01e+00 chirality pdb=" CA HIS A 468 " pdb=" N HIS A 468 " pdb=" C HIS A 468 " pdb=" CB HIS A 468 " both_signs ideal model delta sigma weight residual False 2.51 3.06 -0.55 2.00e-01 2.50e+01 7.62e+00 ... (remaining 2049 not shown) Planarity restraints: 1837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G D 12 " 0.032 2.00e-02 2.50e+03 1.39e-02 5.80e+00 pdb=" N9 G D 12 " -0.031 2.00e-02 2.50e+03 pdb=" C8 G D 12 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G D 12 " 0.004 2.00e-02 2.50e+03 pdb=" C5 G D 12 " -0.004 2.00e-02 2.50e+03 pdb=" C6 G D 12 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G D 12 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G D 12 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G D 12 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G D 12 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G D 12 " -0.012 2.00e-02 2.50e+03 pdb=" C4 G D 12 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 542 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO A 543 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C D 13 " 0.024 2.00e-02 2.50e+03 1.35e-02 4.09e+00 pdb=" N1 C D 13 " -0.032 2.00e-02 2.50e+03 pdb=" C2 C D 13 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C D 13 " -0.000 2.00e-02 2.50e+03 pdb=" N3 C D 13 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C D 13 " -0.000 2.00e-02 2.50e+03 pdb=" N4 C D 13 " 0.007 2.00e-02 2.50e+03 pdb=" C5 C D 13 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C D 13 " -0.000 2.00e-02 2.50e+03 ... (remaining 1834 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 212 2.62 - 3.19: 11379 3.19 - 3.76: 18463 3.76 - 4.33: 25886 4.33 - 4.90: 40241 Nonbonded interactions: 96181 Sorted by model distance: nonbonded pdb=" NZ LYS A 45 " pdb=" OP1 U D 25 " model vdw 2.049 2.520 nonbonded pdb=" OD2 ASP B 551 " pdb="ZN ZN B 801 " model vdw 2.077 2.230 nonbonded pdb=" NZ LYS A 299 " pdb=" OP2 C C 19 " model vdw 2.141 2.520 nonbonded pdb=" O ILE B 606 " pdb=" OH TYR B 650 " model vdw 2.157 2.440 nonbonded pdb=" OG1 THR A 515 " pdb=" O VAL A 569 " model vdw 2.158 2.440 ... (remaining 96176 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 34 through 131 or resid 144 through 170 or (resid 171 thro \ ugh 173 and (name N or name CA or name C or name O or name CB )) or resid 174 th \ rough 292 or (resid 293 through 294 and (name N or name CA or name C or name O o \ r name CB )) or resid 295 through 296 or (resid 297 through 299 and (name N or n \ ame CA or name C or name O or name CB )) or resid 300 through 776 or resid 801)) \ selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 0.010 Extract box with map and model: 4.080 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 39.290 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 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 0.075 12268 Z= 0.483 Angle : 0.823 24.798 16986 Z= 0.449 Chirality : 0.057 1.168 2052 Planarity : 0.004 0.056 1837 Dihedral : 17.029 89.943 4847 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 0.09 % Allowed : 9.10 % Favored : 90.81 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -5.00 (0.19), residues: 1292 helix: -3.04 (0.17), residues: 513 sheet: -3.93 (0.28), residues: 230 loop : -3.12 (0.24), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 452 HIS 0.008 0.002 HIS A 744 PHE 0.033 0.002 PHE A 639 TYR 0.020 0.002 TYR A 650 ARG 0.004 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7679 (mt-10) REVERT: B 484 ILE cc_start: 0.9276 (tp) cc_final: 0.8861 (tp) REVERT: B 591 PHE cc_start: 0.8249 (t80) cc_final: 0.8016 (t80) REVERT: A 106 LYS cc_start: 0.8704 (mttt) cc_final: 0.8172 (mtmt) REVERT: A 219 TYR cc_start: 0.8276 (m-80) cc_final: 0.7847 (m-80) REVERT: A 314 TYR cc_start: 0.8733 (m-80) cc_final: 0.8473 (m-80) REVERT: A 637 MET cc_start: 0.7661 (ttp) cc_final: 0.6338 (tmm) REVERT: A 641 MET cc_start: 0.5650 (ptt) cc_final: 0.5204 (ptt) REVERT: A 681 LYS cc_start: 0.9091 (tttp) cc_final: 0.8851 (tttt) REVERT: A 728 ASN cc_start: 0.8183 (p0) cc_final: 0.7608 (p0) REVERT: A 741 ASP cc_start: 0.7995 (m-30) cc_final: 0.7717 (m-30) outliers start: 1 outliers final: 1 residues processed: 201 average time/residue: 0.2445 time to fit residues: 69.8171 Evaluate side-chains 151 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN B 113 ASN B 566 GLN ** B 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 GLN A 297 ASN A 432 GLN A 444 HIS A 566 GLN A 590 ASN A 657 HIS A 659 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12268 Z= 0.180 Angle : 0.590 8.035 16986 Z= 0.301 Chirality : 0.041 0.160 2052 Planarity : 0.004 0.046 1837 Dihedral : 17.295 92.921 2543 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.61 % Allowed : 16.15 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.22), residues: 1292 helix: -1.02 (0.22), residues: 524 sheet: -3.27 (0.29), residues: 239 loop : -2.31 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 452 HIS 0.006 0.001 HIS B 57 PHE 0.027 0.001 PHE B 324 TYR 0.024 0.001 TYR A 650 ARG 0.007 0.000 ARG B 769 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 188 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 484 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8698 (tp) REVERT: B 563 MET cc_start: 0.7127 (mtt) cc_final: 0.6755 (mmm) REVERT: A 80 ASP cc_start: 0.8097 (m-30) cc_final: 0.7703 (t0) REVERT: A 106 LYS cc_start: 0.8590 (mttt) cc_final: 0.8027 (mtmt) REVERT: A 193 LYS cc_start: 0.9148 (tptt) cc_final: 0.8936 (tttp) REVERT: A 219 TYR cc_start: 0.8101 (m-80) cc_final: 0.7589 (m-10) REVERT: A 261 ILE cc_start: 0.9133 (mt) cc_final: 0.8903 (mm) REVERT: A 314 TYR cc_start: 0.8526 (m-80) cc_final: 0.8299 (m-80) REVERT: A 484 ILE cc_start: 0.9230 (tp) cc_final: 0.8659 (tp) REVERT: A 672 MET cc_start: 0.8948 (mtm) cc_final: 0.8046 (tpt) REVERT: A 681 LYS cc_start: 0.8993 (tttp) cc_final: 0.7972 (tttt) REVERT: A 728 ASN cc_start: 0.8202 (p0) cc_final: 0.7664 (p0) REVERT: A 741 ASP cc_start: 0.7951 (m-30) cc_final: 0.7409 (m-30) outliers start: 18 outliers final: 8 residues processed: 197 average time/residue: 0.2048 time to fit residues: 60.4902 Evaluate side-chains 154 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 145 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 731 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 132 optimal weight: 30.0000 chunk 109 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 571 HIS ** B 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12268 Z= 0.280 Angle : 0.595 9.314 16986 Z= 0.301 Chirality : 0.041 0.149 2052 Planarity : 0.004 0.044 1837 Dihedral : 17.151 92.705 2543 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.39 % Allowed : 18.82 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -2.47 (0.23), residues: 1292 helix: -0.41 (0.23), residues: 531 sheet: -2.97 (0.29), residues: 249 loop : -2.12 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 452 HIS 0.005 0.001 HIS A 744 PHE 0.022 0.002 PHE A 131 TYR 0.022 0.001 TYR A 650 ARG 0.004 0.000 ARG B 504 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 163 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 260 ASP cc_start: 0.8627 (m-30) cc_final: 0.8341 (m-30) REVERT: B 484 ILE cc_start: 0.9083 (tp) cc_final: 0.8583 (tp) REVERT: B 487 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8404 (tp) REVERT: A 80 ASP cc_start: 0.8102 (m-30) cc_final: 0.7709 (t0) REVERT: A 106 LYS cc_start: 0.8642 (mttt) cc_final: 0.8078 (mtmt) REVERT: A 193 LYS cc_start: 0.9211 (tptt) cc_final: 0.8872 (tttt) REVERT: A 219 TYR cc_start: 0.8206 (m-80) cc_final: 0.7807 (m-10) REVERT: A 314 TYR cc_start: 0.8551 (m-80) cc_final: 0.8339 (m-80) REVERT: A 484 ILE cc_start: 0.8973 (tp) cc_final: 0.8481 (tp) REVERT: A 520 LEU cc_start: 0.8084 (mm) cc_final: 0.7777 (mt) REVERT: A 522 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8170 (t0) REVERT: A 637 MET cc_start: 0.7433 (tmm) cc_final: 0.6912 (ptt) REVERT: A 728 ASN cc_start: 0.8271 (p0) cc_final: 0.7702 (p0) outliers start: 38 outliers final: 25 residues processed: 190 average time/residue: 0.1933 time to fit residues: 56.2232 Evaluate side-chains 170 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 749 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.9980 chunk 92 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 chunk 82 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12268 Z= 0.220 Angle : 0.551 10.180 16986 Z= 0.279 Chirality : 0.040 0.159 2052 Planarity : 0.003 0.043 1837 Dihedral : 16.938 89.072 2543 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.10 % Allowed : 19.54 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 (0.24), residues: 1292 helix: -0.04 (0.23), residues: 529 sheet: -2.68 (0.30), residues: 249 loop : -1.88 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 452 HIS 0.005 0.001 HIS B 610 PHE 0.033 0.001 PHE B 324 TYR 0.024 0.001 TYR A 650 ARG 0.005 0.000 ARG B 504 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 158 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 260 ASP cc_start: 0.8729 (m-30) cc_final: 0.8521 (m-30) REVERT: B 484 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8585 (tp) REVERT: B 487 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8364 (tp) REVERT: A 88 ASP cc_start: 0.7674 (p0) cc_final: 0.7052 (p0) REVERT: A 193 LYS cc_start: 0.9183 (tptt) cc_final: 0.8887 (tttt) REVERT: A 219 TYR cc_start: 0.8071 (m-80) cc_final: 0.7626 (m-10) REVERT: A 261 ILE cc_start: 0.9165 (mt) cc_final: 0.8945 (mm) REVERT: A 484 ILE cc_start: 0.8936 (tp) cc_final: 0.8455 (tp) REVERT: A 520 LEU cc_start: 0.8100 (mm) cc_final: 0.7824 (mt) REVERT: A 522 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8042 (t0) REVERT: A 637 MET cc_start: 0.7597 (tmm) cc_final: 0.7096 (tmm) REVERT: A 672 MET cc_start: 0.8988 (mtm) cc_final: 0.8123 (tpt) REVERT: A 728 ASN cc_start: 0.8255 (p0) cc_final: 0.7696 (p0) REVERT: A 741 ASP cc_start: 0.7811 (m-30) cc_final: 0.7595 (m-30) outliers start: 46 outliers final: 30 residues processed: 187 average time/residue: 0.1865 time to fit residues: 54.1819 Evaluate side-chains 182 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 149 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 749 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 1.9990 chunk 74 optimal weight: 0.0370 chunk 1 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.6662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 482 ASN ** B 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 HIS ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12268 Z= 0.245 Angle : 0.557 9.407 16986 Z= 0.282 Chirality : 0.040 0.164 2052 Planarity : 0.003 0.041 1837 Dihedral : 16.709 82.755 2543 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.64 % Allowed : 21.05 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.75 (0.24), residues: 1292 helix: 0.18 (0.24), residues: 531 sheet: -2.55 (0.31), residues: 263 loop : -1.70 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 452 HIS 0.005 0.001 HIS B 610 PHE 0.021 0.001 PHE B 324 TYR 0.023 0.001 TYR A 650 ARG 0.007 0.000 ARG B 478 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 155 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 484 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8621 (tp) REVERT: B 487 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8353 (tp) REVERT: B 676 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.6583 (t80) REVERT: B 680 MET cc_start: 0.7985 (mtt) cc_final: 0.7596 (mtp) REVERT: A 88 ASP cc_start: 0.7743 (p0) cc_final: 0.7116 (p0) REVERT: A 219 TYR cc_start: 0.8168 (m-80) cc_final: 0.7777 (m-80) REVERT: A 261 ILE cc_start: 0.9200 (mt) cc_final: 0.8985 (mm) REVERT: A 297 ASN cc_start: 0.6422 (OUTLIER) cc_final: 0.5882 (t0) REVERT: A 520 LEU cc_start: 0.8211 (mm) cc_final: 0.7929 (mt) REVERT: A 522 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.8053 (t0) REVERT: A 637 MET cc_start: 0.7622 (tmm) cc_final: 0.7094 (tmm) REVERT: A 728 ASN cc_start: 0.8293 (p0) cc_final: 0.7741 (p0) outliers start: 52 outliers final: 37 residues processed: 191 average time/residue: 0.2115 time to fit residues: 62.8917 Evaluate side-chains 189 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 147 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 676 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 749 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 0.0470 chunk 130 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 overall best weight: 1.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12268 Z= 0.209 Angle : 0.533 9.769 16986 Z= 0.270 Chirality : 0.039 0.160 2052 Planarity : 0.003 0.043 1837 Dihedral : 16.509 82.444 2543 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.19 % Allowed : 22.21 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.51 (0.24), residues: 1292 helix: 0.37 (0.24), residues: 530 sheet: -2.41 (0.31), residues: 262 loop : -1.56 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 452 HIS 0.005 0.001 HIS B 610 PHE 0.032 0.001 PHE A 708 TYR 0.022 0.001 TYR A 650 ARG 0.004 0.000 ARG B 504 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 160 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 484 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8591 (tp) REVERT: B 487 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8437 (tp) REVERT: A 88 ASP cc_start: 0.7780 (p0) cc_final: 0.7158 (p0) REVERT: A 219 TYR cc_start: 0.8095 (m-80) cc_final: 0.7665 (m-80) REVERT: A 261 ILE cc_start: 0.9221 (mt) cc_final: 0.8987 (mm) REVERT: A 297 ASN cc_start: 0.6237 (OUTLIER) cc_final: 0.5730 (t0) REVERT: A 450 HIS cc_start: 0.7758 (OUTLIER) cc_final: 0.7220 (t70) REVERT: A 520 LEU cc_start: 0.8169 (mm) cc_final: 0.7853 (mt) REVERT: A 522 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8081 (t0) REVERT: A 637 MET cc_start: 0.7586 (tmm) cc_final: 0.7040 (tmm) REVERT: A 681 LYS cc_start: 0.8765 (tttm) cc_final: 0.8195 (tttt) REVERT: A 728 ASN cc_start: 0.8268 (p0) cc_final: 0.7717 (p0) outliers start: 47 outliers final: 37 residues processed: 193 average time/residue: 0.2026 time to fit residues: 59.9994 Evaluate side-chains 192 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 150 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 749 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 8.9990 chunk 74 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 109 optimal weight: 0.0970 chunk 72 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 81 optimal weight: 0.4980 chunk 79 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 GLN ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12268 Z= 0.152 Angle : 0.531 10.304 16986 Z= 0.265 Chirality : 0.039 0.201 2052 Planarity : 0.003 0.040 1837 Dihedral : 16.332 82.775 2543 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.01 % Allowed : 23.46 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.29 (0.24), residues: 1292 helix: 0.54 (0.24), residues: 530 sheet: -2.25 (0.32), residues: 261 loop : -1.46 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 567 HIS 0.006 0.001 HIS B 610 PHE 0.015 0.001 PHE A 755 TYR 0.028 0.001 TYR A 650 ARG 0.005 0.000 ARG B 478 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 169 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 LEU cc_start: 0.9009 (mt) cc_final: 0.8630 (tt) REVERT: B 260 ASP cc_start: 0.8534 (m-30) cc_final: 0.8248 (m-30) REVERT: B 563 MET cc_start: 0.7375 (mtm) cc_final: 0.5885 (tmm) REVERT: A 62 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8067 (mm-30) REVERT: A 80 ASP cc_start: 0.7860 (m-30) cc_final: 0.7364 (t0) REVERT: A 88 ASP cc_start: 0.7763 (p0) cc_final: 0.7419 (p0) REVERT: A 168 THR cc_start: 0.9123 (p) cc_final: 0.8891 (t) REVERT: A 219 TYR cc_start: 0.8012 (m-80) cc_final: 0.7576 (m-80) REVERT: A 261 ILE cc_start: 0.9227 (mt) cc_final: 0.9007 (mm) REVERT: A 297 ASN cc_start: 0.6385 (OUTLIER) cc_final: 0.5759 (t0) REVERT: A 450 HIS cc_start: 0.7752 (OUTLIER) cc_final: 0.7205 (t70) REVERT: A 484 ILE cc_start: 0.8881 (tp) cc_final: 0.8440 (tp) REVERT: A 533 SER cc_start: 0.8778 (t) cc_final: 0.8426 (t) REVERT: A 637 MET cc_start: 0.7553 (tmm) cc_final: 0.6875 (ptt) REVERT: A 728 ASN cc_start: 0.8203 (p0) cc_final: 0.7674 (p0) outliers start: 45 outliers final: 30 residues processed: 200 average time/residue: 0.1806 time to fit residues: 56.5949 Evaluate side-chains 193 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 161 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 749 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12268 Z= 0.303 Angle : 0.606 11.416 16986 Z= 0.303 Chirality : 0.041 0.168 2052 Planarity : 0.003 0.041 1837 Dihedral : 16.389 82.942 2541 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.46 % Allowed : 23.37 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.24), residues: 1292 helix: 0.34 (0.23), residues: 537 sheet: -2.25 (0.32), residues: 259 loop : -1.51 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 452 HIS 0.005 0.001 HIS A 744 PHE 0.021 0.002 PHE A 755 TYR 0.028 0.002 TYR A 650 ARG 0.005 0.000 ARG B 504 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 158 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 260 ASP cc_start: 0.8794 (m-30) cc_final: 0.8489 (m-30) REVERT: B 301 LYS cc_start: 0.8437 (mmtt) cc_final: 0.7915 (mmtm) REVERT: B 487 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8300 (tp) REVERT: A 88 ASP cc_start: 0.7684 (p0) cc_final: 0.7031 (p0) REVERT: A 106 LYS cc_start: 0.8569 (mttt) cc_final: 0.8037 (mtmt) REVERT: A 219 TYR cc_start: 0.8215 (m-80) cc_final: 0.7869 (m-80) REVERT: A 297 ASN cc_start: 0.6519 (OUTLIER) cc_final: 0.6052 (t0) REVERT: A 314 TYR cc_start: 0.8220 (m-80) cc_final: 0.8010 (m-80) REVERT: A 450 HIS cc_start: 0.7759 (OUTLIER) cc_final: 0.7217 (t70) REVERT: A 520 LEU cc_start: 0.8168 (mm) cc_final: 0.7850 (mt) REVERT: A 637 MET cc_start: 0.7663 (tmm) cc_final: 0.7104 (ptt) REVERT: A 681 LYS cc_start: 0.8814 (tttm) cc_final: 0.8285 (tttt) REVERT: A 728 ASN cc_start: 0.8316 (p0) cc_final: 0.7773 (p0) outliers start: 50 outliers final: 41 residues processed: 196 average time/residue: 0.1913 time to fit residues: 58.1173 Evaluate side-chains 197 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 153 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 749 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 114 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 684 HIS ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12268 Z= 0.229 Angle : 0.576 13.676 16986 Z= 0.286 Chirality : 0.040 0.164 2052 Planarity : 0.003 0.041 1837 Dihedral : 16.309 83.280 2541 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.84 % Allowed : 24.62 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.25), residues: 1292 helix: 0.41 (0.24), residues: 537 sheet: -2.13 (0.33), residues: 258 loop : -1.43 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 452 HIS 0.006 0.001 HIS B 540 PHE 0.022 0.001 PHE A 755 TYR 0.028 0.001 TYR A 650 ARG 0.004 0.000 ARG B 504 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 160 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 260 ASP cc_start: 0.8669 (m-30) cc_final: 0.8363 (m-30) REVERT: B 676 TYR cc_start: 0.7286 (OUTLIER) cc_final: 0.5961 (t80) REVERT: A 219 TYR cc_start: 0.8161 (m-80) cc_final: 0.7816 (m-80) REVERT: A 297 ASN cc_start: 0.6374 (OUTLIER) cc_final: 0.5898 (t0) REVERT: A 314 TYR cc_start: 0.8197 (m-80) cc_final: 0.7991 (m-80) REVERT: A 450 HIS cc_start: 0.7749 (OUTLIER) cc_final: 0.7224 (t70) REVERT: A 520 LEU cc_start: 0.8113 (mm) cc_final: 0.7798 (mt) REVERT: A 637 MET cc_start: 0.7685 (tmm) cc_final: 0.6966 (ptt) REVERT: A 681 LYS cc_start: 0.8810 (tttm) cc_final: 0.8259 (tttt) REVERT: A 728 ASN cc_start: 0.8285 (p0) cc_final: 0.7734 (p0) outliers start: 43 outliers final: 36 residues processed: 194 average time/residue: 0.1833 time to fit residues: 55.7567 Evaluate side-chains 190 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 151 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 676 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 749 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 2.9990 chunk 78 optimal weight: 0.0370 chunk 60 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 85 optimal weight: 8.9990 overall best weight: 1.5264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12268 Z= 0.234 Angle : 0.584 12.812 16986 Z= 0.290 Chirality : 0.040 0.169 2052 Planarity : 0.003 0.040 1837 Dihedral : 16.270 84.162 2541 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.75 % Allowed : 24.80 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.25), residues: 1292 helix: 0.42 (0.24), residues: 537 sheet: -2.05 (0.33), residues: 252 loop : -1.51 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 452 HIS 0.006 0.001 HIS B 540 PHE 0.026 0.001 PHE A 296 TYR 0.026 0.001 TYR A 650 ARG 0.005 0.000 ARG B 504 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 154 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 260 ASP cc_start: 0.8719 (m-30) cc_final: 0.8416 (m-30) REVERT: A 219 TYR cc_start: 0.8184 (m-80) cc_final: 0.7852 (m-80) REVERT: A 297 ASN cc_start: 0.6455 (OUTLIER) cc_final: 0.5947 (t0) REVERT: A 314 TYR cc_start: 0.8226 (m-80) cc_final: 0.8007 (m-80) REVERT: A 450 HIS cc_start: 0.7738 (OUTLIER) cc_final: 0.7219 (t70) REVERT: A 520 LEU cc_start: 0.8122 (mm) cc_final: 0.7813 (mt) REVERT: A 637 MET cc_start: 0.7675 (tmm) cc_final: 0.7112 (ptt) REVERT: A 681 LYS cc_start: 0.8816 (tttm) cc_final: 0.8240 (tttt) REVERT: A 728 ASN cc_start: 0.8304 (p0) cc_final: 0.7775 (p0) outliers start: 42 outliers final: 36 residues processed: 187 average time/residue: 0.1741 time to fit residues: 51.7534 Evaluate side-chains 186 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 148 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 749 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 94 optimal weight: 0.0020 overall best weight: 1.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 HIS ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.140038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.099592 restraints weight = 20574.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.102339 restraints weight = 12967.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.103272 restraints weight = 8591.411| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12268 Z= 0.256 Angle : 0.589 14.210 16986 Z= 0.292 Chirality : 0.041 0.236 2052 Planarity : 0.003 0.042 1837 Dihedral : 16.279 85.397 2541 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.66 % Allowed : 25.16 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.25), residues: 1292 helix: 0.47 (0.24), residues: 531 sheet: -2.01 (0.33), residues: 251 loop : -1.47 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 452 HIS 0.005 0.001 HIS B 540 PHE 0.026 0.001 PHE A 296 TYR 0.025 0.001 TYR A 650 ARG 0.004 0.000 ARG B 504 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2219.41 seconds wall clock time: 41 minutes 38.23 seconds (2498.23 seconds total)