Starting phenix.real_space_refine on Wed Apr 10 17:41:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u86_20678/04_2024/6u86_20678.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u86_20678/04_2024/6u86_20678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u86_20678/04_2024/6u86_20678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u86_20678/04_2024/6u86_20678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u86_20678/04_2024/6u86_20678.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u86_20678/04_2024/6u86_20678.pdb" } resolution = 4.0 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 13180 2.51 5 N 3384 2.21 5 O 3460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 36": "OE1" <-> "OE2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A ARG 539": "NH1" <-> "NH2" Residue "A PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A GLU 561": "OE1" <-> "OE2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "A ARG 617": "NH1" <-> "NH2" Residue "A PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 670": "OE1" <-> "OE2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A ARG 680": "NH1" <-> "NH2" Residue "A ARG 684": "NH1" <-> "NH2" Residue "A ARG 706": "NH1" <-> "NH2" Residue "A GLU 716": "OE1" <-> "OE2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 317": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B GLU 358": "OE1" <-> "OE2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B ARG 371": "NH1" <-> "NH2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B ARG 459": "NH1" <-> "NH2" Residue "B ARG 460": "NH1" <-> "NH2" Residue "B GLU 473": "OE1" <-> "OE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B ARG 535": "NH1" <-> "NH2" Residue "B ARG 539": "NH1" <-> "NH2" Residue "B PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B GLU 561": "OE1" <-> "OE2" Residue "B ARG 591": "NH1" <-> "NH2" Residue "B ARG 617": "NH1" <-> "NH2" Residue "B PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 670": "OE1" <-> "OE2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B ARG 680": "NH1" <-> "NH2" Residue "B ARG 684": "NH1" <-> "NH2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "B GLU 716": "OE1" <-> "OE2" Residue "C GLU 36": "OE1" <-> "OE2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 74": "NH1" <-> "NH2" Residue "C ARG 86": "NH1" <-> "NH2" Residue "C TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "C PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 317": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ARG 371": "NH1" <-> "NH2" Residue "C ARG 388": "NH1" <-> "NH2" Residue "C ARG 459": "NH1" <-> "NH2" Residue "C ARG 460": "NH1" <-> "NH2" Residue "C GLU 473": "OE1" <-> "OE2" Residue "C GLU 495": "OE1" <-> "OE2" Residue "C ARG 535": "NH1" <-> "NH2" Residue "C ARG 539": "NH1" <-> "NH2" Residue "C PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 560": "NH1" <-> "NH2" Residue "C GLU 561": "OE1" <-> "OE2" Residue "C ARG 591": "NH1" <-> "NH2" Residue "C ARG 617": "NH1" <-> "NH2" Residue "C PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 670": "OE1" <-> "OE2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C ARG 680": "NH1" <-> "NH2" Residue "C ARG 684": "NH1" <-> "NH2" Residue "C ARG 706": "NH1" <-> "NH2" Residue "C GLU 716": "OE1" <-> "OE2" Residue "D GLU 36": "OE1" <-> "OE2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 74": "NH1" <-> "NH2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 262": "OE1" <-> "OE2" Residue "D PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 317": "NH1" <-> "NH2" Residue "D ARG 328": "NH1" <-> "NH2" Residue "D ARG 339": "NH1" <-> "NH2" Residue "D GLU 358": "OE1" <-> "OE2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D ARG 371": "NH1" <-> "NH2" Residue "D ARG 388": "NH1" <-> "NH2" Residue "D ARG 459": "NH1" <-> "NH2" Residue "D ARG 460": "NH1" <-> "NH2" Residue "D GLU 473": "OE1" <-> "OE2" Residue "D GLU 495": "OE1" <-> "OE2" Residue "D ARG 535": "NH1" <-> "NH2" Residue "D ARG 539": "NH1" <-> "NH2" Residue "D PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 560": "NH1" <-> "NH2" Residue "D GLU 561": "OE1" <-> "OE2" Residue "D ARG 591": "NH1" <-> "NH2" Residue "D ARG 617": "NH1" <-> "NH2" Residue "D PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 670": "OE1" <-> "OE2" Residue "D ARG 679": "NH1" <-> "NH2" Residue "D ARG 680": "NH1" <-> "NH2" Residue "D ARG 684": "NH1" <-> "NH2" Residue "D ARG 706": "NH1" <-> "NH2" Residue "D GLU 716": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 20140 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 5035 Classifications: {'peptide': 618} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 594} Chain breaks: 4 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 5035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 5035 Classifications: {'peptide': 618} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 594} Chain breaks: 4 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 5035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 5035 Classifications: {'peptide': 618} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 594} Chain breaks: 4 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 5035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 5035 Classifications: {'peptide': 618} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 594} Chain breaks: 4 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 9.71, per 1000 atoms: 0.48 Number of scatterers: 20140 At special positions: 0 Unit cell: (138.86, 138.86, 111.3, 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 116 16.00 O 3460 8.00 N 3384 7.00 C 13180 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.31 Conformation dependent library (CDL) restraints added in 3.3 seconds 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4680 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 4 sheets defined 64.2% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.686A pdb=" N LYS A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 147 removed outlier: 3.642A pdb=" N LEU A 139 " --> pdb=" O CYS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.960A pdb=" N ILE A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 185 removed outlier: 3.581A pdb=" N LEU A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.509A pdb=" N VAL A 226 " --> pdb=" O GLN A 222 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR A 228 " --> pdb=" O ASP A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 308 through 316 removed outlier: 3.625A pdb=" N HIS A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.966A pdb=" N VAL A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 374 " --> pdb=" O HIS A 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 369 through 374' Processing helix chain 'A' and resid 377 through 414 removed outlier: 5.639A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 461 through 466 Processing helix chain 'A' and resid 470 through 492 removed outlier: 3.540A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 3.612A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 517 removed outlier: 4.150A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 532 removed outlier: 4.167A pdb=" N MET A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE A 529 " --> pdb=" O TYR A 525 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 532 " --> pdb=" O MET A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 561 removed outlier: 4.597A pdb=" N LEU A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLU A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 606 Processing helix chain 'A' and resid 618 through 646 removed outlier: 3.658A pdb=" N VAL A 622 " --> pdb=" O PHE A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.613A pdb=" N ASN A 650 " --> pdb=" O GLU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 673 removed outlier: 4.194A pdb=" N SER A 658 " --> pdb=" O ASP A 654 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 719 Processing helix chain 'B' and resid 76 through 87 Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.686A pdb=" N LYS B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 147 removed outlier: 3.642A pdb=" N LEU B 139 " --> pdb=" O CYS B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.960A pdb=" N ILE B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 185 removed outlier: 3.580A pdb=" N LEU B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.509A pdb=" N VAL B 226 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 257 Processing helix chain 'B' and resid 260 through 282 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 308 through 316 removed outlier: 3.625A pdb=" N HIS B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 327 Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.967A pdb=" N VAL B 373 " --> pdb=" O ARG B 369 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL B 374 " --> pdb=" O HIS B 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 369 through 374' Processing helix chain 'B' and resid 377 through 414 removed outlier: 5.639A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 461 through 466 Processing helix chain 'B' and resid 470 through 492 removed outlier: 3.541A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 removed outlier: 3.613A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 removed outlier: 4.150A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 532 removed outlier: 4.167A pdb=" N MET B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE B 529 " --> pdb=" O TYR B 525 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 532 " --> pdb=" O MET B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 561 removed outlier: 4.597A pdb=" N LEU B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE B 551 " --> pdb=" O PHE B 547 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLU B 561 " --> pdb=" O SER B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 606 Processing helix chain 'B' and resid 618 through 646 removed outlier: 3.658A pdb=" N VAL B 622 " --> pdb=" O PHE B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 651 removed outlier: 3.613A pdb=" N ASN B 650 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 673 removed outlier: 4.194A pdb=" N SER B 658 " --> pdb=" O ASP B 654 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 719 Processing helix chain 'C' and resid 76 through 87 Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 94 through 103 Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.686A pdb=" N LYS C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 147 removed outlier: 3.642A pdb=" N LEU C 139 " --> pdb=" O CYS C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 174 removed outlier: 3.960A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 185 removed outlier: 3.581A pdb=" N LEU C 182 " --> pdb=" O GLN C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.509A pdb=" N VAL C 226 " --> pdb=" O GLN C 222 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 257 Processing helix chain 'C' and resid 260 through 282 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 308 through 316 removed outlier: 3.625A pdb=" N HIS C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 327 Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 366 through 368 No H-bonds generated for 'chain 'C' and resid 366 through 368' Processing helix chain 'C' and resid 369 through 374 removed outlier: 3.966A pdb=" N VAL C 373 " --> pdb=" O ARG C 369 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL C 374 " --> pdb=" O HIS C 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 369 through 374' Processing helix chain 'C' and resid 377 through 414 removed outlier: 5.639A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 461 through 466 Processing helix chain 'C' and resid 470 through 492 removed outlier: 3.540A pdb=" N ILE C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 512 removed outlier: 3.612A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 517 removed outlier: 4.150A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 532 removed outlier: 4.167A pdb=" N MET C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE C 529 " --> pdb=" O TYR C 525 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL C 532 " --> pdb=" O MET C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 561 removed outlier: 4.596A pdb=" N LEU C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL C 543 " --> pdb=" O ARG C 539 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE C 551 " --> pdb=" O PHE C 547 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLU C 561 " --> pdb=" O SER C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 606 Processing helix chain 'C' and resid 618 through 646 removed outlier: 3.658A pdb=" N VAL C 622 " --> pdb=" O PHE C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 651 removed outlier: 3.612A pdb=" N ASN C 650 " --> pdb=" O GLU C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 673 removed outlier: 4.193A pdb=" N SER C 658 " --> pdb=" O ASP C 654 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 719 Processing helix chain 'D' and resid 76 through 87 Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.686A pdb=" N LYS D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 147 removed outlier: 3.642A pdb=" N LEU D 139 " --> pdb=" O CYS D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 174 removed outlier: 3.960A pdb=" N ILE D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 185 removed outlier: 3.582A pdb=" N LEU D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 219 Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.510A pdb=" N VAL D 226 " --> pdb=" O GLN D 222 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 257 Processing helix chain 'D' and resid 260 through 282 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 308 through 316 removed outlier: 3.624A pdb=" N HIS D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 366 through 368 No H-bonds generated for 'chain 'D' and resid 366 through 368' Processing helix chain 'D' and resid 369 through 374 removed outlier: 3.967A pdb=" N VAL D 373 " --> pdb=" O ARG D 369 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL D 374 " --> pdb=" O HIS D 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 369 through 374' Processing helix chain 'D' and resid 377 through 414 removed outlier: 5.639A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 461 through 466 Processing helix chain 'D' and resid 470 through 492 removed outlier: 3.541A pdb=" N ILE D 474 " --> pdb=" O SER D 470 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU D 477 " --> pdb=" O GLU D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 512 removed outlier: 3.612A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 517 removed outlier: 4.150A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 532 removed outlier: 4.167A pdb=" N MET D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE D 529 " --> pdb=" O TYR D 525 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 532 " --> pdb=" O MET D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 561 removed outlier: 4.596A pdb=" N LEU D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL D 543 " --> pdb=" O ARG D 539 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE D 551 " --> pdb=" O PHE D 547 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLU D 561 " --> pdb=" O SER D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 606 Processing helix chain 'D' and resid 618 through 646 removed outlier: 3.659A pdb=" N VAL D 622 " --> pdb=" O PHE D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 651 removed outlier: 3.614A pdb=" N ASN D 650 " --> pdb=" O GLU D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 673 removed outlier: 4.194A pdb=" N SER D 658 " --> pdb=" O ASP D 654 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 719 Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 335 removed outlier: 6.697A pdb=" N LYS A 329 " --> pdb=" O ASP A 344 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASP A 344 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N THR A 331 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU A 342 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU A 709 " --> pdb=" O ARG A 339 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER A 341 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL A 707 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG A 702 " --> pdb=" O LEU A 689 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 689 " --> pdb=" O ARG A 702 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 335 removed outlier: 6.697A pdb=" N LYS B 329 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASP B 344 " --> pdb=" O LYS B 329 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N THR B 331 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU B 342 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU B 709 " --> pdb=" O ARG B 339 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER B 341 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL B 707 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG B 702 " --> pdb=" O LEU B 689 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 689 " --> pdb=" O ARG B 702 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 335 removed outlier: 6.697A pdb=" N LYS C 329 " --> pdb=" O ASP C 344 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASP C 344 " --> pdb=" O LYS C 329 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N THR C 331 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU C 342 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU C 709 " --> pdb=" O ARG C 339 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER C 341 " --> pdb=" O VAL C 707 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL C 707 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG C 702 " --> pdb=" O LEU C 689 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 689 " --> pdb=" O ARG C 702 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 335 removed outlier: 6.698A pdb=" N LYS D 329 " --> pdb=" O ASP D 344 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASP D 344 " --> pdb=" O LYS D 329 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N THR D 331 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU D 342 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU D 709 " --> pdb=" O ARG D 339 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER D 341 " --> pdb=" O VAL D 707 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL D 707 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG D 702 " --> pdb=" O LEU D 689 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 689 " --> pdb=" O ARG D 702 " (cutoff:3.500A) 1060 hydrogen bonds defined for protein. 3084 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: 5.47 Time building geometry restraints manager: 8.01 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: 6304 1.34 - 1.46: 4308 1.46 - 1.57: 9860 1.57 - 1.69: 0 1.69 - 1.81: 180 Bond restraints: 20652 Sorted by residual: bond pdb=" CB PRO B 377 " pdb=" CG PRO B 377 " ideal model delta sigma weight residual 1.506 1.450 0.056 3.90e-02 6.57e+02 2.05e+00 bond pdb=" CB PRO C 377 " pdb=" CG PRO C 377 " ideal model delta sigma weight residual 1.506 1.450 0.056 3.90e-02 6.57e+02 2.05e+00 bond pdb=" CB PRO A 377 " pdb=" CG PRO A 377 " ideal model delta sigma weight residual 1.506 1.450 0.056 3.90e-02 6.57e+02 2.05e+00 bond pdb=" CB PRO D 377 " pdb=" CG PRO D 377 " ideal model delta sigma weight residual 1.506 1.451 0.055 3.90e-02 6.57e+02 2.00e+00 bond pdb=" CG LEU B 253 " pdb=" CD2 LEU B 253 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.50e+00 ... (remaining 20647 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.56: 555 106.56 - 113.42: 11361 113.42 - 120.29: 7487 120.29 - 127.15: 8311 127.15 - 134.02: 294 Bond angle restraints: 28008 Sorted by residual: angle pdb=" N LEU C 513 " pdb=" CA LEU C 513 " pdb=" C LEU C 513 " ideal model delta sigma weight residual 114.64 110.87 3.77 1.52e+00 4.33e-01 6.14e+00 angle pdb=" N LEU B 513 " pdb=" CA LEU B 513 " pdb=" C LEU B 513 " ideal model delta sigma weight residual 114.64 110.88 3.76 1.52e+00 4.33e-01 6.12e+00 angle pdb=" N LEU D 513 " pdb=" CA LEU D 513 " pdb=" C LEU D 513 " ideal model delta sigma weight residual 114.64 110.88 3.76 1.52e+00 4.33e-01 6.12e+00 angle pdb=" N LEU A 513 " pdb=" CA LEU A 513 " pdb=" C LEU A 513 " ideal model delta sigma weight residual 114.64 110.90 3.74 1.52e+00 4.33e-01 6.05e+00 angle pdb=" CA LEU D 498 " pdb=" C LEU D 498 " pdb=" N PRO D 499 " ideal model delta sigma weight residual 120.81 118.94 1.87 8.60e-01 1.35e+00 4.71e+00 ... (remaining 28003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 10924 17.58 - 35.16: 1046 35.16 - 52.75: 154 52.75 - 70.33: 12 70.33 - 87.91: 12 Dihedral angle restraints: 12148 sinusoidal: 4916 harmonic: 7232 Sorted by residual: dihedral pdb=" CA LEU C 534 " pdb=" C LEU C 534 " pdb=" N ARG C 535 " pdb=" CA ARG C 535 " ideal model delta harmonic sigma weight residual 180.00 157.78 22.22 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA LEU D 534 " pdb=" C LEU D 534 " pdb=" N ARG D 535 " pdb=" CA ARG D 535 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA LEU A 534 " pdb=" C LEU A 534 " pdb=" N ARG A 535 " pdb=" CA ARG A 535 " ideal model delta harmonic sigma weight residual 180.00 157.80 22.20 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 12145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1801 0.028 - 0.056: 850 0.056 - 0.084: 349 0.084 - 0.112: 123 0.112 - 0.140: 17 Chirality restraints: 3140 Sorted by residual: chirality pdb=" CA GLN C 520 " pdb=" N GLN C 520 " pdb=" C GLN C 520 " pdb=" CB GLN C 520 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA GLN D 520 " pdb=" N GLN D 520 " pdb=" C GLN D 520 " pdb=" CB GLN D 520 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA GLN A 520 " pdb=" N GLN A 520 " pdb=" C GLN A 520 " pdb=" CB GLN A 520 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 3137 not shown) Planarity restraints: 3468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 99 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.24e+00 pdb=" C LEU A 99 " -0.053 2.00e-02 2.50e+03 pdb=" O LEU A 99 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG A 100 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 99 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.19e+00 pdb=" C LEU D 99 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU D 99 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG D 100 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 99 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C LEU C 99 " 0.052 2.00e-02 2.50e+03 pdb=" O LEU C 99 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG C 100 " -0.018 2.00e-02 2.50e+03 ... (remaining 3465 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2293 2.74 - 3.28: 22154 3.28 - 3.82: 32317 3.82 - 4.36: 37178 4.36 - 4.90: 62184 Nonbonded interactions: 156126 Sorted by model distance: nonbonded pdb=" OD1 ASP A 159 " pdb=" N GLU A 160 " model vdw 2.198 2.520 nonbonded pdb=" OD1 ASP B 159 " pdb=" N GLU B 160 " model vdw 2.199 2.520 nonbonded pdb=" OD1 ASP C 159 " pdb=" N GLU C 160 " model vdw 2.199 2.520 nonbonded pdb=" OD1 ASP D 159 " pdb=" N GLU D 160 " model vdw 2.199 2.520 nonbonded pdb=" O LEU D 513 " pdb=" OG1 THR D 516 " model vdw 2.237 2.440 ... (remaining 156121 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' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 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: 6.240 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 48.690 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 20652 Z= 0.431 Angle : 0.664 5.634 28008 Z= 0.375 Chirality : 0.039 0.140 3140 Planarity : 0.004 0.035 3468 Dihedral : 13.343 87.911 7468 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.18 % Allowed : 3.30 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.14), residues: 2432 helix: -2.06 (0.11), residues: 1488 sheet: None (None), residues: 0 loop : -3.30 (0.17), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 715 HIS 0.008 0.002 HIS C 438 PHE 0.016 0.002 PHE D 705 TYR 0.013 0.002 TYR B 514 ARG 0.007 0.001 ARG B 684 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 510 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TYR cc_start: 0.8789 (m-80) cc_final: 0.8483 (m-80) REVERT: A 487 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8459 (mm-40) REVERT: A 507 LEU cc_start: 0.8873 (mt) cc_final: 0.8431 (mm) REVERT: A 511 ASN cc_start: 0.8127 (m-40) cc_final: 0.7787 (m-40) REVERT: A 591 ARG cc_start: 0.8513 (tpp-160) cc_final: 0.8303 (tpp80) REVERT: B 162 TYR cc_start: 0.8814 (m-80) cc_final: 0.8502 (m-80) REVERT: B 487 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8388 (mm-40) REVERT: B 507 LEU cc_start: 0.8918 (mt) cc_final: 0.8481 (mm) REVERT: B 511 ASN cc_start: 0.8179 (m-40) cc_final: 0.7852 (m-40) REVERT: C 162 TYR cc_start: 0.8809 (m-80) cc_final: 0.8496 (m-80) REVERT: C 487 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8397 (mm-40) REVERT: C 507 LEU cc_start: 0.8923 (mt) cc_final: 0.8494 (mm) REVERT: C 511 ASN cc_start: 0.8183 (m-40) cc_final: 0.7865 (m-40) REVERT: D 162 TYR cc_start: 0.8762 (m-80) cc_final: 0.8494 (m-80) REVERT: D 487 GLN cc_start: 0.8893 (mm-40) cc_final: 0.8404 (mm-40) REVERT: D 507 LEU cc_start: 0.8893 (mt) cc_final: 0.8443 (mm) REVERT: D 511 ASN cc_start: 0.8192 (m-40) cc_final: 0.7851 (m-40) REVERT: D 591 ARG cc_start: 0.8493 (tpp-160) cc_final: 0.8288 (tpp80) outliers start: 4 outliers final: 4 residues processed: 514 average time/residue: 0.3442 time to fit residues: 263.7778 Evaluate side-chains 298 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 294 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain D residue 258 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 4.9990 chunk 184 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 191 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 221 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 316 GLN A 452 GLN A 530 GLN B 154 ASN B 452 GLN B 530 GLN C 154 ASN C 452 GLN C 530 GLN D 154 ASN D 452 GLN D 530 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20652 Z= 0.185 Angle : 0.606 8.571 28008 Z= 0.296 Chirality : 0.039 0.173 3140 Planarity : 0.004 0.037 3468 Dihedral : 4.224 20.399 2704 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.29 % Allowed : 11.81 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.68 (0.16), residues: 2432 helix: 0.49 (0.13), residues: 1496 sheet: None (None), residues: 0 loop : -2.01 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 101 HIS 0.015 0.001 HIS A 413 PHE 0.012 0.001 PHE C 311 TYR 0.015 0.001 TYR C 412 ARG 0.003 0.000 ARG A 617 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 413 time to evaluate : 2.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8288 (mmm) cc_final: 0.7990 (mmm) REVERT: A 162 TYR cc_start: 0.8991 (m-80) cc_final: 0.8742 (m-80) REVERT: A 215 SER cc_start: 0.9429 (m) cc_final: 0.8899 (t) REVERT: A 264 SER cc_start: 0.9198 (m) cc_final: 0.8992 (p) REVERT: A 299 LEU cc_start: 0.8544 (tp) cc_final: 0.8339 (tp) REVERT: A 507 LEU cc_start: 0.9109 (mt) cc_final: 0.8718 (mm) REVERT: A 511 ASN cc_start: 0.8381 (m-40) cc_final: 0.8009 (m110) REVERT: A 662 LEU cc_start: 0.9400 (tp) cc_final: 0.9095 (tp) REVERT: B 122 MET cc_start: 0.8321 (mmm) cc_final: 0.8019 (mmm) REVERT: B 162 TYR cc_start: 0.9015 (m-80) cc_final: 0.8770 (m-80) REVERT: B 215 SER cc_start: 0.9454 (m) cc_final: 0.9001 (t) REVERT: B 264 SER cc_start: 0.9175 (m) cc_final: 0.8937 (p) REVERT: B 387 ASP cc_start: 0.7755 (m-30) cc_final: 0.7499 (m-30) REVERT: B 434 LEU cc_start: 0.8193 (tt) cc_final: 0.7976 (mm) REVERT: B 507 LEU cc_start: 0.9122 (mt) cc_final: 0.8725 (mm) REVERT: B 511 ASN cc_start: 0.8353 (m-40) cc_final: 0.7976 (m110) REVERT: B 599 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7490 (tp30) REVERT: C 122 MET cc_start: 0.8322 (mmm) cc_final: 0.8011 (mmm) REVERT: C 162 TYR cc_start: 0.9010 (m-80) cc_final: 0.8769 (m-80) REVERT: C 215 SER cc_start: 0.9448 (m) cc_final: 0.8993 (t) REVERT: C 264 SER cc_start: 0.9154 (m) cc_final: 0.8934 (p) REVERT: C 387 ASP cc_start: 0.7761 (m-30) cc_final: 0.7482 (m-30) REVERT: C 434 LEU cc_start: 0.8181 (tt) cc_final: 0.7973 (mm) REVERT: C 507 LEU cc_start: 0.9123 (mt) cc_final: 0.8728 (mm) REVERT: C 511 ASN cc_start: 0.8362 (m-40) cc_final: 0.7979 (m110) REVERT: D 122 MET cc_start: 0.8262 (mmm) cc_final: 0.7939 (mmm) REVERT: D 162 TYR cc_start: 0.8987 (m-80) cc_final: 0.8749 (m-80) REVERT: D 215 SER cc_start: 0.9427 (m) cc_final: 0.8958 (t) REVERT: D 264 SER cc_start: 0.9173 (m) cc_final: 0.8967 (p) REVERT: D 312 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.8033 (tmm-80) REVERT: D 387 ASP cc_start: 0.7750 (m-30) cc_final: 0.7526 (m-30) REVERT: D 507 LEU cc_start: 0.9099 (mt) cc_final: 0.8714 (mm) REVERT: D 511 ASN cc_start: 0.8366 (m-40) cc_final: 0.7951 (m110) outliers start: 50 outliers final: 23 residues processed: 436 average time/residue: 0.2929 time to fit residues: 202.6904 Evaluate side-chains 336 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 312 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 675 TYR Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 605 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 221 optimal weight: 0.5980 chunk 239 optimal weight: 4.9990 chunk 197 optimal weight: 7.9990 chunk 220 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 154 ASN ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 GLN B 148 ASN B 154 ASN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 GLN B 530 GLN C 148 ASN C 154 ASN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 GLN C 530 GLN D 148 ASN D 154 ASN ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 HIS D 530 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 20652 Z= 0.349 Angle : 0.700 9.517 28008 Z= 0.339 Chirality : 0.042 0.129 3140 Planarity : 0.004 0.038 3468 Dihedral : 4.478 19.121 2696 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.58 % Allowed : 17.45 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.00 (0.16), residues: 2432 helix: 1.02 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -1.79 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 351 HIS 0.007 0.001 HIS A 413 PHE 0.016 0.002 PHE D 209 TYR 0.016 0.002 TYR C 514 ARG 0.009 0.001 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 346 time to evaluate : 2.302 Fit side-chains REVERT: A 108 ASP cc_start: 0.8405 (t70) cc_final: 0.7792 (m-30) REVERT: A 215 SER cc_start: 0.9532 (m) cc_final: 0.9131 (t) REVERT: A 264 SER cc_start: 0.9361 (m) cc_final: 0.9117 (p) REVERT: A 289 GLU cc_start: 0.7386 (tm-30) cc_final: 0.7056 (tm-30) REVERT: A 412 TYR cc_start: 0.7533 (OUTLIER) cc_final: 0.7313 (t80) REVERT: A 507 LEU cc_start: 0.8995 (mt) cc_final: 0.8733 (tp) REVERT: A 511 ASN cc_start: 0.8074 (m-40) cc_final: 0.7841 (m-40) REVERT: A 540 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.8263 (t80) REVERT: A 662 LEU cc_start: 0.9417 (tp) cc_final: 0.9054 (tp) REVERT: B 215 SER cc_start: 0.9528 (m) cc_final: 0.9142 (t) REVERT: B 264 SER cc_start: 0.9323 (m) cc_final: 0.9086 (p) REVERT: B 289 GLU cc_start: 0.7382 (tm-30) cc_final: 0.7065 (tm-30) REVERT: B 412 TYR cc_start: 0.7396 (OUTLIER) cc_final: 0.6938 (t80) REVERT: B 507 LEU cc_start: 0.9018 (mt) cc_final: 0.8754 (tp) REVERT: B 511 ASN cc_start: 0.8058 (m-40) cc_final: 0.7823 (m-40) REVERT: B 512 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9157 (tt) REVERT: B 540 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.8267 (t80) REVERT: B 599 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7492 (tp30) REVERT: B 662 LEU cc_start: 0.9448 (tp) cc_final: 0.9088 (tp) REVERT: C 215 SER cc_start: 0.9513 (m) cc_final: 0.9134 (t) REVERT: C 264 SER cc_start: 0.9305 (m) cc_final: 0.9095 (p) REVERT: C 289 GLU cc_start: 0.7378 (tm-30) cc_final: 0.7061 (tm-30) REVERT: C 412 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.6986 (t80) REVERT: C 507 LEU cc_start: 0.9023 (mt) cc_final: 0.8756 (tp) REVERT: C 511 ASN cc_start: 0.8077 (m-40) cc_final: 0.7834 (m-40) REVERT: C 512 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9169 (tt) REVERT: C 540 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.8270 (t80) REVERT: C 662 LEU cc_start: 0.9455 (tp) cc_final: 0.9093 (tp) REVERT: D 215 SER cc_start: 0.9532 (m) cc_final: 0.9106 (t) REVERT: D 264 SER cc_start: 0.9305 (m) cc_final: 0.9075 (p) REVERT: D 289 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7229 (tm-30) REVERT: D 312 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7490 (ttm-80) REVERT: D 412 TYR cc_start: 0.7465 (OUTLIER) cc_final: 0.6926 (t80) REVERT: D 507 LEU cc_start: 0.9031 (mt) cc_final: 0.8754 (tp) REVERT: D 511 ASN cc_start: 0.8073 (m-40) cc_final: 0.7830 (m-40) REVERT: D 512 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9177 (tt) REVERT: D 662 LEU cc_start: 0.9454 (tp) cc_final: 0.9091 (tp) outliers start: 100 outliers final: 57 residues processed: 408 average time/residue: 0.2496 time to fit residues: 171.8002 Evaluate side-chains 376 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 308 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 675 TYR Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 412 TYR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 675 TYR Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 412 TYR Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 675 TYR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 412 TYR Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 675 TYR Chi-restraints excluded: chain D residue 710 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 chunk 222 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 211 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN B 154 ASN C 154 ASN D 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20652 Z= 0.161 Angle : 0.566 9.760 28008 Z= 0.269 Chirality : 0.037 0.122 3140 Planarity : 0.003 0.036 3468 Dihedral : 3.871 16.103 2696 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.49 % Allowed : 20.56 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.78 (0.17), residues: 2432 helix: 1.60 (0.14), residues: 1484 sheet: None (None), residues: 0 loop : -1.26 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 351 HIS 0.016 0.001 HIS D 413 PHE 0.012 0.001 PHE D 311 TYR 0.014 0.001 TYR D 412 ARG 0.002 0.000 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 380 time to evaluate : 2.025 Fit side-chains REVERT: A 215 SER cc_start: 0.9444 (m) cc_final: 0.9000 (t) REVERT: A 247 ASN cc_start: 0.8545 (m-40) cc_final: 0.8048 (m110) REVERT: A 264 SER cc_start: 0.9357 (m) cc_final: 0.9088 (p) REVERT: A 289 GLU cc_start: 0.7425 (tm-30) cc_final: 0.7107 (tm-30) REVERT: A 331 THR cc_start: 0.9461 (m) cc_final: 0.9182 (p) REVERT: A 540 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.8158 (t80) REVERT: A 662 LEU cc_start: 0.9381 (tp) cc_final: 0.9085 (tp) REVERT: B 215 SER cc_start: 0.9404 (m) cc_final: 0.8949 (t) REVERT: B 247 ASN cc_start: 0.8560 (m-40) cc_final: 0.8067 (m110) REVERT: B 264 SER cc_start: 0.9350 (m) cc_final: 0.9080 (p) REVERT: B 289 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7142 (tm-30) REVERT: B 331 THR cc_start: 0.9462 (m) cc_final: 0.9165 (p) REVERT: B 439 ILE cc_start: 0.8798 (mm) cc_final: 0.8474 (pt) REVERT: B 540 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.8153 (t80) REVERT: B 607 MET cc_start: 0.8046 (tmm) cc_final: 0.7743 (tmm) REVERT: B 662 LEU cc_start: 0.9415 (tp) cc_final: 0.9125 (tp) REVERT: C 215 SER cc_start: 0.9396 (m) cc_final: 0.8947 (t) REVERT: C 247 ASN cc_start: 0.8574 (m-40) cc_final: 0.8076 (m110) REVERT: C 264 SER cc_start: 0.9337 (m) cc_final: 0.9086 (p) REVERT: C 289 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7152 (tm-30) REVERT: C 331 THR cc_start: 0.9471 (m) cc_final: 0.9171 (p) REVERT: C 540 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.8156 (t80) REVERT: C 607 MET cc_start: 0.7938 (tmm) cc_final: 0.7651 (tmm) REVERT: C 662 LEU cc_start: 0.9425 (tp) cc_final: 0.9135 (tp) REVERT: D 215 SER cc_start: 0.9431 (m) cc_final: 0.8965 (t) REVERT: D 247 ASN cc_start: 0.8689 (m-40) cc_final: 0.8184 (m110) REVERT: D 264 SER cc_start: 0.9333 (m) cc_final: 0.9070 (p) REVERT: D 289 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7251 (tm-30) REVERT: D 312 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7330 (ttm-80) REVERT: D 331 THR cc_start: 0.9392 (m) cc_final: 0.9157 (p) REVERT: D 439 ILE cc_start: 0.8743 (mm) cc_final: 0.8531 (pt) REVERT: D 662 LEU cc_start: 0.9423 (tp) cc_final: 0.9117 (tp) outliers start: 98 outliers final: 45 residues processed: 446 average time/residue: 0.2473 time to fit residues: 187.0759 Evaluate side-chains 371 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 322 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 639 ASN Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 639 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 6.9990 chunk 133 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 201 optimal weight: 8.9990 chunk 163 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 chunk 211 optimal weight: 4.9990 chunk 59 optimal weight: 0.4980 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN B 413 HIS C 154 ASN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 HIS D 154 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20652 Z= 0.298 Angle : 0.673 10.994 28008 Z= 0.317 Chirality : 0.040 0.128 3140 Planarity : 0.004 0.039 3468 Dihedral : 4.089 17.343 2696 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.08 % Allowed : 22.34 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.69 (0.17), residues: 2432 helix: 1.54 (0.14), residues: 1472 sheet: None (None), residues: 0 loop : -1.29 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 351 HIS 0.009 0.001 HIS D 413 PHE 0.016 0.002 PHE D 311 TYR 0.014 0.002 TYR A 525 ARG 0.006 0.001 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 297 time to evaluate : 2.220 Fit side-chains REVERT: A 162 TYR cc_start: 0.9059 (m-10) cc_final: 0.8765 (m-80) REVERT: A 215 SER cc_start: 0.9494 (m) cc_final: 0.9117 (t) REVERT: A 264 SER cc_start: 0.9390 (m) cc_final: 0.9116 (p) REVERT: A 289 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7204 (tm-30) REVERT: A 540 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.8220 (t80) REVERT: A 607 MET cc_start: 0.8010 (tmm) cc_final: 0.7648 (tmm) REVERT: A 662 LEU cc_start: 0.9402 (tp) cc_final: 0.9071 (tp) REVERT: B 162 TYR cc_start: 0.9053 (m-10) cc_final: 0.8762 (m-80) REVERT: B 215 SER cc_start: 0.9455 (m) cc_final: 0.9089 (t) REVERT: B 264 SER cc_start: 0.9397 (m) cc_final: 0.9114 (p) REVERT: B 289 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7206 (tm-30) REVERT: B 662 LEU cc_start: 0.9432 (tp) cc_final: 0.9107 (tp) REVERT: C 162 TYR cc_start: 0.9067 (m-10) cc_final: 0.8794 (m-80) REVERT: C 215 SER cc_start: 0.9458 (m) cc_final: 0.9093 (t) REVERT: C 264 SER cc_start: 0.9381 (m) cc_final: 0.9132 (p) REVERT: C 289 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7206 (tm-30) REVERT: C 662 LEU cc_start: 0.9445 (tp) cc_final: 0.9117 (tp) REVERT: D 162 TYR cc_start: 0.9037 (m-10) cc_final: 0.8700 (m-80) REVERT: D 215 SER cc_start: 0.9491 (m) cc_final: 0.9117 (t) REVERT: D 264 SER cc_start: 0.9389 (m) cc_final: 0.9117 (p) REVERT: D 289 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7193 (tm-30) REVERT: D 331 THR cc_start: 0.9441 (m) cc_final: 0.9211 (p) REVERT: D 387 ASP cc_start: 0.7839 (m-30) cc_final: 0.7629 (m-30) REVERT: D 433 MET cc_start: 0.5053 (ttp) cc_final: 0.4782 (ttt) REVERT: D 439 ILE cc_start: 0.8806 (mm) cc_final: 0.8553 (pt) REVERT: D 662 LEU cc_start: 0.9438 (tp) cc_final: 0.9103 (tp) outliers start: 89 outliers final: 77 residues processed: 363 average time/residue: 0.2492 time to fit residues: 153.5326 Evaluate side-chains 372 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 294 time to evaluate : 2.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 639 ASN Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 438 HIS Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 639 ASN Chi-restraints excluded: chain D residue 718 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 9.9990 chunk 212 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 236 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN B 154 ASN C 154 ASN D 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20652 Z= 0.221 Angle : 0.616 11.732 28008 Z= 0.285 Chirality : 0.038 0.130 3140 Planarity : 0.003 0.037 3468 Dihedral : 3.924 16.655 2696 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.21 % Allowed : 22.66 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.82 (0.17), residues: 2432 helix: 1.56 (0.14), residues: 1480 sheet: None (None), residues: 0 loop : -1.11 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 351 HIS 0.006 0.001 HIS D 413 PHE 0.013 0.001 PHE D 311 TYR 0.013 0.001 TYR A 471 ARG 0.004 0.000 ARG C 684 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 311 time to evaluate : 2.272 Fit side-chains REVERT: A 122 MET cc_start: 0.8728 (mmm) cc_final: 0.8469 (mmm) REVERT: A 215 SER cc_start: 0.9447 (m) cc_final: 0.9075 (t) REVERT: A 247 ASN cc_start: 0.8777 (m-40) cc_final: 0.8256 (m110) REVERT: A 264 SER cc_start: 0.9461 (m) cc_final: 0.9082 (p) REVERT: A 289 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7159 (tm-30) REVERT: A 331 THR cc_start: 0.9467 (m) cc_final: 0.9249 (p) REVERT: A 479 GLN cc_start: 0.9097 (tm-30) cc_final: 0.8780 (tm-30) REVERT: A 607 MET cc_start: 0.7873 (tmm) cc_final: 0.7640 (tmm) REVERT: A 640 MET cc_start: 0.7736 (tmm) cc_final: 0.7109 (tmm) REVERT: A 662 LEU cc_start: 0.9397 (tp) cc_final: 0.9101 (tp) REVERT: B 122 MET cc_start: 0.8737 (mmm) cc_final: 0.8478 (mmm) REVERT: B 215 SER cc_start: 0.9413 (m) cc_final: 0.9052 (t) REVERT: B 247 ASN cc_start: 0.8782 (m-40) cc_final: 0.8254 (m110) REVERT: B 264 SER cc_start: 0.9386 (m) cc_final: 0.9085 (p) REVERT: B 289 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7169 (tm-30) REVERT: B 331 THR cc_start: 0.9469 (m) cc_final: 0.9248 (p) REVERT: B 479 GLN cc_start: 0.9089 (tm-30) cc_final: 0.8787 (tm-30) REVERT: B 599 GLU cc_start: 0.7982 (tp30) cc_final: 0.7745 (tp30) REVERT: B 662 LEU cc_start: 0.9433 (tp) cc_final: 0.9147 (tp) REVERT: C 122 MET cc_start: 0.8722 (mmm) cc_final: 0.8496 (mmm) REVERT: C 215 SER cc_start: 0.9413 (m) cc_final: 0.9045 (t) REVERT: C 247 ASN cc_start: 0.8800 (m-40) cc_final: 0.8263 (m110) REVERT: C 264 SER cc_start: 0.9343 (m) cc_final: 0.9092 (p) REVERT: C 289 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7157 (tm-30) REVERT: C 331 THR cc_start: 0.9484 (m) cc_final: 0.9251 (p) REVERT: C 479 GLN cc_start: 0.9089 (tm-30) cc_final: 0.8787 (tm-30) REVERT: C 662 LEU cc_start: 0.9449 (tp) cc_final: 0.9155 (tp) REVERT: D 215 SER cc_start: 0.9427 (m) cc_final: 0.9043 (t) REVERT: D 247 ASN cc_start: 0.8796 (m-40) cc_final: 0.8255 (m110) REVERT: D 264 SER cc_start: 0.9455 (m) cc_final: 0.9095 (p) REVERT: D 289 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7199 (tm-30) REVERT: D 331 THR cc_start: 0.9443 (m) cc_final: 0.9220 (p) REVERT: D 433 MET cc_start: 0.5057 (ttp) cc_final: 0.4768 (ttt) REVERT: D 479 GLN cc_start: 0.9080 (tm-30) cc_final: 0.8791 (tm-30) REVERT: D 662 LEU cc_start: 0.9441 (tp) cc_final: 0.9142 (tp) outliers start: 92 outliers final: 73 residues processed: 384 average time/residue: 0.2490 time to fit residues: 162.9129 Evaluate side-chains 372 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 299 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 438 HIS Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 639 ASN Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 438 HIS Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 438 HIS Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 639 ASN Chi-restraints excluded: chain D residue 718 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 0.0370 chunk 26 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 198 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 235 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN B 154 ASN C 154 ASN D 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20652 Z= 0.142 Angle : 0.587 11.275 28008 Z= 0.265 Chirality : 0.036 0.137 3140 Planarity : 0.003 0.036 3468 Dihedral : 3.596 15.448 2696 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.43 % Allowed : 23.58 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.01 (0.17), residues: 2432 helix: 1.76 (0.14), residues: 1472 sheet: None (None), residues: 0 loop : -1.09 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 351 HIS 0.006 0.001 HIS D 413 PHE 0.023 0.001 PHE C 462 TYR 0.012 0.001 TYR C 412 ARG 0.003 0.000 ARG C 684 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 347 time to evaluate : 2.280 Fit side-chains REVERT: A 122 MET cc_start: 0.8732 (mmm) cc_final: 0.8453 (mmm) REVERT: A 215 SER cc_start: 0.9384 (m) cc_final: 0.9025 (t) REVERT: A 247 ASN cc_start: 0.8632 (m-40) cc_final: 0.8164 (m110) REVERT: A 264 SER cc_start: 0.9436 (m) cc_final: 0.9022 (p) REVERT: A 331 THR cc_start: 0.9458 (m) cc_final: 0.9227 (p) REVERT: A 479 GLN cc_start: 0.9059 (tm-30) cc_final: 0.8740 (tm-30) REVERT: A 540 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.8133 (t80) REVERT: A 640 MET cc_start: 0.7726 (tmm) cc_final: 0.7080 (tmm) REVERT: A 662 LEU cc_start: 0.9374 (tp) cc_final: 0.9105 (tp) REVERT: B 122 MET cc_start: 0.8739 (mmm) cc_final: 0.8449 (mmm) REVERT: B 215 SER cc_start: 0.9352 (m) cc_final: 0.9004 (t) REVERT: B 247 ASN cc_start: 0.8629 (m-40) cc_final: 0.8163 (m110) REVERT: B 264 SER cc_start: 0.9431 (m) cc_final: 0.9042 (p) REVERT: B 331 THR cc_start: 0.9469 (m) cc_final: 0.9223 (p) REVERT: B 479 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8748 (tm-30) REVERT: B 662 LEU cc_start: 0.9394 (tp) cc_final: 0.9171 (tp) REVERT: C 122 MET cc_start: 0.8679 (mmm) cc_final: 0.8462 (mmm) REVERT: C 215 SER cc_start: 0.9339 (m) cc_final: 0.8998 (t) REVERT: C 247 ASN cc_start: 0.8653 (m-40) cc_final: 0.8170 (m110) REVERT: C 264 SER cc_start: 0.9348 (m) cc_final: 0.9049 (p) REVERT: C 331 THR cc_start: 0.9473 (m) cc_final: 0.9228 (p) REVERT: C 479 GLN cc_start: 0.9049 (tm-30) cc_final: 0.8749 (tm-30) REVERT: C 662 LEU cc_start: 0.9411 (tp) cc_final: 0.9182 (tp) REVERT: D 122 MET cc_start: 0.8646 (mmm) cc_final: 0.8421 (mmm) REVERT: D 215 SER cc_start: 0.9367 (m) cc_final: 0.9007 (t) REVERT: D 247 ASN cc_start: 0.8615 (m-40) cc_final: 0.8134 (m110) REVERT: D 264 SER cc_start: 0.9428 (m) cc_final: 0.9041 (p) REVERT: D 289 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7163 (tm-30) REVERT: D 331 THR cc_start: 0.9431 (m) cc_final: 0.9174 (p) REVERT: D 433 MET cc_start: 0.5119 (ttp) cc_final: 0.4777 (ttt) REVERT: D 479 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8742 (tm-30) REVERT: D 597 SER cc_start: 0.8985 (m) cc_final: 0.8738 (p) REVERT: D 607 MET cc_start: 0.7727 (ppp) cc_final: 0.7373 (ppp) REVERT: D 662 LEU cc_start: 0.9404 (tp) cc_final: 0.9160 (tp) outliers start: 75 outliers final: 55 residues processed: 399 average time/residue: 0.2528 time to fit residues: 169.6914 Evaluate side-chains 371 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 315 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 639 ASN Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 438 HIS Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 639 ASN Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 438 HIS Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 438 HIS Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 627 LEU Chi-restraints excluded: chain D residue 639 ASN Chi-restraints excluded: chain D residue 718 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 6.9990 chunk 93 optimal weight: 0.5980 chunk 140 optimal weight: 6.9990 chunk 70 optimal weight: 0.4980 chunk 46 optimal weight: 0.0270 chunk 45 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 160 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20652 Z= 0.156 Angle : 0.596 11.014 28008 Z= 0.269 Chirality : 0.036 0.120 3140 Planarity : 0.003 0.034 3468 Dihedral : 3.553 15.550 2696 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.43 % Allowed : 25.23 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.08 (0.17), residues: 2432 helix: 1.75 (0.14), residues: 1480 sheet: None (None), residues: 0 loop : -0.97 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 351 HIS 0.005 0.001 HIS C 438 PHE 0.016 0.001 PHE A 462 TYR 0.012 0.001 TYR D 455 ARG 0.003 0.000 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 315 time to evaluate : 2.288 Fit side-chains REVERT: A 122 MET cc_start: 0.8752 (mmm) cc_final: 0.8435 (mmm) REVERT: A 215 SER cc_start: 0.9380 (m) cc_final: 0.9017 (t) REVERT: A 247 ASN cc_start: 0.8627 (m-40) cc_final: 0.8159 (m110) REVERT: A 264 SER cc_start: 0.9419 (m) cc_final: 0.9028 (p) REVERT: A 640 MET cc_start: 0.7705 (tmm) cc_final: 0.7080 (tmm) REVERT: A 662 LEU cc_start: 0.9388 (tp) cc_final: 0.9110 (tp) REVERT: B 122 MET cc_start: 0.8743 (mmm) cc_final: 0.8435 (mmm) REVERT: B 215 SER cc_start: 0.9370 (m) cc_final: 0.9037 (t) REVERT: B 247 ASN cc_start: 0.8574 (m-40) cc_final: 0.8129 (m110) REVERT: B 264 SER cc_start: 0.9433 (m) cc_final: 0.9038 (p) REVERT: B 479 GLN cc_start: 0.9121 (tm-30) cc_final: 0.8816 (tm-30) REVERT: B 662 LEU cc_start: 0.9400 (tp) cc_final: 0.9169 (tp) REVERT: C 122 MET cc_start: 0.8662 (mmm) cc_final: 0.8409 (mmm) REVERT: C 215 SER cc_start: 0.9367 (m) cc_final: 0.9025 (t) REVERT: C 247 ASN cc_start: 0.8589 (m-40) cc_final: 0.8131 (m110) REVERT: C 264 SER cc_start: 0.9415 (m) cc_final: 0.9044 (p) REVERT: C 479 GLN cc_start: 0.9116 (tm-30) cc_final: 0.8820 (tm-30) REVERT: C 598 LEU cc_start: 0.8827 (tt) cc_final: 0.8578 (tp) REVERT: C 662 LEU cc_start: 0.9418 (tp) cc_final: 0.9177 (tp) REVERT: D 122 MET cc_start: 0.8797 (mmm) cc_final: 0.8546 (mmm) REVERT: D 215 SER cc_start: 0.9369 (m) cc_final: 0.9002 (t) REVERT: D 247 ASN cc_start: 0.8616 (m-40) cc_final: 0.8107 (m110) REVERT: D 264 SER cc_start: 0.9401 (m) cc_final: 0.9028 (p) REVERT: D 331 THR cc_start: 0.9412 (m) cc_final: 0.9181 (p) REVERT: D 433 MET cc_start: 0.5136 (ttp) cc_final: 0.4787 (ttt) REVERT: D 479 GLN cc_start: 0.9092 (tm-30) cc_final: 0.8803 (tm-30) REVERT: D 597 SER cc_start: 0.9018 (m) cc_final: 0.8761 (p) REVERT: D 607 MET cc_start: 0.7807 (ppp) cc_final: 0.7465 (ppp) REVERT: D 662 LEU cc_start: 0.9401 (tp) cc_final: 0.9157 (tp) outliers start: 75 outliers final: 67 residues processed: 370 average time/residue: 0.2694 time to fit residues: 169.5455 Evaluate side-chains 371 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 304 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 639 ASN Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 438 HIS Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 438 HIS Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 438 HIS Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 627 LEU Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 639 ASN Chi-restraints excluded: chain D residue 718 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.8980 chunk 225 optimal weight: 2.9990 chunk 205 optimal weight: 10.0000 chunk 219 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 172 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 218 optimal weight: 8.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN B 154 ASN C 154 ASN D 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20652 Z= 0.200 Angle : 0.613 10.354 28008 Z= 0.279 Chirality : 0.037 0.119 3140 Planarity : 0.003 0.033 3468 Dihedral : 3.657 15.896 2696 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.43 % Allowed : 26.01 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.10 (0.17), residues: 2432 helix: 1.79 (0.14), residues: 1476 sheet: None (None), residues: 0 loop : -0.99 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 351 HIS 0.005 0.001 HIS C 438 PHE 0.014 0.001 PHE B 612 TYR 0.019 0.001 TYR A 525 ARG 0.007 0.000 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 295 time to evaluate : 2.163 Fit side-chains REVERT: A 122 MET cc_start: 0.8793 (mmm) cc_final: 0.8538 (mmm) REVERT: A 215 SER cc_start: 0.9411 (m) cc_final: 0.9051 (t) REVERT: A 247 ASN cc_start: 0.8712 (m-40) cc_final: 0.8168 (m110) REVERT: A 264 SER cc_start: 0.9453 (m) cc_final: 0.9030 (p) REVERT: A 528 MET cc_start: 0.7362 (mmm) cc_final: 0.6917 (tpp) REVERT: A 612 PHE cc_start: 0.6138 (p90) cc_final: 0.5629 (p90) REVERT: A 662 LEU cc_start: 0.9397 (tp) cc_final: 0.9121 (tp) REVERT: B 122 MET cc_start: 0.8793 (mmm) cc_final: 0.8527 (mmm) REVERT: B 215 SER cc_start: 0.9395 (m) cc_final: 0.9047 (t) REVERT: B 247 ASN cc_start: 0.8714 (m-40) cc_final: 0.8185 (m110) REVERT: B 264 SER cc_start: 0.9452 (m) cc_final: 0.9054 (p) REVERT: B 439 ILE cc_start: 0.8694 (mm) cc_final: 0.8346 (pt) REVERT: B 528 MET cc_start: 0.7383 (mmm) cc_final: 0.6961 (tpp) REVERT: B 662 LEU cc_start: 0.9426 (tp) cc_final: 0.9170 (tp) REVERT: C 122 MET cc_start: 0.8767 (mmm) cc_final: 0.8512 (mmm) REVERT: C 215 SER cc_start: 0.9389 (m) cc_final: 0.9038 (t) REVERT: C 247 ASN cc_start: 0.8726 (m-40) cc_final: 0.8195 (m110) REVERT: C 264 SER cc_start: 0.9442 (m) cc_final: 0.9054 (p) REVERT: C 439 ILE cc_start: 0.8680 (mm) cc_final: 0.8334 (pt) REVERT: C 530 GLN cc_start: 0.5970 (OUTLIER) cc_final: 0.5721 (mt0) REVERT: C 598 LEU cc_start: 0.8895 (tt) cc_final: 0.8686 (tp) REVERT: C 662 LEU cc_start: 0.9442 (tp) cc_final: 0.9159 (tp) REVERT: D 122 MET cc_start: 0.8753 (mmm) cc_final: 0.8551 (mmm) REVERT: D 215 SER cc_start: 0.9404 (m) cc_final: 0.9041 (t) REVERT: D 247 ASN cc_start: 0.8754 (m-40) cc_final: 0.8227 (m110) REVERT: D 264 SER cc_start: 0.9421 (m) cc_final: 0.9038 (p) REVERT: D 331 THR cc_start: 0.9383 (m) cc_final: 0.9175 (p) REVERT: D 433 MET cc_start: 0.5229 (ttp) cc_final: 0.4865 (ttt) REVERT: D 597 SER cc_start: 0.9000 (m) cc_final: 0.8775 (p) REVERT: D 607 MET cc_start: 0.7890 (ppp) cc_final: 0.7588 (ppp) REVERT: D 662 LEU cc_start: 0.9429 (tp) cc_final: 0.9157 (tp) outliers start: 75 outliers final: 65 residues processed: 350 average time/residue: 0.2542 time to fit residues: 151.3721 Evaluate side-chains 353 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 287 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 639 ASN Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 438 HIS Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 639 ASN Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 438 HIS Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 438 HIS Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 627 LEU Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 639 ASN Chi-restraints excluded: chain D residue 718 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 4.9990 chunk 231 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 243 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 193 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 118 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN B 154 ASN C 154 ASN D 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 20652 Z= 0.202 Angle : 0.619 10.486 28008 Z= 0.281 Chirality : 0.037 0.122 3140 Planarity : 0.003 0.033 3468 Dihedral : 3.701 15.811 2696 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.48 % Allowed : 26.47 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.10 (0.17), residues: 2432 helix: 1.77 (0.14), residues: 1476 sheet: None (None), residues: 0 loop : -0.96 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 351 HIS 0.005 0.001 HIS C 438 PHE 0.014 0.001 PHE C 603 TYR 0.030 0.001 TYR C 525 ARG 0.005 0.000 ARG B 684 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 287 time to evaluate : 2.217 Fit side-chains REVERT: A 122 MET cc_start: 0.8810 (mmm) cc_final: 0.8535 (mmm) REVERT: A 215 SER cc_start: 0.9407 (m) cc_final: 0.9057 (t) REVERT: A 247 ASN cc_start: 0.8706 (m-40) cc_final: 0.8190 (m110) REVERT: A 264 SER cc_start: 0.9455 (m) cc_final: 0.9036 (p) REVERT: A 528 MET cc_start: 0.7330 (mmm) cc_final: 0.6896 (tpp) REVERT: A 662 LEU cc_start: 0.9397 (tp) cc_final: 0.9125 (tp) REVERT: B 122 MET cc_start: 0.8793 (mmm) cc_final: 0.8526 (mmm) REVERT: B 215 SER cc_start: 0.9395 (m) cc_final: 0.9043 (t) REVERT: B 247 ASN cc_start: 0.8693 (m-40) cc_final: 0.8194 (m110) REVERT: B 264 SER cc_start: 0.9460 (m) cc_final: 0.9059 (p) REVERT: B 439 ILE cc_start: 0.8705 (mm) cc_final: 0.8358 (pt) REVERT: B 528 MET cc_start: 0.7314 (mmm) cc_final: 0.6913 (tpp) REVERT: B 599 GLU cc_start: 0.7982 (tp30) cc_final: 0.7744 (tm-30) REVERT: B 662 LEU cc_start: 0.9425 (tp) cc_final: 0.9182 (tp) REVERT: C 122 MET cc_start: 0.8753 (mmm) cc_final: 0.8525 (mmm) REVERT: C 215 SER cc_start: 0.9389 (m) cc_final: 0.9033 (t) REVERT: C 247 ASN cc_start: 0.8711 (m-40) cc_final: 0.8212 (m110) REVERT: C 264 SER cc_start: 0.9388 (m) cc_final: 0.9018 (p) REVERT: C 439 ILE cc_start: 0.8696 (mm) cc_final: 0.8377 (pt) REVERT: C 598 LEU cc_start: 0.8895 (tt) cc_final: 0.8671 (tp) REVERT: C 662 LEU cc_start: 0.9442 (tp) cc_final: 0.9174 (tp) REVERT: D 122 MET cc_start: 0.8800 (mmm) cc_final: 0.8522 (mmm) REVERT: D 215 SER cc_start: 0.9401 (m) cc_final: 0.9041 (t) REVERT: D 247 ASN cc_start: 0.8785 (m-40) cc_final: 0.8271 (m110) REVERT: D 264 SER cc_start: 0.9429 (m) cc_final: 0.9044 (p) REVERT: D 433 MET cc_start: 0.5240 (ttp) cc_final: 0.4874 (ttt) REVERT: D 597 SER cc_start: 0.9010 (m) cc_final: 0.8771 (p) REVERT: D 607 MET cc_start: 0.7938 (ppp) cc_final: 0.7537 (ppp) REVERT: D 662 LEU cc_start: 0.9428 (tp) cc_final: 0.9167 (tp) outliers start: 76 outliers final: 66 residues processed: 344 average time/residue: 0.2497 time to fit residues: 145.9369 Evaluate side-chains 348 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 282 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 639 ASN Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 438 HIS Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 639 ASN Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 438 HIS Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 438 HIS Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 627 LEU Chi-restraints excluded: chain D residue 639 ASN Chi-restraints excluded: chain D residue 718 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 2.9990 chunk 206 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 178 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 193 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 199 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN B 154 ASN C 154 ASN D 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.107410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.093983 restraints weight = 41770.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.096424 restraints weight = 24176.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.098058 restraints weight = 16269.697| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20652 Z= 0.173 Angle : 0.607 10.453 28008 Z= 0.273 Chirality : 0.037 0.122 3140 Planarity : 0.003 0.032 3468 Dihedral : 3.597 15.499 2696 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.39 % Allowed : 26.56 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.16 (0.17), residues: 2432 helix: 1.81 (0.14), residues: 1476 sheet: None (None), residues: 0 loop : -0.92 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 351 HIS 0.005 0.001 HIS C 438 PHE 0.025 0.001 PHE D 462 TYR 0.026 0.001 TYR C 525 ARG 0.004 0.000 ARG C 684 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3886.83 seconds wall clock time: 72 minutes 14.21 seconds (4334.21 seconds total)