Starting phenix.real_space_refine on Tue Apr 9 19:49:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epd_31238/04_2024/7epd_31238.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epd_31238/04_2024/7epd_31238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epd_31238/04_2024/7epd_31238.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epd_31238/04_2024/7epd_31238.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epd_31238/04_2024/7epd_31238.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epd_31238/04_2024/7epd_31238.pdb" } resolution = 3.9 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6655 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 6699 2.51 5 N 1925 2.21 5 O 2028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 63": "OE1" <-> "OE2" Residue "A ARG 71": "NH1" <-> "NH2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ASP 131": "OD1" <-> "OD2" Residue "A ASP 188": "OD1" <-> "OD2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ASP 274": "OD1" <-> "OD2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A GLU 312": "OE1" <-> "OE2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A ARG 411": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 417": "NH1" <-> "NH2" Residue "A ARG 433": "NH1" <-> "NH2" Residue "A ARG 467": "NH1" <-> "NH2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 531": "NH1" <-> "NH2" Residue "B ASP 69": "OD1" <-> "OD2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 289": "OD1" <-> "OD2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B ASP 387": "OD1" <-> "OD2" Residue "B ASP 478": "OD1" <-> "OD2" Residue "B GLU 517": "OE1" <-> "OE2" Residue "B PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10710 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 777, 5332 Classifications: {'peptide': 777} Incomplete info: {'truncation_to_alanine': 196} Link IDs: {'PTRANS': 37, 'TRANS': 739} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 756 Unresolved non-hydrogen angles: 978 Unresolved non-hydrogen dihedrals: 632 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 11, 'ASN:plan1': 6, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 16, 'GLU:plan': 13, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 425 Chain: "B" Number of atoms: 5378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 5378 Classifications: {'peptide': 792} Incomplete info: {'truncation_to_alanine': 245} Link IDs: {'PTRANS': 37, 'TRANS': 754} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 901 Unresolved non-hydrogen angles: 1150 Unresolved non-hydrogen dihedrals: 733 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 12, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 16, 'PHE:plan': 16, 'GLU:plan': 18, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 483 Time building chain proxies: 6.13, per 1000 atoms: 0.57 Number of scatterers: 10710 At special positions: 0 Unit cell: (132.715, 118.085, 181.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 2028 8.00 N 1925 7.00 C 6699 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 362 " distance=2.03 Simple disulfide: pdb=" SG CYS A 400 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 519 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 522 " distance=2.04 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 537 " distance=2.03 Simple disulfide: pdb=" SG CYS A 540 " - pdb=" SG CYS A 553 " distance=2.03 Simple disulfide: pdb=" SG CYS A 632 " - pdb=" SG CYS A 721 " distance=2.03 Simple disulfide: pdb=" SG CYS B 67 " - pdb=" SG CYS B 109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 249 " - pdb=" SG CYS B 541 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 390 " distance=2.03 Simple disulfide: pdb=" SG CYS B 430 " - pdb=" SG CYS B 437 " distance=2.03 Simple disulfide: pdb=" SG CYS B 523 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 527 " - pdb=" SG CYS B 545 " distance=2.03 Simple disulfide: pdb=" SG CYS B 548 " - pdb=" SG CYS B 560 " distance=2.03 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 655 " - pdb=" SG CYS B 749 " 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: 4.13 Conformation dependent library (CDL) restraints added in 2.1 seconds 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2922 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 6 sheets defined 47.6% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 59 through 74 Processing helix chain 'A' and resid 95 through 108 removed outlier: 4.164A pdb=" N ASP A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.930A pdb=" N LEU A 172 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 173 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP A 174 " --> pdb=" O LYS A 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 169 through 174' Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 190 through 202 removed outlier: 4.091A pdb=" N ALA A 194 " --> pdb=" O PHE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 232 Processing helix chain 'A' and resid 246 through 259 removed outlier: 3.771A pdb=" N PHE A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 285 removed outlier: 4.160A pdb=" N GLU A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 298 Processing helix chain 'A' and resid 324 through 333 Processing helix chain 'A' and resid 342 through 353 Processing helix chain 'A' and resid 377 through 400 Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 564 through 592 removed outlier: 4.170A pdb=" N GLY A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Proline residue: A 571 - end of helix Processing helix chain 'A' and resid 595 through 600 Processing helix chain 'A' and resid 602 through 623 removed outlier: 3.577A pdb=" N TYR A 617 " --> pdb=" O VAL A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 661 removed outlier: 3.608A pdb=" N PHE A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 701 removed outlier: 3.793A pdb=" N CYS A 683 " --> pdb=" O GLN A 679 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 684 " --> pdb=" O VAL A 680 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY A 689 " --> pdb=" O ALA A 685 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN A 690 " --> pdb=" O LEU A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 747 removed outlier: 3.976A pdb=" N GLY A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 783 Proline residue: A 778 - end of helix Processing helix chain 'A' and resid 784 through 786 No H-bonds generated for 'chain 'A' and resid 784 through 786' Processing helix chain 'A' and resid 788 through 817 removed outlier: 3.760A pdb=" N LEU A 809 " --> pdb=" O VAL A 805 " (cutoff:3.500A) Proline residue: A 812 - end of helix Processing helix chain 'B' and resid 72 through 77 Processing helix chain 'B' and resid 78 through 90 Processing helix chain 'B' and resid 113 through 128 removed outlier: 4.026A pdb=" N PHE B 122 " --> pdb=" O GLN B 118 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL B 123 " --> pdb=" O SER B 119 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 125 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 126 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 172 removed outlier: 4.105A pdb=" N ILE B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE B 168 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU B 171 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 removed outlier: 3.999A pdb=" N LEU B 186 " --> pdb=" O ALA B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 229 through 245 removed outlier: 4.188A pdb=" N LYS B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU B 244 " --> pdb=" O GLN B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 277 removed outlier: 3.613A pdb=" N ASP B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG B 269 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B 272 " --> pdb=" O ASP B 268 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR B 277 " --> pdb=" O GLN B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 303 removed outlier: 3.787A pdb=" N GLN B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 350 Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.512A pdb=" N GLU B 369 " --> pdb=" O GLU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 3.639A pdb=" N LYS B 398 " --> pdb=" O GLU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 430 removed outlier: 3.974A pdb=" N ILE B 412 " --> pdb=" O VAL B 408 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP B 413 " --> pdb=" O GLN B 409 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA B 414 " --> pdb=" O PHE B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 441 removed outlier: 3.525A pdb=" N GLU B 441 " --> pdb=" O PRO B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 454 removed outlier: 4.137A pdb=" N LEU B 448 " --> pdb=" O GLY B 444 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN B 454 " --> pdb=" O LYS B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 509 removed outlier: 4.403A pdb=" N MET B 509 " --> pdb=" O ILE B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 600 Processing helix chain 'B' and resid 600 through 613 removed outlier: 4.254A pdb=" N ALA B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE B 613 " --> pdb=" O MET B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 removed outlier: 3.662A pdb=" N ARG B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER B 624 " --> pdb=" O ILE B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 646 removed outlier: 3.655A pdb=" N SER B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR B 630 " --> pdb=" O ARG B 626 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 659 Processing helix chain 'B' and resid 660 through 684 removed outlier: 3.545A pdb=" N GLY B 665 " --> pdb=" O PHE B 661 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET B 666 " --> pdb=" O LEU B 662 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 669 " --> pdb=" O GLY B 665 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR B 670 " --> pdb=" O MET B 666 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 671 " --> pdb=" O CYS B 667 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA B 672 " --> pdb=" O ILE B 668 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU B 673 " --> pdb=" O SER B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 722 Processing helix chain 'B' and resid 752 through 778 removed outlier: 4.420A pdb=" N TYR B 762 " --> pdb=" O CYS B 758 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N SER B 763 " --> pdb=" O SER B 759 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 765 " --> pdb=" O GLY B 761 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 809 Proline residue: B 806 - end of helix Processing helix chain 'B' and resid 816 through 819 Processing helix chain 'B' and resid 820 through 841 Processing helix chain 'B' and resid 841 through 850 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 3.526A pdb=" N ALA A 86 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU A 34 " --> pdb=" O HIS A 87 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU A 89 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N GLY A 36 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 238 through 241 removed outlier: 7.489A pdb=" N THR A 209 " --> pdb=" O GLU A 239 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N VAL A 241 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA A 211 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 315 through 319 removed outlier: 6.352A pdb=" N TYR A 453 " --> pdb=" O TYR A 473 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TYR A 473 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE A 455 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG A 467 " --> pdb=" O LEU A 459 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 473 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 479 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 43 through 45 removed outlier: 3.757A pdb=" N ALA B 103 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 49 " --> pdb=" O GLY B 102 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ARG B 104 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU B 51 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU B 106 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N GLY B 53 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N THR B 50 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLY B 152 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 249 through 256 removed outlier: 5.633A pdb=" N VAL B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN B 252 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 225 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ALA B 282 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TRP B 310 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE B 336 " --> pdb=" O TRP B 310 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY B 312 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLY B 496 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLN B 481 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU B 494 " --> pdb=" O GLN B 481 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 553 through 555 removed outlier: 3.833A pdb=" N THR B 559 " --> pdb=" O PHE B 555 " (cutoff:3.500A) 519 hydrogen bonds defined for protein. 1524 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: 3.25 Time building geometry restraints manager: 4.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3704 1.34 - 1.46: 2459 1.46 - 1.58: 4681 1.58 - 1.70: 0 1.70 - 1.81: 75 Bond restraints: 10919 Sorted by residual: bond pdb=" C SER B 588 " pdb=" N PRO B 589 " ideal model delta sigma weight residual 1.335 1.344 -0.008 1.30e-02 5.92e+03 4.19e-01 bond pdb=" CA ILE B 518 " pdb=" C ILE B 518 " ideal model delta sigma weight residual 1.524 1.531 -0.007 1.05e-02 9.07e+03 4.03e-01 bond pdb=" C ARG A 411 " pdb=" N PRO A 412 " ideal model delta sigma weight residual 1.334 1.348 -0.014 2.34e-02 1.83e+03 3.73e-01 bond pdb=" C ALA A 710 " pdb=" N PRO A 711 " ideal model delta sigma weight residual 1.330 1.337 -0.007 1.22e-02 6.72e+03 3.63e-01 bond pdb=" CZ ARG A 183 " pdb=" NH2 ARG A 183 " ideal model delta sigma weight residual 1.330 1.322 0.008 1.30e-02 5.92e+03 3.41e-01 ... (remaining 10914 not shown) Histogram of bond angle deviations from ideal: 100.28 - 107.04: 323 107.04 - 113.79: 6025 113.79 - 120.55: 4410 120.55 - 127.30: 4060 127.30 - 134.06: 118 Bond angle restraints: 14936 Sorted by residual: angle pdb=" N ILE B 722 " pdb=" CA ILE B 722 " pdb=" C ILE B 722 " ideal model delta sigma weight residual 112.98 110.05 2.93 1.25e+00 6.40e-01 5.48e+00 angle pdb=" N ILE B 518 " pdb=" CA ILE B 518 " pdb=" C ILE B 518 " ideal model delta sigma weight residual 108.88 113.85 -4.97 2.16e+00 2.14e-01 5.30e+00 angle pdb=" C PRO B 278 " pdb=" N ASN B 279 " pdb=" CA ASN B 279 " ideal model delta sigma weight residual 121.54 125.63 -4.09 1.91e+00 2.74e-01 4.58e+00 angle pdb=" CA ILE B 518 " pdb=" C ILE B 518 " pdb=" N PRO B 519 " ideal model delta sigma weight residual 118.88 122.15 -3.27 1.54e+00 4.22e-01 4.50e+00 angle pdb=" N GLY B 317 " pdb=" CA GLY B 317 " pdb=" C GLY B 317 " ideal model delta sigma weight residual 110.77 114.48 -3.71 1.93e+00 2.68e-01 3.70e+00 ... (remaining 14931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 6036 17.91 - 35.81: 394 35.81 - 53.72: 58 53.72 - 71.63: 13 71.63 - 89.54: 7 Dihedral angle restraints: 6508 sinusoidal: 1986 harmonic: 4522 Sorted by residual: dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 92 " pdb=" CB CYS A 92 " ideal model delta sinusoidal sigma weight residual 93.00 11.26 81.74 1 1.00e+01 1.00e-02 8.22e+01 dihedral pdb=" CB CYS A 504 " pdb=" SG CYS A 504 " pdb=" SG CYS A 522 " pdb=" CB CYS A 522 " ideal model delta sinusoidal sigma weight residual -86.00 -167.45 81.45 1 1.00e+01 1.00e-02 8.17e+01 dihedral pdb=" CB CYS A 632 " pdb=" SG CYS A 632 " pdb=" SG CYS A 721 " pdb=" CB CYS A 721 " ideal model delta sinusoidal sigma weight residual -86.00 -17.68 -68.32 1 1.00e+01 1.00e-02 6.05e+01 ... (remaining 6505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1059 0.029 - 0.059: 460 0.059 - 0.088: 136 0.088 - 0.117: 68 0.117 - 0.146: 10 Chirality restraints: 1733 Sorted by residual: chirality pdb=" CB ILE A 160 " pdb=" CA ILE A 160 " pdb=" CG1 ILE A 160 " pdb=" CG2 ILE A 160 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA ILE B 154 " pdb=" N ILE B 154 " pdb=" C ILE B 154 " pdb=" CB ILE B 154 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA ILE A 485 " pdb=" N ILE A 485 " pdb=" C ILE A 485 " pdb=" CB ILE A 485 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 1730 not shown) Planarity restraints: 1994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 720 " -0.010 2.00e-02 2.50e+03 1.00e-02 2.50e+00 pdb=" CG TRP B 720 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP B 720 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP B 720 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 720 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 720 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 720 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 720 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 720 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 720 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 739 " -0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO B 740 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 740 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 740 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 370 " 0.017 5.00e-02 4.00e+02 2.52e-02 1.02e+00 pdb=" N PRO A 371 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 371 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 371 " 0.014 5.00e-02 4.00e+02 ... (remaining 1991 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1950 2.77 - 3.30: 10441 3.30 - 3.83: 17804 3.83 - 4.37: 18655 4.37 - 4.90: 32519 Nonbonded interactions: 81369 Sorted by model distance: nonbonded pdb=" OG SER A 143 " pdb=" OH TYR A 165 " model vdw 2.232 2.440 nonbonded pdb=" O SER B 698 " pdb=" OG SER B 698 " model vdw 2.305 2.440 nonbonded pdb=" OG SER B 698 " pdb=" OG SER B 701 " model vdw 2.313 2.440 nonbonded pdb=" O TYR B 114 " pdb=" NE2 GLN B 118 " model vdw 2.319 2.520 nonbonded pdb=" NE2 GLN B 252 " pdb=" OE1 GLN B 273 " model vdw 2.349 2.520 ... (remaining 81364 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 6.620 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.200 Find NCS groups from input model: 0.400 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: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 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 : 0.002 0.020 10919 Z= 0.106 Angle : 0.448 6.199 14936 Z= 0.248 Chirality : 0.039 0.146 1733 Planarity : 0.003 0.036 1994 Dihedral : 12.271 89.537 3529 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Cbeta Deviations : 0.00 % 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: -2.46 (0.18), residues: 1557 helix: -0.34 (0.18), residues: 696 sheet: -2.45 (0.43), residues: 124 loop : -2.83 (0.18), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 720 HIS 0.002 0.000 HIS A 119 PHE 0.008 0.001 PHE A 189 TYR 0.008 0.001 TYR B 114 ARG 0.002 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8152 (tp) cc_final: 0.7948 (tt) REVERT: A 295 ASP cc_start: 0.7284 (t0) cc_final: 0.6712 (t0) REVERT: A 427 LYS cc_start: 0.5214 (tptp) cc_final: 0.4963 (mmmm) REVERT: B 170 ARG cc_start: 0.7112 (ttp-110) cc_final: 0.6864 (ttm170) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2416 time to fit residues: 47.0587 Evaluate side-chains 97 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 10.0000 chunk 118 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 40 optimal weight: 0.0970 chunk 79 optimal weight: 9.9990 chunk 63 optimal weight: 50.0000 chunk 122 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 74 optimal weight: 40.0000 chunk 91 optimal weight: 0.9980 chunk 141 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 HIS A 396 HIS A 439 ASN A 454 ASN B 98 ASN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 HIS B 505 ASN B 567 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10919 Z= 0.209 Angle : 0.495 6.248 14936 Z= 0.253 Chirality : 0.040 0.147 1733 Planarity : 0.004 0.043 1994 Dihedral : 3.215 16.024 1657 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.47 % Allowed : 13.02 % Favored : 85.50 % Cbeta Deviations : 0.00 % 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: -1.05 (0.21), residues: 1557 helix: 1.14 (0.19), residues: 706 sheet: -2.08 (0.45), residues: 129 loop : -2.42 (0.20), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 720 HIS 0.004 0.001 HIS A 41 PHE 0.019 0.001 PHE B 480 TYR 0.010 0.001 TYR B 114 ARG 0.007 0.001 ARG B 568 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: A 295 ASP cc_start: 0.7725 (t0) cc_final: 0.7073 (t0) REVERT: A 427 LYS cc_start: 0.5537 (tptp) cc_final: 0.5172 (tptp) REVERT: A 466 TYR cc_start: 0.5761 (m-80) cc_final: 0.5204 (m-80) REVERT: B 418 MET cc_start: 0.8116 (mtp) cc_final: 0.7836 (mtp) REVERT: B 738 MET cc_start: 0.2536 (pmm) cc_final: 0.2272 (ptp) outliers start: 13 outliers final: 9 residues processed: 114 average time/residue: 0.2081 time to fit residues: 35.7795 Evaluate side-chains 98 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 499 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 141 optimal weight: 7.9990 chunk 153 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 48 optimal weight: 0.0980 chunk 113 optimal weight: 0.0470 overall best weight: 0.4880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN B 561 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10919 Z= 0.168 Angle : 0.467 7.301 14936 Z= 0.237 Chirality : 0.039 0.142 1733 Planarity : 0.003 0.039 1994 Dihedral : 3.186 18.491 1657 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.81 % Allowed : 16.76 % Favored : 81.43 % Cbeta Deviations : 0.00 % 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: -0.44 (0.21), residues: 1557 helix: 1.81 (0.20), residues: 702 sheet: -2.19 (0.43), residues: 130 loop : -2.17 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 349 HIS 0.002 0.000 HIS A 41 PHE 0.010 0.001 PHE B 480 TYR 0.013 0.001 TYR B 433 ARG 0.008 0.000 ARG B 568 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 1.186 Fit side-chains revert: symmetry clash REVERT: A 295 ASP cc_start: 0.7723 (t0) cc_final: 0.7077 (t0) REVERT: A 427 LYS cc_start: 0.5764 (tptp) cc_final: 0.5331 (tptp) REVERT: A 466 TYR cc_start: 0.6077 (m-80) cc_final: 0.5764 (m-80) outliers start: 16 outliers final: 9 residues processed: 106 average time/residue: 0.1973 time to fit residues: 32.2632 Evaluate side-chains 100 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 411 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 9.9990 chunk 106 optimal weight: 0.7980 chunk 73 optimal weight: 30.0000 chunk 15 optimal weight: 0.2980 chunk 67 optimal weight: 0.0770 chunk 95 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 chunk 150 optimal weight: 7.9990 chunk 74 optimal weight: 50.0000 chunk 134 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 HIS ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 HIS ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10919 Z= 0.295 Angle : 0.538 6.925 14936 Z= 0.275 Chirality : 0.041 0.158 1733 Planarity : 0.004 0.047 1994 Dihedral : 3.623 19.154 1657 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.28 % Allowed : 19.14 % Favored : 77.58 % Cbeta Deviations : 0.00 % 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: -0.23 (0.22), residues: 1557 helix: 1.91 (0.20), residues: 713 sheet: -2.39 (0.42), residues: 138 loop : -1.95 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 218 HIS 0.003 0.001 HIS A 56 PHE 0.015 0.002 PHE A 289 TYR 0.013 0.001 TYR B 179 ARG 0.006 0.000 ARG B 568 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 95 time to evaluate : 1.206 Fit side-chains revert: symmetry clash REVERT: A 295 ASP cc_start: 0.7825 (t0) cc_final: 0.7140 (t0) REVERT: A 395 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6537 (ppp) REVERT: A 466 TYR cc_start: 0.6219 (m-80) cc_final: 0.5532 (m-80) REVERT: B 440 MET cc_start: 0.7485 (mmm) cc_final: 0.6634 (mmt) REVERT: B 518 ILE cc_start: 0.5181 (OUTLIER) cc_final: 0.4907 (pt) outliers start: 29 outliers final: 20 residues processed: 116 average time/residue: 0.1897 time to fit residues: 33.6816 Evaluate side-chains 111 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 611 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.4980 chunk 85 optimal weight: 0.0770 chunk 2 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 30.0000 chunk 128 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 40.0000 chunk 135 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10919 Z= 0.293 Angle : 0.524 6.618 14936 Z= 0.270 Chirality : 0.041 0.169 1733 Planarity : 0.004 0.042 1994 Dihedral : 3.699 20.173 1657 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.08 % Allowed : 19.59 % Favored : 76.33 % Cbeta Deviations : 0.00 % 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: -0.15 (0.22), residues: 1557 helix: 1.98 (0.20), residues: 724 sheet: -2.44 (0.42), residues: 138 loop : -1.95 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 218 HIS 0.005 0.001 HIS A 56 PHE 0.015 0.002 PHE B 172 TYR 0.013 0.001 TYR B 84 ARG 0.005 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 98 time to evaluate : 1.239 Fit side-chains revert: symmetry clash REVERT: A 225 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7343 (mm-30) REVERT: A 291 TRP cc_start: 0.7853 (p90) cc_final: 0.7257 (p90) REVERT: A 295 ASP cc_start: 0.7724 (t0) cc_final: 0.6884 (t0) REVERT: A 466 TYR cc_start: 0.6500 (m-80) cc_final: 0.5990 (m-80) REVERT: B 440 MET cc_start: 0.7678 (mmm) cc_final: 0.7192 (mmt) REVERT: B 518 ILE cc_start: 0.5690 (OUTLIER) cc_final: 0.5476 (pt) REVERT: B 731 ASP cc_start: 0.3033 (OUTLIER) cc_final: 0.2019 (p0) outliers start: 36 outliers final: 22 residues processed: 129 average time/residue: 0.2004 time to fit residues: 39.3833 Evaluate side-chains 114 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 731 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.8980 chunk 135 optimal weight: 30.0000 chunk 29 optimal weight: 0.0060 chunk 88 optimal weight: 0.2980 chunk 37 optimal weight: 0.0070 chunk 150 optimal weight: 20.0000 chunk 125 optimal weight: 0.2980 chunk 69 optimal weight: 30.0000 chunk 12 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.2414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10919 Z= 0.134 Angle : 0.474 6.781 14936 Z= 0.241 Chirality : 0.039 0.137 1733 Planarity : 0.003 0.040 1994 Dihedral : 3.417 17.686 1657 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.83 % Allowed : 20.72 % Favored : 76.44 % Cbeta Deviations : 0.00 % 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: 0.08 (0.22), residues: 1557 helix: 2.26 (0.20), residues: 707 sheet: -2.42 (0.42), residues: 138 loop : -1.82 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 368 HIS 0.002 0.000 HIS B 735 PHE 0.013 0.001 PHE B 480 TYR 0.012 0.001 TYR B 84 ARG 0.003 0.000 ARG B 568 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 101 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: A 291 TRP cc_start: 0.7832 (p90) cc_final: 0.7492 (p90) REVERT: A 295 ASP cc_start: 0.7600 (t0) cc_final: 0.6693 (t0) REVERT: A 410 MET cc_start: 0.6842 (tpp) cc_final: 0.6608 (tpt) REVERT: A 466 TYR cc_start: 0.6460 (m-80) cc_final: 0.5928 (m-80) REVERT: B 440 MET cc_start: 0.7610 (mmm) cc_final: 0.7174 (mmt) REVERT: B 518 ILE cc_start: 0.5382 (OUTLIER) cc_final: 0.5157 (pt) outliers start: 25 outliers final: 18 residues processed: 120 average time/residue: 0.1979 time to fit residues: 36.5230 Evaluate side-chains 112 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 840 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 110 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 150 optimal weight: 40.0000 chunk 94 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 69 optimal weight: 30.0000 chunk 93 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10919 Z= 0.261 Angle : 0.512 6.739 14936 Z= 0.263 Chirality : 0.040 0.150 1733 Planarity : 0.003 0.042 1994 Dihedral : 3.586 19.531 1657 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.19 % Allowed : 20.39 % Favored : 75.42 % Cbeta Deviations : 0.00 % 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: 0.07 (0.22), residues: 1557 helix: 2.14 (0.20), residues: 723 sheet: -2.43 (0.42), residues: 138 loop : -1.79 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 218 HIS 0.007 0.001 HIS A 56 PHE 0.011 0.001 PHE B 172 TYR 0.015 0.001 TYR B 84 ARG 0.004 0.000 ARG B 568 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 91 time to evaluate : 1.151 Fit side-chains REVERT: A 225 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7323 (mm-30) REVERT: A 259 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.7165 (mt0) REVERT: A 295 ASP cc_start: 0.7615 (t0) cc_final: 0.6855 (t0) REVERT: A 427 LYS cc_start: 0.6081 (tptp) cc_final: 0.5623 (tptp) REVERT: A 466 TYR cc_start: 0.6675 (m-80) cc_final: 0.6138 (m-80) REVERT: B 440 MET cc_start: 0.7525 (mmm) cc_final: 0.7046 (mmt) REVERT: B 518 ILE cc_start: 0.5797 (OUTLIER) cc_final: 0.5596 (pt) outliers start: 37 outliers final: 28 residues processed: 123 average time/residue: 0.1961 time to fit residues: 37.1957 Evaluate side-chains 118 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 88 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 611 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 50.0000 chunk 89 optimal weight: 0.0870 chunk 45 optimal weight: 0.2980 chunk 29 optimal weight: 0.0050 chunk 95 optimal weight: 0.0470 chunk 102 optimal weight: 2.9990 chunk 74 optimal weight: 40.0000 chunk 14 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 136 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.2870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 191 GLN ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN B 481 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10919 Z= 0.142 Angle : 0.488 10.366 14936 Z= 0.247 Chirality : 0.039 0.168 1733 Planarity : 0.003 0.042 1994 Dihedral : 3.412 19.633 1657 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.28 % Allowed : 21.52 % Favored : 75.20 % Cbeta Deviations : 0.00 % 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: 0.18 (0.22), residues: 1557 helix: 2.29 (0.20), residues: 714 sheet: -2.44 (0.43), residues: 131 loop : -1.75 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 218 HIS 0.003 0.001 HIS B 735 PHE 0.011 0.001 PHE A 422 TYR 0.015 0.001 TYR B 433 ARG 0.004 0.000 ARG B 568 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 98 time to evaluate : 1.099 Fit side-chains revert: symmetry clash REVERT: A 225 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7364 (mm-30) REVERT: A 295 ASP cc_start: 0.7402 (t0) cc_final: 0.6647 (t0) REVERT: A 466 TYR cc_start: 0.6588 (m-80) cc_final: 0.6055 (m-80) REVERT: B 169 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.7775 (mp) REVERT: B 440 MET cc_start: 0.7467 (mmm) cc_final: 0.7003 (mmt) REVERT: B 518 ILE cc_start: 0.5676 (OUTLIER) cc_final: 0.5439 (pt) REVERT: B 738 MET cc_start: 0.1082 (ptp) cc_final: 0.0821 (ptp) outliers start: 29 outliers final: 21 residues processed: 122 average time/residue: 0.1898 time to fit residues: 35.1633 Evaluate side-chains 118 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 611 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 chunk 110 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 132 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 HIS ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 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 : 0.006 0.070 10919 Z= 0.425 Angle : 0.623 12.744 14936 Z= 0.320 Chirality : 0.044 0.209 1733 Planarity : 0.004 0.048 1994 Dihedral : 4.072 21.505 1657 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.53 % Allowed : 21.18 % Favored : 74.29 % Cbeta Deviations : 0.00 % 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: 0.02 (0.22), residues: 1557 helix: 2.01 (0.20), residues: 737 sheet: -2.24 (0.43), residues: 132 loop : -1.86 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 218 HIS 0.012 0.001 HIS A 390 PHE 0.016 0.002 PHE B 122 TYR 0.022 0.002 TYR B 84 ARG 0.007 0.001 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 93 time to evaluate : 1.213 Fit side-chains REVERT: A 225 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7398 (mm-30) REVERT: A 259 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7244 (mt0) REVERT: A 295 ASP cc_start: 0.7609 (t0) cc_final: 0.6856 (t0) REVERT: A 337 TRP cc_start: 0.7075 (OUTLIER) cc_final: 0.5777 (m100) REVERT: B 440 MET cc_start: 0.7729 (mmm) cc_final: 0.7161 (mmt) REVERT: B 518 ILE cc_start: 0.5935 (OUTLIER) cc_final: 0.5727 (pt) outliers start: 40 outliers final: 28 residues processed: 129 average time/residue: 0.1737 time to fit residues: 35.2310 Evaluate side-chains 120 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 89 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 337 TRP Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 611 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 chunk 70 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 155 optimal weight: 20.0000 chunk 143 optimal weight: 0.0030 chunk 123 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 95 optimal weight: 0.0030 chunk 75 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 HIS ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10919 Z= 0.172 Angle : 0.536 12.485 14936 Z= 0.272 Chirality : 0.040 0.184 1733 Planarity : 0.003 0.043 1994 Dihedral : 3.745 21.000 1657 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.06 % Allowed : 22.76 % Favored : 74.18 % Cbeta Deviations : 0.00 % 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: 0.06 (0.22), residues: 1557 helix: 2.13 (0.20), residues: 730 sheet: -2.46 (0.40), residues: 138 loop : -1.82 (0.22), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 291 HIS 0.007 0.001 HIS A 390 PHE 0.013 0.001 PHE A 67 TYR 0.017 0.001 TYR B 433 ARG 0.004 0.000 ARG B 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 92 time to evaluate : 1.181 Fit side-chains REVERT: A 295 ASP cc_start: 0.7365 (t0) cc_final: 0.6659 (t0) REVERT: A 337 TRP cc_start: 0.7013 (OUTLIER) cc_final: 0.5837 (m100) REVERT: B 440 MET cc_start: 0.7647 (mmm) cc_final: 0.7219 (mmt) REVERT: B 518 ILE cc_start: 0.5759 (OUTLIER) cc_final: 0.5549 (pt) REVERT: B 738 MET cc_start: 0.1261 (ptp) cc_final: 0.0875 (ptp) outliers start: 27 outliers final: 23 residues processed: 117 average time/residue: 0.1743 time to fit residues: 32.1634 Evaluate side-chains 113 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 88 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 337 TRP Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 611 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 0.1980 chunk 123 optimal weight: 0.1980 chunk 51 optimal weight: 7.9990 chunk 127 optimal weight: 0.6980 chunk 15 optimal weight: 0.0970 chunk 22 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.136795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.115288 restraints weight = 27148.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.113870 restraints weight = 37711.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.114956 restraints weight = 35111.369| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10919 Z= 0.162 Angle : 0.518 8.710 14936 Z= 0.262 Chirality : 0.040 0.169 1733 Planarity : 0.003 0.040 1994 Dihedral : 3.577 20.422 1657 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.06 % Allowed : 22.54 % Favored : 74.41 % Cbeta Deviations : 0.00 % 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: 0.18 (0.22), residues: 1557 helix: 2.25 (0.20), residues: 723 sheet: -2.46 (0.42), residues: 125 loop : -1.76 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 291 HIS 0.005 0.001 HIS A 390 PHE 0.011 0.001 PHE B 480 TYR 0.018 0.001 TYR B 433 ARG 0.004 0.000 ARG B 568 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2038.20 seconds wall clock time: 37 minutes 58.22 seconds (2278.22 seconds total)