Starting phenix.real_space_refine on Wed Feb 14 17:54:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p48_20246/02_2024/6p48_20246.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p48_20246/02_2024/6p48_20246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p48_20246/02_2024/6p48_20246.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p48_20246/02_2024/6p48_20246.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p48_20246/02_2024/6p48_20246.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p48_20246/02_2024/6p48_20246.pdb" } resolution = 3.2 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= 0.003 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: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 68 5.16 5 C 6592 2.51 5 N 1586 2.21 5 O 1688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A GLU 395": "OE1" <-> "OE2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A ARG 478": "NH1" <-> "NH2" Residue "A ARG 636": "NH1" <-> "NH2" Residue "A ARG 701": "NH1" <-> "NH2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A GLU 717": "OE1" <-> "OE2" Residue "A ARG 808": "NH1" <-> "NH2" Residue "A ARG 810": "NH1" <-> "NH2" Residue "A PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B ARG 209": "NH1" <-> "NH2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 277": "NH1" <-> "NH2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 360": "NH1" <-> "NH2" Residue "B GLU 395": "OE1" <-> "OE2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B ARG 478": "NH1" <-> "NH2" Residue "B ARG 636": "NH1" <-> "NH2" Residue "B ARG 701": "NH1" <-> "NH2" Residue "B ARG 712": "NH1" <-> "NH2" Residue "B GLU 717": "OE1" <-> "OE2" Residue "B ARG 808": "NH1" <-> "NH2" Residue "B ARG 810": "NH1" <-> "NH2" Residue "B PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 9936 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4967 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 577} Chain breaks: 9 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 4967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4967 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 577} Chain breaks: 9 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.64, per 1000 atoms: 0.57 Number of scatterers: 9936 At special positions: 0 Unit cell: (85.779, 112.254, 109.077, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 68 16.00 O 1688 8.00 N 1586 7.00 C 6592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 356 " distance=2.04 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " distance=2.04 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 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: 3.83 Conformation dependent library (CDL) restraints added in 1.7 seconds 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2296 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 2 sheets defined 60.1% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 91 through 104 removed outlier: 3.994A pdb=" N LYS A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N TYR A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASN A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 220 removed outlier: 3.787A pdb=" N ARG A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG A 219 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.626A pdb=" N VAL A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 238 " --> pdb=" O ASN A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 272 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.685A pdb=" N TRP A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN A 308 " --> pdb=" O GLY A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 326 removed outlier: 3.834A pdb=" N VAL A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 325 " --> pdb=" O PHE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 removed outlier: 3.837A pdb=" N SER A 376 " --> pdb=" O CYS A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 408 removed outlier: 3.856A pdb=" N GLU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.558A pdb=" N CYS A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 452 through 456' Processing helix chain 'A' and resid 456 through 480 removed outlier: 3.729A pdb=" N PHE A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 465 " --> pdb=" O PHE A 461 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE A 475 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 486 removed outlier: 3.648A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 537 removed outlier: 3.818A pdb=" N PHE A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 535 " --> pdb=" O VAL A 531 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.906A pdb=" N TYR A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ASN A 549 " --> pdb=" O THR A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 573 removed outlier: 4.589A pdb=" N LEU A 557 " --> pdb=" O MET A 553 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A 572 " --> pdb=" O PHE A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 589 removed outlier: 3.583A pdb=" N LEU A 588 " --> pdb=" O VAL A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 614 removed outlier: 3.535A pdb=" N LEU A 605 " --> pdb=" O CYS A 601 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 620 Processing helix chain 'A' and resid 638 through 646 removed outlier: 3.555A pdb=" N GLY A 642 " --> pdb=" O LYS A 638 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 644 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 654 removed outlier: 3.543A pdb=" N ASP A 653 " --> pdb=" O ARG A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 679 removed outlier: 3.765A pdb=" N GLU A 670 " --> pdb=" O TYR A 666 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET A 671 " --> pdb=" O GLU A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.597A pdb=" N ASN A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE A 700 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 747 removed outlier: 3.518A pdb=" N ALA A 741 " --> pdb=" O VAL A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 760 removed outlier: 3.603A pdb=" N TYR A 756 " --> pdb=" O PRO A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 857 removed outlier: 3.511A pdb=" N SER A 848 " --> pdb=" O HIS A 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 104 removed outlier: 3.995A pdb=" N LYS B 97 " --> pdb=" O LYS B 93 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TYR B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU B 102 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASN B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 220 removed outlier: 3.787A pdb=" N ARG B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL B 213 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG B 219 " --> pdb=" O PHE B 215 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 239 removed outlier: 3.626A pdb=" N VAL B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER B 238 " --> pdb=" O ASN B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 272 Processing helix chain 'B' and resid 285 through 290 Processing helix chain 'B' and resid 296 through 310 removed outlier: 3.685A pdb=" N TRP B 302 " --> pdb=" O ILE B 298 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN B 308 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 326 removed outlier: 3.834A pdb=" N VAL B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS B 320 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR B 325 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 376 removed outlier: 3.837A pdb=" N SER B 376 " --> pdb=" O CYS B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 408 removed outlier: 3.856A pdb=" N GLU B 395 " --> pdb=" O THR B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 456 removed outlier: 3.557A pdb=" N CYS B 456 " --> pdb=" O ARG B 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 452 through 456' Processing helix chain 'B' and resid 456 through 480 removed outlier: 3.728A pdb=" N PHE B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU B 465 " --> pdb=" O PHE B 461 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 470 " --> pdb=" O LEU B 466 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE B 475 " --> pdb=" O VAL B 471 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B 477 " --> pdb=" O GLY B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 486 removed outlier: 3.648A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 537 removed outlier: 3.818A pdb=" N PHE B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE B 535 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 551 removed outlier: 3.906A pdb=" N TYR B 547 " --> pdb=" O THR B 543 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ASN B 549 " --> pdb=" O THR B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 573 removed outlier: 4.590A pdb=" N LEU B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR B 569 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE B 572 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.583A pdb=" N LEU B 588 " --> pdb=" O VAL B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 removed outlier: 3.535A pdb=" N LEU B 605 " --> pdb=" O CYS B 601 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN B 608 " --> pdb=" O GLU B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 620 Processing helix chain 'B' and resid 638 through 646 removed outlier: 3.555A pdb=" N GLY B 642 " --> pdb=" O LYS B 638 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 644 " --> pdb=" O VAL B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 654 removed outlier: 3.542A pdb=" N ASP B 653 " --> pdb=" O ARG B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 679 removed outlier: 3.765A pdb=" N GLU B 670 " --> pdb=" O TYR B 666 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET B 671 " --> pdb=" O GLU B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.597A pdb=" N ASN B 696 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE B 700 " --> pdb=" O ASN B 696 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA B 704 " --> pdb=" O ILE B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 747 removed outlier: 3.518A pdb=" N ALA B 741 " --> pdb=" O VAL B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 760 removed outlier: 3.602A pdb=" N TYR B 756 " --> pdb=" O PRO B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 857 removed outlier: 3.510A pdb=" N SER B 848 " --> pdb=" O HIS B 844 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 76 removed outlier: 3.534A pdb=" N ALA A 244 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 73 through 76 removed outlier: 3.534A pdb=" N ALA B 244 " --> pdb=" O VAL B 76 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1248 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: 2.64 Time building geometry restraints manager: 4.15 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: 2934 1.34 - 1.47: 2832 1.47 - 1.59: 4334 1.59 - 1.72: 0 1.72 - 1.84: 106 Bond restraints: 10206 Sorted by residual: bond pdb=" CA ALA A 571 " pdb=" C ALA A 571 " ideal model delta sigma weight residual 1.524 1.577 -0.054 1.16e-02 7.43e+03 2.15e+01 bond pdb=" CA ALA B 571 " pdb=" C ALA B 571 " ideal model delta sigma weight residual 1.524 1.577 -0.053 1.16e-02 7.43e+03 2.12e+01 bond pdb=" CA PHE A 812 " pdb=" CB PHE A 812 " ideal model delta sigma weight residual 1.526 1.464 0.063 1.53e-02 4.27e+03 1.68e+01 bond pdb=" CA PHE B 812 " pdb=" CB PHE B 812 " ideal model delta sigma weight residual 1.526 1.464 0.063 1.53e-02 4.27e+03 1.68e+01 bond pdb=" N PRO B 648 " pdb=" CD PRO B 648 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.51e+01 ... (remaining 10201 not shown) Histogram of bond angle deviations from ideal: 93.22 - 101.70: 50 101.70 - 110.19: 2136 110.19 - 118.67: 5759 118.67 - 127.16: 5761 127.16 - 135.64: 138 Bond angle restraints: 13844 Sorted by residual: angle pdb=" N ARG A 478 " pdb=" CA ARG A 478 " pdb=" C ARG A 478 " ideal model delta sigma weight residual 113.88 100.31 13.57 1.23e+00 6.61e-01 1.22e+02 angle pdb=" N ARG B 478 " pdb=" CA ARG B 478 " pdb=" C ARG B 478 " ideal model delta sigma weight residual 113.88 100.33 13.55 1.23e+00 6.61e-01 1.21e+02 angle pdb=" N ALA A 274 " pdb=" CA ALA A 274 " pdb=" C ALA A 274 " ideal model delta sigma weight residual 112.68 126.47 -13.79 1.33e+00 5.65e-01 1.07e+02 angle pdb=" N ALA B 274 " pdb=" CA ALA B 274 " pdb=" C ALA B 274 " ideal model delta sigma weight residual 112.68 126.44 -13.76 1.33e+00 5.65e-01 1.07e+02 angle pdb=" N LEU B 664 " pdb=" CA LEU B 664 " pdb=" C LEU B 664 " ideal model delta sigma weight residual 112.59 100.75 11.84 1.22e+00 6.72e-01 9.42e+01 ... (remaining 13839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 5026 16.48 - 32.95: 728 32.95 - 49.43: 164 49.43 - 65.90: 50 65.90 - 82.38: 8 Dihedral angle restraints: 5976 sinusoidal: 2410 harmonic: 3566 Sorted by residual: dihedral pdb=" CA ILE A 786 " pdb=" C ILE A 786 " pdb=" N THR A 787 " pdb=" CA THR A 787 " ideal model delta harmonic sigma weight residual 180.00 152.07 27.93 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ILE B 786 " pdb=" C ILE B 786 " pdb=" N THR B 787 " pdb=" CA THR B 787 " ideal model delta harmonic sigma weight residual 180.00 152.09 27.91 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ASP A 375 " pdb=" C ASP A 375 " pdb=" N SER A 376 " pdb=" CA SER A 376 " ideal model delta harmonic sigma weight residual -180.00 -152.43 -27.57 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 5973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1318 0.105 - 0.210: 162 0.210 - 0.315: 30 0.315 - 0.421: 24 0.421 - 0.526: 4 Chirality restraints: 1538 Sorted by residual: chirality pdb=" CA ALA B 274 " pdb=" N ALA B 274 " pdb=" C ALA B 274 " pdb=" CB ALA B 274 " both_signs ideal model delta sigma weight residual False 2.48 1.96 0.53 2.00e-01 2.50e+01 6.91e+00 chirality pdb=" CA ALA A 274 " pdb=" N ALA A 274 " pdb=" C ALA A 274 " pdb=" CB ALA A 274 " both_signs ideal model delta sigma weight residual False 2.48 1.96 0.53 2.00e-01 2.50e+01 6.90e+00 chirality pdb=" CA PRO A 340 " pdb=" N PRO A 340 " pdb=" C PRO A 340 " pdb=" CB PRO A 340 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.67e+00 ... (remaining 1535 not shown) Planarity restraints: 1686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 541 " 0.021 2.00e-02 2.50e+03 4.27e-02 1.83e+01 pdb=" C PRO A 541 " -0.074 2.00e-02 2.50e+03 pdb=" O PRO A 541 " 0.030 2.00e-02 2.50e+03 pdb=" N ARG A 542 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 541 " 0.021 2.00e-02 2.50e+03 4.27e-02 1.82e+01 pdb=" C PRO B 541 " -0.074 2.00e-02 2.50e+03 pdb=" O PRO B 541 " 0.029 2.00e-02 2.50e+03 pdb=" N ARG B 542 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 647 " -0.069 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO A 648 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO A 648 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 648 " -0.055 5.00e-02 4.00e+02 ... (remaining 1683 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 156 2.59 - 3.17: 8430 3.17 - 3.75: 16032 3.75 - 4.32: 22064 4.32 - 4.90: 34337 Nonbonded interactions: 81019 Sorted by model distance: nonbonded pdb=" CD1 LEU A 627 " pdb=" CD PRO A 628 " model vdw 2.014 3.860 nonbonded pdb=" CD1 LEU B 627 " pdb=" CD PRO B 628 " model vdw 2.014 3.860 nonbonded pdb=" CB HIS B 275 " pdb=" CD PRO B 276 " model vdw 2.171 3.840 nonbonded pdb=" CB HIS A 275 " pdb=" CD PRO A 276 " model vdw 2.171 3.840 nonbonded pdb=" O HIS B 275 " pdb=" O SER B 278 " model vdw 2.200 3.040 ... (remaining 81014 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.700 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: 4.210 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 28.870 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 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 : 0.011 0.100 10206 Z= 0.675 Angle : 1.556 15.195 13844 Z= 0.962 Chirality : 0.091 0.526 1538 Planarity : 0.011 0.103 1686 Dihedral : 16.573 82.380 3656 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.86 % Allowed : 6.51 % Favored : 92.64 % Rotamer: Outliers : 3.53 % Allowed : 14.68 % Favored : 81.78 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.05 (0.17), residues: 1168 helix: -4.12 (0.11), residues: 696 sheet: -3.70 (1.03), residues: 18 loop : -3.59 (0.25), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP B 463 HIS 0.008 0.002 HIS A 844 PHE 0.028 0.004 PHE B 760 TYR 0.037 0.004 TYR A 809 ARG 0.008 0.001 ARG B 209 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 200 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 HIS cc_start: 0.5230 (OUTLIER) cc_final: 0.4889 (t70) REVERT: A 298 ILE cc_start: 0.8456 (tp) cc_final: 0.8144 (tt) REVERT: A 396 PHE cc_start: 0.6698 (t80) cc_final: 0.6483 (t80) REVERT: A 403 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7517 (tm-30) REVERT: A 588 LEU cc_start: 0.6165 (OUTLIER) cc_final: 0.5903 (mm) REVERT: A 590 LYS cc_start: 0.4367 (OUTLIER) cc_final: 0.3613 (mppt) REVERT: A 671 MET cc_start: 0.8217 (mmm) cc_final: 0.7676 (mmm) REVERT: A 742 MET cc_start: 0.7116 (mmt) cc_final: 0.6810 (tpp) REVERT: A 826 ILE cc_start: 0.5232 (OUTLIER) cc_final: 0.4985 (pt) REVERT: A 853 ILE cc_start: 0.8491 (mm) cc_final: 0.8249 (mt) REVERT: B 275 HIS cc_start: 0.5514 (OUTLIER) cc_final: 0.4570 (t70) REVERT: B 298 ILE cc_start: 0.8361 (tp) cc_final: 0.8095 (tt) REVERT: B 403 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7410 (tm-30) REVERT: B 590 LYS cc_start: 0.4209 (OUTLIER) cc_final: 0.3396 (mmtt) REVERT: B 649 ARG cc_start: 0.6494 (pmt170) cc_final: 0.6141 (ptt-90) REVERT: B 750 MET cc_start: 0.5962 (mmp) cc_final: 0.5059 (ttm) outliers start: 38 outliers final: 9 residues processed: 233 average time/residue: 0.2534 time to fit residues: 80.1031 Evaluate side-chains 153 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 138 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 94 optimal weight: 0.0170 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 129 HIS A 275 HIS A 283 GLN A 620 ASN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN A 726 GLN A 740 ASN ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN B 129 HIS B 275 HIS B 620 ASN ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN B 726 GLN B 740 ASN ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 830 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10206 Z= 0.230 Angle : 0.799 15.181 13844 Z= 0.422 Chirality : 0.046 0.189 1538 Planarity : 0.007 0.067 1686 Dihedral : 8.541 58.389 1361 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.51 % Favored : 93.32 % Rotamer: Outliers : 4.55 % Allowed : 15.71 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -4.44 (0.20), residues: 1168 helix: -2.72 (0.15), residues: 704 sheet: -3.49 (0.77), residues: 26 loop : -3.06 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 629 HIS 0.002 0.001 HIS B 818 PHE 0.022 0.002 PHE A 851 TYR 0.036 0.002 TYR B 477 ARG 0.006 0.001 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 191 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 HIS cc_start: 0.6011 (OUTLIER) cc_final: 0.4817 (t-90) REVERT: A 298 ILE cc_start: 0.8066 (tp) cc_final: 0.7735 (tt) REVERT: A 522 MET cc_start: 0.6827 (mmp) cc_final: 0.6580 (mmm) REVERT: A 588 LEU cc_start: 0.5998 (OUTLIER) cc_final: 0.5732 (mm) REVERT: A 742 MET cc_start: 0.7172 (mmt) cc_final: 0.6781 (tpp) REVERT: A 842 MET cc_start: 0.6261 (mmt) cc_final: 0.6013 (mmt) REVERT: B 270 TYR cc_start: 0.5081 (t80) cc_final: 0.4686 (t80) REVERT: B 275 HIS cc_start: 0.6629 (OUTLIER) cc_final: 0.5213 (t-90) REVERT: B 286 ASP cc_start: 0.6591 (OUTLIER) cc_final: 0.6371 (m-30) REVERT: B 298 ILE cc_start: 0.8057 (tp) cc_final: 0.7744 (tt) REVERT: B 590 LYS cc_start: 0.4656 (OUTLIER) cc_final: 0.3662 (mmtt) outliers start: 49 outliers final: 22 residues processed: 229 average time/residue: 0.2064 time to fit residues: 68.0953 Evaluate side-chains 174 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 147 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 730 GLN Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 818 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 108 optimal weight: 0.0980 chunk 37 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN B 99 GLN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 ASN ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10206 Z= 0.209 Angle : 0.709 9.772 13844 Z= 0.378 Chirality : 0.046 0.213 1538 Planarity : 0.006 0.070 1686 Dihedral : 7.344 59.973 1340 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.05 % Favored : 91.78 % Rotamer: Outliers : 4.65 % Allowed : 18.40 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.09 % 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: -3.63 (0.22), residues: 1168 helix: -2.05 (0.17), residues: 712 sheet: -3.40 (0.77), residues: 26 loop : -2.75 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 629 HIS 0.007 0.001 HIS B 275 PHE 0.031 0.002 PHE A 461 TYR 0.040 0.002 TYR B 323 ARG 0.007 0.001 ARG A 478 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 171 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 HIS cc_start: 0.6205 (OUTLIER) cc_final: 0.5167 (t-90) REVERT: A 298 ILE cc_start: 0.7879 (tp) cc_final: 0.7510 (tt) REVERT: A 586 TYR cc_start: 0.4962 (OUTLIER) cc_final: 0.3642 (t80) REVERT: A 588 LEU cc_start: 0.5718 (OUTLIER) cc_final: 0.5486 (mm) REVERT: A 590 LYS cc_start: 0.5031 (OUTLIER) cc_final: 0.3596 (mppt) REVERT: A 742 MET cc_start: 0.7137 (mmt) cc_final: 0.6806 (tpp) REVERT: A 842 MET cc_start: 0.6218 (mmt) cc_final: 0.6016 (mmt) REVERT: B 275 HIS cc_start: 0.6711 (OUTLIER) cc_final: 0.5196 (t-90) REVERT: B 298 ILE cc_start: 0.7993 (tp) cc_final: 0.7670 (tt) REVERT: B 323 TYR cc_start: 0.7826 (p90) cc_final: 0.7598 (p90) REVERT: B 586 TYR cc_start: 0.4751 (OUTLIER) cc_final: 0.3764 (t80) REVERT: B 590 LYS cc_start: 0.5008 (OUTLIER) cc_final: 0.3433 (mppt) REVERT: B 666 TYR cc_start: 0.8316 (m-10) cc_final: 0.8094 (m-80) REVERT: B 730 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7489 (mt0) REVERT: B 753 ARG cc_start: 0.6052 (ttm-80) cc_final: 0.5535 (mtp-110) outliers start: 50 outliers final: 27 residues processed: 211 average time/residue: 0.1842 time to fit residues: 57.3111 Evaluate side-chains 180 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 145 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 730 GLN Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 831 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 56 optimal weight: 0.0040 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10206 Z= 0.201 Angle : 0.682 12.413 13844 Z= 0.357 Chirality : 0.044 0.167 1538 Planarity : 0.005 0.076 1686 Dihedral : 7.083 57.272 1340 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.73 % Favored : 91.10 % Rotamer: Outliers : 4.46 % Allowed : 21.10 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.18 % 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: -3.12 (0.23), residues: 1168 helix: -1.65 (0.18), residues: 720 sheet: -3.40 (0.76), residues: 26 loop : -2.52 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 629 HIS 0.004 0.001 HIS B 275 PHE 0.022 0.002 PHE A 556 TYR 0.033 0.001 TYR B 323 ARG 0.008 0.000 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 163 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 HIS cc_start: 0.6361 (OUTLIER) cc_final: 0.5179 (t-90) REVERT: A 586 TYR cc_start: 0.4887 (OUTLIER) cc_final: 0.3638 (t80) REVERT: A 588 LEU cc_start: 0.5688 (OUTLIER) cc_final: 0.5434 (mm) REVERT: A 595 GLU cc_start: 0.6450 (mp0) cc_final: 0.6059 (mp0) REVERT: B 323 TYR cc_start: 0.7866 (p90) cc_final: 0.7540 (p90) REVERT: B 586 TYR cc_start: 0.4607 (OUTLIER) cc_final: 0.3529 (t80) REVERT: B 730 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7407 (mt0) REVERT: B 753 ARG cc_start: 0.6155 (ttm-80) cc_final: 0.5768 (mtp-110) outliers start: 48 outliers final: 28 residues processed: 200 average time/residue: 0.1797 time to fit residues: 54.0660 Evaluate side-chains 179 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 146 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 730 GLN Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 831 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN B 695 ASN ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10206 Z= 0.207 Angle : 0.675 11.744 13844 Z= 0.352 Chirality : 0.044 0.162 1538 Planarity : 0.005 0.075 1686 Dihedral : 6.809 55.501 1332 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.82 % Favored : 91.01 % Rotamer: Outliers : 4.83 % Allowed : 22.86 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.18 % 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: -2.78 (0.24), residues: 1168 helix: -1.39 (0.18), residues: 708 sheet: -3.41 (0.75), residues: 26 loop : -2.34 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 629 HIS 0.004 0.001 HIS B 768 PHE 0.024 0.002 PHE B 382 TYR 0.028 0.001 TYR B 323 ARG 0.003 0.000 ARG A 478 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 158 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 HIS cc_start: 0.6550 (OUTLIER) cc_final: 0.5478 (t-90) REVERT: A 586 TYR cc_start: 0.4918 (OUTLIER) cc_final: 0.3652 (t80) REVERT: A 595 GLU cc_start: 0.6463 (mp0) cc_final: 0.6083 (mp0) REVERT: A 842 MET cc_start: 0.6417 (mmt) cc_final: 0.6207 (mmt) REVERT: A 857 ILE cc_start: 0.6713 (tp) cc_final: 0.6494 (tt) REVERT: B 565 SER cc_start: 0.6965 (OUTLIER) cc_final: 0.6434 (p) REVERT: B 586 TYR cc_start: 0.4768 (OUTLIER) cc_final: 0.3705 (t80) REVERT: B 666 TYR cc_start: 0.8394 (m-10) cc_final: 0.8189 (m-80) REVERT: B 753 ARG cc_start: 0.6505 (ttm-80) cc_final: 0.6230 (mtp-110) outliers start: 52 outliers final: 36 residues processed: 195 average time/residue: 0.1752 time to fit residues: 51.2492 Evaluate side-chains 184 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 144 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 831 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 20.0000 chunk 104 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.0270 chunk 60 optimal weight: 5.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN B 695 ASN ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10206 Z= 0.192 Angle : 0.652 10.658 13844 Z= 0.340 Chirality : 0.044 0.162 1538 Planarity : 0.005 0.073 1686 Dihedral : 6.559 53.616 1330 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.90 % Favored : 90.92 % Rotamer: Outliers : 5.20 % Allowed : 23.23 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.18 % 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: -2.57 (0.24), residues: 1168 helix: -1.23 (0.18), residues: 720 sheet: -3.43 (0.74), residues: 26 loop : -2.24 (0.33), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 629 HIS 0.003 0.001 HIS A 818 PHE 0.023 0.002 PHE B 382 TYR 0.028 0.001 TYR A 528 ARG 0.003 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 161 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 HIS cc_start: 0.6500 (OUTLIER) cc_final: 0.5599 (t-90) REVERT: A 298 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7413 (tt) REVERT: A 565 SER cc_start: 0.6884 (OUTLIER) cc_final: 0.6484 (p) REVERT: A 586 TYR cc_start: 0.4910 (OUTLIER) cc_final: 0.3664 (t80) REVERT: A 595 GLU cc_start: 0.6422 (mp0) cc_final: 0.6023 (mp0) REVERT: B 138 TYR cc_start: 0.4158 (m-80) cc_final: 0.3856 (m-80) REVERT: B 298 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7540 (tt) REVERT: B 478 ARG cc_start: 0.5516 (mmt90) cc_final: 0.4669 (mmp80) REVERT: B 565 SER cc_start: 0.6879 (OUTLIER) cc_final: 0.6482 (p) REVERT: B 586 TYR cc_start: 0.4636 (OUTLIER) cc_final: 0.3558 (t80) outliers start: 56 outliers final: 39 residues processed: 205 average time/residue: 0.1835 time to fit residues: 55.8597 Evaluate side-chains 194 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 148 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 857 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 66 optimal weight: 0.0270 chunk 84 optimal weight: 0.1980 chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10206 Z= 0.197 Angle : 0.673 13.953 13844 Z= 0.346 Chirality : 0.044 0.157 1538 Planarity : 0.005 0.067 1686 Dihedral : 6.435 52.485 1330 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.08 % Favored : 90.75 % Rotamer: Outliers : 5.58 % Allowed : 24.44 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.18 % 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: -2.35 (0.24), residues: 1168 helix: -0.94 (0.19), residues: 700 sheet: -3.40 (0.74), residues: 26 loop : -2.35 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 629 HIS 0.003 0.001 HIS A 818 PHE 0.022 0.002 PHE B 382 TYR 0.035 0.002 TYR A 528 ARG 0.003 0.000 ARG A 649 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 160 time to evaluate : 1.160 Fit side-chains revert: symmetry clash REVERT: A 275 HIS cc_start: 0.6523 (OUTLIER) cc_final: 0.5925 (t-90) REVERT: A 298 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7401 (tt) REVERT: A 565 SER cc_start: 0.6801 (OUTLIER) cc_final: 0.6415 (p) REVERT: A 586 TYR cc_start: 0.4936 (OUTLIER) cc_final: 0.3685 (t80) REVERT: B 138 TYR cc_start: 0.4321 (m-80) cc_final: 0.3975 (m-80) REVERT: B 298 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7606 (tt) REVERT: B 478 ARG cc_start: 0.5314 (mmt90) cc_final: 0.4553 (mmp80) REVERT: B 565 SER cc_start: 0.6840 (OUTLIER) cc_final: 0.6482 (p) REVERT: B 586 TYR cc_start: 0.4674 (OUTLIER) cc_final: 0.3588 (t80) REVERT: B 742 MET cc_start: 0.7452 (tpp) cc_final: 0.7032 (mmt) outliers start: 60 outliers final: 42 residues processed: 205 average time/residue: 0.1891 time to fit residues: 57.8121 Evaluate side-chains 197 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 148 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 857 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 0.1980 chunk 105 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10206 Z= 0.198 Angle : 0.684 15.352 13844 Z= 0.348 Chirality : 0.043 0.160 1538 Planarity : 0.005 0.067 1686 Dihedral : 6.374 51.228 1330 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.39 % Favored : 91.44 % Rotamer: Outliers : 4.74 % Allowed : 25.37 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.18 % 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: -2.21 (0.24), residues: 1168 helix: -0.79 (0.19), residues: 710 sheet: -3.39 (0.75), residues: 26 loop : -2.38 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 629 HIS 0.003 0.001 HIS A 818 PHE 0.026 0.002 PHE B 558 TYR 0.044 0.002 TYR B 528 ARG 0.003 0.000 ARG B 753 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 159 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: A 275 HIS cc_start: 0.6584 (OUTLIER) cc_final: 0.6129 (t-90) REVERT: A 298 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7451 (tt) REVERT: A 586 TYR cc_start: 0.4923 (OUTLIER) cc_final: 0.3683 (t80) REVERT: B 291 TYR cc_start: 0.5903 (t80) cc_final: 0.5699 (t80) REVERT: B 298 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7605 (tt) REVERT: B 478 ARG cc_start: 0.5360 (mmt90) cc_final: 0.4638 (mmp80) REVERT: B 565 SER cc_start: 0.6847 (OUTLIER) cc_final: 0.6543 (p) REVERT: B 586 TYR cc_start: 0.4678 (OUTLIER) cc_final: 0.3595 (t80) REVERT: B 730 GLN cc_start: 0.7487 (mm-40) cc_final: 0.7231 (mp10) REVERT: B 742 MET cc_start: 0.7501 (tpp) cc_final: 0.7129 (mmt) outliers start: 51 outliers final: 41 residues processed: 199 average time/residue: 0.1794 time to fit residues: 53.1959 Evaluate side-chains 196 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 149 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 857 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 107 optimal weight: 0.3980 chunk 64 optimal weight: 9.9990 chunk 46 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 69 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: ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN B 275 HIS ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6325 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10206 Z= 0.204 Angle : 0.703 17.205 13844 Z= 0.356 Chirality : 0.044 0.229 1538 Planarity : 0.005 0.065 1686 Dihedral : 6.154 49.603 1328 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.50 % Favored : 90.33 % Rotamer: Outliers : 4.83 % Allowed : 25.09 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.09 % 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: -2.17 (0.24), residues: 1168 helix: -0.69 (0.19), residues: 720 sheet: -3.36 (0.76), residues: 26 loop : -2.55 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 629 HIS 0.003 0.001 HIS A 818 PHE 0.029 0.002 PHE A 556 TYR 0.033 0.001 TYR A 528 ARG 0.003 0.000 ARG B 753 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 157 time to evaluate : 1.218 Fit side-chains revert: symmetry clash REVERT: A 275 HIS cc_start: 0.6351 (OUTLIER) cc_final: 0.6082 (t-90) REVERT: A 524 LEU cc_start: 0.7980 (tt) cc_final: 0.7762 (pp) REVERT: A 565 SER cc_start: 0.6759 (OUTLIER) cc_final: 0.6480 (p) REVERT: A 586 TYR cc_start: 0.4847 (OUTLIER) cc_final: 0.3678 (t80) REVERT: A 595 GLU cc_start: 0.6725 (mp0) cc_final: 0.6310 (mp0) REVERT: A 629 TRP cc_start: 0.5713 (m-90) cc_final: 0.5346 (m-90) REVERT: A 730 GLN cc_start: 0.7525 (mp10) cc_final: 0.7309 (mp10) REVERT: B 298 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7640 (tt) REVERT: B 478 ARG cc_start: 0.5340 (mmt90) cc_final: 0.4655 (mmp80) REVERT: B 565 SER cc_start: 0.6844 (OUTLIER) cc_final: 0.6563 (p) REVERT: B 586 TYR cc_start: 0.4624 (OUTLIER) cc_final: 0.3554 (t80) REVERT: B 742 MET cc_start: 0.7515 (tpp) cc_final: 0.7143 (mmt) outliers start: 52 outliers final: 36 residues processed: 198 average time/residue: 0.1839 time to fit residues: 53.8937 Evaluate side-chains 192 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 150 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 857 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.0970 chunk 79 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 345 GLN ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 HIS B 308 GLN ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10206 Z= 0.206 Angle : 0.703 14.080 13844 Z= 0.358 Chirality : 0.044 0.237 1538 Planarity : 0.005 0.066 1686 Dihedral : 6.075 48.315 1328 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.65 % Favored : 91.18 % Rotamer: Outliers : 4.37 % Allowed : 26.21 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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 (0.24), residues: 1168 helix: -0.57 (0.19), residues: 720 sheet: -3.33 (0.76), residues: 26 loop : -2.52 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 629 HIS 0.004 0.001 HIS A 818 PHE 0.032 0.002 PHE A 556 TYR 0.026 0.001 TYR B 323 ARG 0.004 0.000 ARG B 277 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 157 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: A 298 ILE cc_start: 0.7822 (tp) cc_final: 0.7419 (tt) REVERT: A 565 SER cc_start: 0.6726 (OUTLIER) cc_final: 0.6468 (p) REVERT: A 586 TYR cc_start: 0.4776 (OUTLIER) cc_final: 0.3662 (t80) REVERT: A 595 GLU cc_start: 0.6723 (mp0) cc_final: 0.6348 (mp0) REVERT: A 629 TRP cc_start: 0.5792 (m-90) cc_final: 0.5392 (m-90) REVERT: B 298 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7615 (tt) REVERT: B 478 ARG cc_start: 0.5299 (mmt90) cc_final: 0.4657 (mmp80) REVERT: B 565 SER cc_start: 0.6842 (OUTLIER) cc_final: 0.6555 (p) REVERT: B 586 TYR cc_start: 0.4560 (OUTLIER) cc_final: 0.3503 (t80) REVERT: B 742 MET cc_start: 0.7508 (tpp) cc_final: 0.7135 (mmt) REVERT: B 825 ASN cc_start: 0.6119 (m110) cc_final: 0.5587 (t0) outliers start: 47 outliers final: 35 residues processed: 190 average time/residue: 0.1907 time to fit residues: 53.8882 Evaluate side-chains 188 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 148 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 857 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 HIS B 308 GLN ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.234077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.204008 restraints weight = 14711.885| |-----------------------------------------------------------------------------| r_work (start): 0.4539 rms_B_bonded: 3.21 r_work: 0.4297 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10206 Z= 0.239 Angle : 0.724 14.635 13844 Z= 0.372 Chirality : 0.045 0.152 1538 Planarity : 0.006 0.075 1686 Dihedral : 5.985 42.799 1326 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.93 % Favored : 89.90 % Rotamer: Outliers : 4.55 % Allowed : 26.67 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -2.11 (0.24), residues: 1168 helix: -0.54 (0.19), residues: 708 sheet: -3.48 (0.75), residues: 26 loop : -2.65 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 629 HIS 0.004 0.001 HIS B 824 PHE 0.033 0.002 PHE B 556 TYR 0.026 0.002 TYR B 323 ARG 0.005 0.000 ARG B 753 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2310.25 seconds wall clock time: 42 minutes 50.76 seconds (2570.76 seconds total)