Starting phenix.real_space_refine on Wed Apr 10 20:28:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u84_20677/04_2024/6u84_20677.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u84_20677/04_2024/6u84_20677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u84_20677/04_2024/6u84_20677.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u84_20677/04_2024/6u84_20677.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u84_20677/04_2024/6u84_20677.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u84_20677/04_2024/6u84_20677.pdb" } resolution = 3.7 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 13360 2.51 5 N 3452 2.21 5 O 3532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 31": "OE1" <-> "OE2" Residue "A GLU 36": "OE1" <-> "OE2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 328": "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 PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 517": "NH1" <-> "NH2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A ARG 563": "NH1" <-> "NH2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "A GLU 609": "OE1" <-> "OE2" Residue "A ARG 617": "NH1" <-> "NH2" Residue "A GLU 672": "OE1" <-> "OE2" Residue "A ARG 706": "NH1" <-> "NH2" Residue "A GLU 716": "OE1" <-> "OE2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B ARG 317": "NH1" <-> "NH2" Residue "B ARG 328": "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 517": "NH1" <-> "NH2" Residue "B ARG 535": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 563": "NH1" <-> "NH2" Residue "B ARG 591": "NH1" <-> "NH2" Residue "B GLU 609": "OE1" <-> "OE2" Residue "B ARG 617": "NH1" <-> "NH2" Residue "B GLU 672": "OE1" <-> "OE2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "B GLU 716": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C GLU 36": "OE1" <-> "OE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 74": "NH1" <-> "NH2" Residue "C ARG 86": "NH1" <-> "NH2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "C ARG 317": "NH1" <-> "NH2" Residue "C ARG 328": "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 517": "NH1" <-> "NH2" Residue "C ARG 535": "NH1" <-> "NH2" Residue "C ARG 560": "NH1" <-> "NH2" Residue "C ARG 563": "NH1" <-> "NH2" Residue "C ARG 591": "NH1" <-> "NH2" Residue "C GLU 609": "OE1" <-> "OE2" Residue "C ARG 617": "NH1" <-> "NH2" Residue "C GLU 672": "OE1" <-> "OE2" Residue "C ARG 706": "NH1" <-> "NH2" Residue "C GLU 716": "OE1" <-> "OE2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D GLU 36": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 74": "NH1" <-> "NH2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D GLU 262": "OE1" <-> "OE2" Residue "D ARG 317": "NH1" <-> "NH2" Residue "D ARG 328": "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 517": "NH1" <-> "NH2" Residue "D ARG 535": "NH1" <-> "NH2" Residue "D ARG 560": "NH1" <-> "NH2" Residue "D ARG 563": "NH1" <-> "NH2" Residue "D ARG 591": "NH1" <-> "NH2" Residue "D GLU 609": "OE1" <-> "OE2" Residue "D ARG 617": "NH1" <-> "NH2" Residue "D GLU 672": "OE1" <-> "OE2" 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: 20460 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 5115 Classifications: {'peptide': 630} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 606} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 5115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 5115 Classifications: {'peptide': 630} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 606} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 5115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 5115 Classifications: {'peptide': 630} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 606} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 5115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 5115 Classifications: {'peptide': 630} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 606} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 10.82, per 1000 atoms: 0.53 Number of scatterers: 20460 At special positions: 0 Unit cell: (136.74, 136.74, 114.48, 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 3532 8.00 N 3452 7.00 C 13360 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: 8.20 Conformation dependent library (CDL) restraints added in 3.7 seconds 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4760 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 4 sheets defined 62.1% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.966A pdb=" N ARG A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 87 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 94 through 103 removed outlier: 3.637A pdb=" N TYR A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.680A pdb=" N LYS A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 147 Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 166 through 174 removed outlier: 4.246A pdb=" N ILE A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 185 removed outlier: 3.963A pdb=" N LEU A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.508A pdb=" N THR A 227 " --> pdb=" O TRP A 223 " (cutoff:3.500A) removed outlier: 3.668A 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 removed outlier: 3.601A pdb=" N GLY A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 316 removed outlier: 3.924A pdb=" N HIS A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 377 through 413 removed outlier: 5.400A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.443A 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 466 through 492 removed outlier: 6.946A pdb=" N PHE A 472 " --> pdb=" O MET A 468 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU A 473 " --> pdb=" O ASP A 469 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 4.009A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 removed outlier: 3.538A pdb=" N THR A 516 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY A 518 " --> pdb=" O TYR A 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 513 through 518' Processing helix chain 'A' and resid 519 through 530 removed outlier: 4.093A pdb=" N TYR A 525 " --> pdb=" O HIS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 560 removed outlier: 3.829A pdb=" N ASP A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 removed outlier: 3.633A pdb=" N ALA A 596 " --> pdb=" O SER A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 649 Processing helix chain 'A' and resid 655 through 672 Processing helix chain 'A' and resid 711 through 719 removed outlier: 3.602A pdb=" N THR A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 719 " --> pdb=" O TRP A 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 87 removed outlier: 3.966A pdb=" N ARG B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY B 87 " --> pdb=" O VAL B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 94 through 103 removed outlier: 3.637A pdb=" N TYR B 98 " --> pdb=" O GLY B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.681A pdb=" N LYS B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 147 Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 166 through 174 removed outlier: 4.247A pdb=" N ILE B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 185 removed outlier: 3.962A pdb=" N LEU B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.508A pdb=" N THR B 227 " --> pdb=" O TRP B 223 " (cutoff:3.500A) removed outlier: 3.668A 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 removed outlier: 3.601A pdb=" N GLY B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 316 removed outlier: 3.923A pdb=" N HIS B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'B' and resid 377 through 413 removed outlier: 5.399A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.444A 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 466 through 492 removed outlier: 6.946A pdb=" N PHE B 472 " --> pdb=" O MET B 468 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU B 473 " --> pdb=" O ASP B 469 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 removed outlier: 4.008A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 removed outlier: 3.538A pdb=" N THR B 516 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY B 518 " --> pdb=" O TYR B 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 513 through 518' Processing helix chain 'B' and resid 519 through 530 removed outlier: 4.094A pdb=" N TYR B 525 " --> pdb=" O HIS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 560 removed outlier: 3.829A pdb=" N ASP B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG B 539 " --> pdb=" O ARG B 535 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE B 540 " --> pdb=" O ASP B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 removed outlier: 3.634A pdb=" N ALA B 596 " --> pdb=" O SER B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 649 Processing helix chain 'B' and resid 655 through 672 Processing helix chain 'B' and resid 711 through 719 removed outlier: 3.602A pdb=" N THR B 718 " --> pdb=" O ALA B 714 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 719 " --> pdb=" O TRP B 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 removed outlier: 3.966A pdb=" N ARG C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY C 87 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 94 through 103 removed outlier: 3.637A pdb=" N TYR C 98 " --> pdb=" O GLY C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.680A pdb=" N LYS C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 147 Processing helix chain 'C' and resid 151 through 155 Processing helix chain 'C' and resid 166 through 174 removed outlier: 4.246A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 185 removed outlier: 3.963A pdb=" N LEU C 182 " --> pdb=" O GLN C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.508A pdb=" N THR C 227 " --> pdb=" O TRP C 223 " (cutoff:3.500A) removed outlier: 3.667A 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 removed outlier: 3.602A pdb=" N GLY C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 316 removed outlier: 3.923A pdb=" N HIS C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 377 through 413 removed outlier: 5.399A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.444A 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 466 through 492 removed outlier: 6.946A pdb=" N PHE C 472 " --> pdb=" O MET C 468 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU C 473 " --> pdb=" O ASP C 469 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 512 removed outlier: 4.009A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 518 removed outlier: 3.538A pdb=" N THR C 516 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY C 518 " --> pdb=" O TYR C 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 513 through 518' Processing helix chain 'C' and resid 519 through 530 removed outlier: 4.094A pdb=" N TYR C 525 " --> pdb=" O HIS C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 560 removed outlier: 3.829A pdb=" N ASP C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE C 540 " --> pdb=" O ASP C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 602 removed outlier: 3.633A pdb=" N ALA C 596 " --> pdb=" O SER C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 649 Processing helix chain 'C' and resid 655 through 672 Processing helix chain 'C' and resid 711 through 719 removed outlier: 3.603A pdb=" N THR C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 719 " --> pdb=" O TRP C 715 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 87 removed outlier: 3.965A pdb=" N ARG D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY D 87 " --> pdb=" O VAL D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 94 through 103 removed outlier: 3.637A pdb=" N TYR D 98 " --> pdb=" O GLY D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.681A pdb=" N LYS D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 147 Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 166 through 174 removed outlier: 4.247A pdb=" N ILE D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 185 removed outlier: 3.963A pdb=" N LEU D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.508A pdb=" N THR D 227 " --> pdb=" O TRP D 223 " (cutoff:3.500A) removed outlier: 3.667A 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 removed outlier: 3.602A pdb=" N GLY D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 316 removed outlier: 3.923A pdb=" N HIS D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 368 through 372 Processing helix chain 'D' and resid 377 through 413 removed outlier: 5.399A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.445A 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 466 through 492 removed outlier: 6.947A pdb=" N PHE D 472 " --> pdb=" O MET D 468 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU D 473 " --> pdb=" O ASP D 469 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE D 474 " --> pdb=" O SER D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 512 removed outlier: 4.008A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 removed outlier: 3.537A pdb=" N THR D 516 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY D 518 " --> pdb=" O TYR D 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 513 through 518' Processing helix chain 'D' and resid 519 through 530 removed outlier: 4.093A pdb=" N TYR D 525 " --> pdb=" O HIS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 560 removed outlier: 3.830A pdb=" N ASP D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE D 540 " --> pdb=" O ASP D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 602 removed outlier: 3.633A pdb=" N ALA D 596 " --> pdb=" O SER D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 649 Processing helix chain 'D' and resid 655 through 672 Processing helix chain 'D' and resid 711 through 719 removed outlier: 3.602A pdb=" N THR D 718 " --> pdb=" O ALA D 714 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 719 " --> pdb=" O TRP D 715 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 335 removed outlier: 6.575A pdb=" N LYS A 329 " --> pdb=" O ASP A 344 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASP A 344 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N THR A 331 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU A 342 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP A 700 " --> pdb=" O VAL A 691 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 335 removed outlier: 6.574A pdb=" N LYS B 329 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASP B 344 " --> pdb=" O LYS B 329 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N THR B 331 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU B 342 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASP B 700 " --> pdb=" O VAL B 691 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 335 removed outlier: 6.574A pdb=" N LYS C 329 " --> pdb=" O ASP C 344 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASP C 344 " --> pdb=" O LYS C 329 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N THR C 331 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU C 342 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASP C 700 " --> pdb=" O VAL C 691 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 335 removed outlier: 6.574A pdb=" N LYS D 329 " --> pdb=" O ASP D 344 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASP D 344 " --> pdb=" O LYS D 329 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N THR D 331 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU D 342 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASP D 700 " --> pdb=" O VAL D 691 " (cutoff:3.500A) 1084 hydrogen bonds defined for protein. 3156 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: 6.39 Time building geometry restraints manager: 8.95 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: 6447 1.34 - 1.46: 5003 1.46 - 1.57: 9346 1.57 - 1.69: 0 1.69 - 1.81: 180 Bond restraints: 20976 Sorted by residual: bond pdb=" CB VAL C 356 " pdb=" CG2 VAL C 356 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.94e+00 bond pdb=" CB VAL A 356 " pdb=" CG2 VAL A 356 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.94e+00 bond pdb=" CB VAL B 356 " pdb=" CG2 VAL B 356 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.85e+00 bond pdb=" CB VAL D 356 " pdb=" CG2 VAL D 356 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.85e+00 bond pdb=" CG LEU D 558 " pdb=" CD1 LEU D 558 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.76e+00 ... (remaining 20971 not shown) Histogram of bond angle deviations from ideal: 98.35 - 105.48: 351 105.48 - 112.61: 11032 112.61 - 119.75: 6901 119.75 - 126.88: 9830 126.88 - 134.01: 342 Bond angle restraints: 28456 Sorted by residual: angle pdb=" C GLU B 332 " pdb=" N TRP B 333 " pdb=" CA TRP B 333 " ideal model delta sigma weight residual 121.89 118.30 3.59 1.74e+00 3.30e-01 4.27e+00 angle pdb=" C GLU A 332 " pdb=" N TRP A 333 " pdb=" CA TRP A 333 " ideal model delta sigma weight residual 121.89 118.30 3.59 1.74e+00 3.30e-01 4.26e+00 angle pdb=" C GLU D 332 " pdb=" N TRP D 333 " pdb=" CA TRP D 333 " ideal model delta sigma weight residual 121.89 118.30 3.59 1.74e+00 3.30e-01 4.26e+00 angle pdb=" C GLU C 332 " pdb=" N TRP C 333 " pdb=" CA TRP C 333 " ideal model delta sigma weight residual 121.89 118.33 3.56 1.74e+00 3.30e-01 4.19e+00 angle pdb=" CA TYR C 271 " pdb=" CB TYR C 271 " pdb=" CG TYR C 271 " ideal model delta sigma weight residual 113.90 117.39 -3.49 1.80e+00 3.09e-01 3.76e+00 ... (remaining 28451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 10841 18.03 - 36.06: 1245 36.06 - 54.10: 210 54.10 - 72.13: 40 72.13 - 90.16: 12 Dihedral angle restraints: 12348 sinusoidal: 4984 harmonic: 7364 Sorted by residual: dihedral pdb=" CA ASN C 247 " pdb=" C ASN C 247 " pdb=" N THR C 248 " pdb=" CA THR C 248 " ideal model delta harmonic sigma weight residual 180.00 158.60 21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ASN B 247 " pdb=" C ASN B 247 " pdb=" N THR B 248 " pdb=" CA THR B 248 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ASN D 247 " pdb=" C ASN D 247 " pdb=" N THR D 248 " pdb=" CA THR D 248 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 12345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1882 0.036 - 0.072: 882 0.072 - 0.107: 330 0.107 - 0.143: 80 0.143 - 0.179: 14 Chirality restraints: 3188 Sorted by residual: chirality pdb=" CB VAL C 338 " pdb=" CA VAL C 338 " pdb=" CG1 VAL C 338 " pdb=" CG2 VAL C 338 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.01e-01 chirality pdb=" CB VAL A 338 " pdb=" CA VAL A 338 " pdb=" CG1 VAL A 338 " pdb=" CG2 VAL A 338 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CB VAL D 338 " pdb=" CA VAL D 338 " pdb=" CG1 VAL D 338 " pdb=" CG2 VAL D 338 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.85e-01 ... (remaining 3185 not shown) Planarity restraints: 3540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 250 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C LEU C 250 " 0.028 2.00e-02 2.50e+03 pdb=" O LEU C 250 " -0.011 2.00e-02 2.50e+03 pdb=" N HIS C 251 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 250 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.54e+00 pdb=" C LEU A 250 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU A 250 " 0.010 2.00e-02 2.50e+03 pdb=" N HIS A 251 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 250 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.52e+00 pdb=" C LEU D 250 " -0.027 2.00e-02 2.50e+03 pdb=" O LEU D 250 " 0.010 2.00e-02 2.50e+03 pdb=" N HIS D 251 " 0.009 2.00e-02 2.50e+03 ... (remaining 3537 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3763 2.75 - 3.29: 20686 3.29 - 3.83: 33063 3.83 - 4.36: 37465 4.36 - 4.90: 66280 Nonbonded interactions: 161257 Sorted by model distance: nonbonded pdb=" O LEU D 216 " pdb=" OG1 THR D 220 " model vdw 2.214 2.440 nonbonded pdb=" O LEU B 216 " pdb=" OG1 THR B 220 " model vdw 2.215 2.440 nonbonded pdb=" O LEU A 216 " pdb=" OG1 THR A 220 " model vdw 2.215 2.440 nonbonded pdb=" O LEU C 216 " pdb=" OG1 THR C 220 " model vdw 2.215 2.440 nonbonded pdb=" O ILE A 529 " pdb=" ND2 ASN B 639 " model vdw 2.243 2.520 ... (remaining 161252 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: 1.020 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: 0.020 Extract box with map and model: 6.290 Check model and map are aligned: 0.300 Set scattering table: 0.200 Process input model: 53.690 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.120 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: 0.020 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.066 20976 Z= 0.715 Angle : 0.743 5.023 28456 Z= 0.400 Chirality : 0.047 0.179 3188 Planarity : 0.004 0.033 3540 Dihedral : 15.058 90.159 7588 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.90 % Allowed : 8.77 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.15), residues: 2488 helix: -1.02 (0.12), residues: 1416 sheet: -1.26 (0.62), residues: 64 loop : -2.01 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 715 HIS 0.005 0.001 HIS B 269 PHE 0.025 0.003 PHE A 362 TYR 0.023 0.003 TYR C 162 ARG 0.010 0.001 ARG B 560 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 267 time to evaluate : 2.210 Fit side-chains REVERT: A 193 ARG cc_start: 0.8379 (ptp90) cc_final: 0.8114 (ptp-110) REVERT: A 640 MET cc_start: 0.8498 (tmm) cc_final: 0.8187 (ttp) REVERT: A 667 SER cc_start: 0.9184 (t) cc_final: 0.8962 (p) REVERT: B 193 ARG cc_start: 0.8388 (ptp90) cc_final: 0.8115 (ptp-110) REVERT: B 614 GLU cc_start: 0.7028 (pp20) cc_final: 0.6353 (pp20) REVERT: B 640 MET cc_start: 0.8363 (tmm) cc_final: 0.8074 (ttp) REVERT: B 667 SER cc_start: 0.9219 (t) cc_final: 0.8973 (p) REVERT: C 193 ARG cc_start: 0.8381 (ptp90) cc_final: 0.8113 (ptp-110) REVERT: C 614 GLU cc_start: 0.7030 (pp20) cc_final: 0.6353 (pp20) REVERT: C 640 MET cc_start: 0.8365 (tmm) cc_final: 0.8071 (ttp) REVERT: C 667 SER cc_start: 0.9221 (t) cc_final: 0.8973 (p) REVERT: D 193 ARG cc_start: 0.8385 (ptp90) cc_final: 0.8111 (ptp-110) REVERT: D 314 ILE cc_start: 0.8762 (mt) cc_final: 0.8493 (mt) REVERT: D 614 GLU cc_start: 0.7035 (pp20) cc_final: 0.6350 (pp20) REVERT: D 640 MET cc_start: 0.8359 (tmm) cc_final: 0.8071 (ttp) REVERT: D 667 SER cc_start: 0.9220 (t) cc_final: 0.8974 (p) outliers start: 20 outliers final: 12 residues processed: 283 average time/residue: 0.3723 time to fit residues: 156.9712 Evaluate side-chains 216 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 204 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 710 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 228 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 269 HIS ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 ASN B 269 HIS ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN C 269 HIS ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 GLN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN D 269 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20976 Z= 0.204 Angle : 0.514 6.874 28456 Z= 0.257 Chirality : 0.036 0.122 3188 Planarity : 0.003 0.031 3540 Dihedral : 4.215 31.125 2772 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.31 % Allowed : 14.24 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.11 (0.17), residues: 2488 helix: 0.76 (0.14), residues: 1452 sheet: -1.14 (0.54), residues: 64 loop : -1.24 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 676 HIS 0.007 0.001 HIS A 269 PHE 0.017 0.001 PHE B 491 TYR 0.009 0.001 TYR D 228 ARG 0.004 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 267 time to evaluate : 2.453 Fit side-chains REVERT: A 193 ARG cc_start: 0.8302 (ptp90) cc_final: 0.8040 (ptp-110) REVERT: A 491 PHE cc_start: 0.7709 (t80) cc_final: 0.7489 (t80) REVERT: A 614 GLU cc_start: 0.7090 (pp20) cc_final: 0.6598 (pp20) REVERT: B 193 ARG cc_start: 0.8317 (ptp90) cc_final: 0.8062 (ptp-110) REVERT: B 491 PHE cc_start: 0.7751 (t80) cc_final: 0.7540 (t80) REVERT: C 193 ARG cc_start: 0.8315 (ptp90) cc_final: 0.8061 (ptp-110) REVERT: C 491 PHE cc_start: 0.7767 (t80) cc_final: 0.7566 (t80) REVERT: D 193 ARG cc_start: 0.8312 (ptp90) cc_final: 0.8057 (ptp-110) REVERT: D 314 ILE cc_start: 0.8998 (mt) cc_final: 0.8777 (mt) REVERT: D 491 PHE cc_start: 0.7761 (t80) cc_final: 0.7555 (t80) outliers start: 29 outliers final: 15 residues processed: 288 average time/residue: 0.3087 time to fit residues: 140.2098 Evaluate side-chains 231 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 216 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain D residue 710 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 190 optimal weight: 5.9990 chunk 155 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 229 optimal weight: 4.9990 chunk 247 optimal weight: 4.9990 chunk 204 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 183 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20976 Z= 0.180 Angle : 0.474 6.554 28456 Z= 0.238 Chirality : 0.036 0.117 3188 Planarity : 0.003 0.030 3540 Dihedral : 3.718 20.891 2760 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.26 % Allowed : 16.41 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.65 (0.17), residues: 2488 helix: 1.48 (0.14), residues: 1436 sheet: -0.80 (0.55), residues: 64 loop : -1.07 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 676 HIS 0.002 0.000 HIS A 269 PHE 0.010 0.001 PHE D 311 TYR 0.007 0.001 TYR D 403 ARG 0.004 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 270 time to evaluate : 2.465 Fit side-chains REVERT: A 193 ARG cc_start: 0.8357 (ptp90) cc_final: 0.8103 (ptp-110) REVERT: A 277 MET cc_start: 0.7464 (mtp) cc_final: 0.7251 (mtt) REVERT: A 491 PHE cc_start: 0.7556 (t80) cc_final: 0.7236 (t80) REVERT: A 614 GLU cc_start: 0.7086 (pp20) cc_final: 0.6565 (pp20) REVERT: A 636 LEU cc_start: 0.8785 (tp) cc_final: 0.8534 (tt) REVERT: B 193 ARG cc_start: 0.8395 (ptp90) cc_final: 0.8085 (ptp-110) REVERT: B 332 GLU cc_start: 0.8138 (tt0) cc_final: 0.7729 (tt0) REVERT: B 491 PHE cc_start: 0.7571 (t80) cc_final: 0.7282 (t80) REVERT: B 636 LEU cc_start: 0.8766 (tp) cc_final: 0.8532 (tt) REVERT: B 670 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7563 (tm-30) REVERT: C 193 ARG cc_start: 0.8389 (ptp90) cc_final: 0.8086 (ptp-110) REVERT: C 332 GLU cc_start: 0.8141 (tt0) cc_final: 0.7735 (tt0) REVERT: C 491 PHE cc_start: 0.7582 (t80) cc_final: 0.7294 (t80) REVERT: C 636 LEU cc_start: 0.8738 (tp) cc_final: 0.8481 (tt) REVERT: C 670 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7567 (tm-30) REVERT: D 193 ARG cc_start: 0.8389 (ptp90) cc_final: 0.8087 (ptp-110) REVERT: D 314 ILE cc_start: 0.9018 (mt) cc_final: 0.8767 (mt) REVERT: D 332 GLU cc_start: 0.8135 (tt0) cc_final: 0.7734 (tt0) REVERT: D 491 PHE cc_start: 0.7567 (t80) cc_final: 0.7278 (t80) REVERT: D 636 LEU cc_start: 0.8758 (tp) cc_final: 0.8511 (tt) REVERT: D 670 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7563 (tm-30) outliers start: 50 outliers final: 33 residues processed: 318 average time/residue: 0.2944 time to fit residues: 150.7716 Evaluate side-chains 251 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 218 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 667 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 230 optimal weight: 0.9980 chunk 243 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 218 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN C 368 ASN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN D 368 ASN D 414 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20976 Z= 0.264 Angle : 0.532 8.029 28456 Z= 0.265 Chirality : 0.037 0.118 3188 Planarity : 0.003 0.029 3540 Dihedral : 3.731 14.554 2756 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.98 % Allowed : 18.49 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.79 (0.17), residues: 2488 helix: 1.57 (0.14), residues: 1436 sheet: -0.51 (0.59), residues: 64 loop : -0.98 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 676 HIS 0.002 0.001 HIS A 202 PHE 0.008 0.001 PHE D 540 TYR 0.011 0.001 TYR B 271 ARG 0.002 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 242 time to evaluate : 2.439 Fit side-chains REVERT: A 453 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9081 (mm) REVERT: A 491 PHE cc_start: 0.7622 (t80) cc_final: 0.7289 (t80) REVERT: A 614 GLU cc_start: 0.7175 (pp20) cc_final: 0.6645 (pp20) REVERT: A 636 LEU cc_start: 0.8897 (tp) cc_final: 0.8618 (tt) REVERT: B 453 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9027 (mm) REVERT: B 491 PHE cc_start: 0.7605 (t80) cc_final: 0.7297 (t80) REVERT: B 636 LEU cc_start: 0.8899 (tp) cc_final: 0.8624 (tt) REVERT: C 453 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9031 (mm) REVERT: C 491 PHE cc_start: 0.7611 (t80) cc_final: 0.7316 (t80) REVERT: C 636 LEU cc_start: 0.8899 (tp) cc_final: 0.8619 (tt) REVERT: D 453 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9028 (mm) REVERT: D 491 PHE cc_start: 0.7602 (t80) cc_final: 0.7297 (t80) REVERT: D 636 LEU cc_start: 0.8898 (tp) cc_final: 0.8620 (tt) outliers start: 88 outliers final: 57 residues processed: 322 average time/residue: 0.2664 time to fit residues: 142.6410 Evaluate side-chains 286 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 225 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 7.9990 chunk 138 optimal weight: 0.9990 chunk 3 optimal weight: 0.0470 chunk 181 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20976 Z= 0.198 Angle : 0.498 8.341 28456 Z= 0.245 Chirality : 0.036 0.115 3188 Planarity : 0.003 0.034 3540 Dihedral : 3.578 14.039 2756 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.48 % Allowed : 20.98 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.06 (0.17), residues: 2488 helix: 1.78 (0.14), residues: 1436 sheet: -0.69 (0.55), residues: 64 loop : -0.82 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 676 HIS 0.002 0.000 HIS A 202 PHE 0.007 0.001 PHE C 311 TYR 0.009 0.001 TYR A 228 ARG 0.002 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 258 time to evaluate : 2.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 491 PHE cc_start: 0.7644 (t80) cc_final: 0.7378 (t80) REVERT: A 614 GLU cc_start: 0.7173 (pp20) cc_final: 0.6643 (pp20) REVERT: B 453 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8965 (mm) REVERT: B 491 PHE cc_start: 0.7643 (t80) cc_final: 0.7322 (t80) REVERT: B 670 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7531 (tm-30) REVERT: C 453 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8970 (mm) REVERT: C 491 PHE cc_start: 0.7632 (t80) cc_final: 0.7378 (t80) REVERT: C 670 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7526 (tm-30) REVERT: D 453 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8975 (mm) REVERT: D 491 PHE cc_start: 0.7621 (t80) cc_final: 0.7359 (t80) REVERT: D 670 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7517 (tm-30) outliers start: 77 outliers final: 58 residues processed: 327 average time/residue: 0.2800 time to fit residues: 148.8399 Evaluate side-chains 291 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 230 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 8.9990 chunk 219 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 243 optimal weight: 0.5980 chunk 202 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20976 Z= 0.249 Angle : 0.536 9.416 28456 Z= 0.260 Chirality : 0.037 0.122 3188 Planarity : 0.003 0.036 3540 Dihedral : 3.635 14.603 2756 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.75 % Allowed : 21.88 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2488 helix: 1.78 (0.14), residues: 1436 sheet: -0.91 (0.54), residues: 64 loop : -0.77 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 676 HIS 0.002 0.001 HIS A 165 PHE 0.007 0.001 PHE D 612 TYR 0.010 0.001 TYR D 271 ARG 0.002 0.000 ARG B 517 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 241 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9025 (mm) REVERT: A 491 PHE cc_start: 0.7662 (t80) cc_final: 0.7404 (t80) REVERT: A 614 GLU cc_start: 0.7202 (pp20) cc_final: 0.6678 (pp20) REVERT: B 453 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8982 (mm) REVERT: B 491 PHE cc_start: 0.7657 (t80) cc_final: 0.7404 (t80) REVERT: C 453 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8986 (mm) REVERT: C 491 PHE cc_start: 0.7662 (t80) cc_final: 0.7412 (t80) REVERT: D 453 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9002 (mm) REVERT: D 491 PHE cc_start: 0.7651 (t80) cc_final: 0.7399 (t80) outliers start: 83 outliers final: 63 residues processed: 315 average time/residue: 0.2751 time to fit residues: 143.8953 Evaluate side-chains 298 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 231 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 205 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 242 optimal weight: 2.9990 chunk 152 optimal weight: 0.0980 chunk 148 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20976 Z= 0.269 Angle : 0.545 10.093 28456 Z= 0.266 Chirality : 0.037 0.122 3188 Planarity : 0.003 0.039 3540 Dihedral : 3.671 15.287 2756 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.93 % Allowed : 22.74 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2488 helix: 1.77 (0.14), residues: 1436 sheet: -1.03 (0.54), residues: 64 loop : -0.75 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 676 HIS 0.002 0.001 HIS D 202 PHE 0.007 0.001 PHE D 311 TYR 0.010 0.001 TYR C 271 ARG 0.002 0.000 ARG D 517 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 237 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 453 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8986 (mm) REVERT: A 491 PHE cc_start: 0.7648 (t80) cc_final: 0.7436 (t80) REVERT: A 492 MET cc_start: 0.7294 (ttt) cc_final: 0.7009 (ttt) REVERT: A 614 GLU cc_start: 0.7195 (pp20) cc_final: 0.6679 (pp20) REVERT: B 214 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8658 (tt) REVERT: B 453 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8990 (mm) REVERT: B 491 PHE cc_start: 0.7638 (t80) cc_final: 0.7420 (t80) REVERT: B 670 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7599 (tm-30) REVERT: C 214 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8664 (tt) REVERT: C 453 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8996 (mm) REVERT: C 491 PHE cc_start: 0.7642 (t80) cc_final: 0.7423 (t80) REVERT: C 670 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7591 (tm-30) REVERT: D 214 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8666 (tt) REVERT: D 453 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9002 (mm) REVERT: D 491 PHE cc_start: 0.7631 (t80) cc_final: 0.7404 (t80) REVERT: D 670 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7587 (tm-30) outliers start: 87 outliers final: 65 residues processed: 313 average time/residue: 0.2109 time to fit residues: 109.8140 Evaluate side-chains 303 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 231 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 154 optimal weight: 0.6980 chunk 165 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 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 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20976 Z= 0.184 Angle : 0.505 11.004 28456 Z= 0.246 Chirality : 0.036 0.123 3188 Planarity : 0.003 0.041 3540 Dihedral : 3.510 14.157 2756 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.75 % Allowed : 23.06 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.19 (0.17), residues: 2488 helix: 1.90 (0.14), residues: 1436 sheet: -1.06 (0.54), residues: 64 loop : -0.75 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 676 HIS 0.001 0.000 HIS A 165 PHE 0.007 0.001 PHE B 311 TYR 0.012 0.001 TYR D 98 ARG 0.001 0.000 ARG D 517 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 243 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 GLU cc_start: 0.8186 (tt0) cc_final: 0.7760 (tt0) REVERT: A 453 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8907 (mm) REVERT: A 491 PHE cc_start: 0.7640 (t80) cc_final: 0.7428 (t80) REVERT: A 492 MET cc_start: 0.7343 (ttt) cc_final: 0.7019 (ttt) REVERT: A 614 GLU cc_start: 0.7132 (pp20) cc_final: 0.6638 (pp20) REVERT: B 453 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8985 (mm) REVERT: B 491 PHE cc_start: 0.7652 (t80) cc_final: 0.7395 (t80) REVERT: B 670 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7521 (tm-30) REVERT: C 453 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8971 (mm) REVERT: C 491 PHE cc_start: 0.7659 (t80) cc_final: 0.7401 (t80) REVERT: C 670 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7530 (tm-30) REVERT: D 453 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8947 (mm) REVERT: D 491 PHE cc_start: 0.7643 (t80) cc_final: 0.7385 (t80) REVERT: D 670 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7521 (tm-30) outliers start: 83 outliers final: 65 residues processed: 309 average time/residue: 0.2727 time to fit residues: 138.3510 Evaluate side-chains 299 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 230 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 3.9990 chunk 212 optimal weight: 0.4980 chunk 226 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 177 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 204 optimal weight: 0.6980 chunk 214 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 20976 Z= 0.160 Angle : 0.510 11.449 28456 Z= 0.249 Chirality : 0.035 0.124 3188 Planarity : 0.003 0.042 3540 Dihedral : 3.375 13.009 2756 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.35 % Allowed : 23.24 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.32 (0.17), residues: 2488 helix: 2.01 (0.14), residues: 1436 sheet: -0.91 (0.54), residues: 64 loop : -0.71 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 676 HIS 0.001 0.000 HIS B 165 PHE 0.007 0.001 PHE C 311 TYR 0.012 0.001 TYR D 98 ARG 0.001 0.000 ARG D 517 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 260 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 GLU cc_start: 0.8159 (tt0) cc_final: 0.7809 (tt0) REVERT: A 453 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8907 (mm) REVERT: A 491 PHE cc_start: 0.7670 (t80) cc_final: 0.7435 (t80) REVERT: A 614 GLU cc_start: 0.7029 (pp20) cc_final: 0.6526 (pp20) REVERT: B 345 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8369 (pt) REVERT: B 453 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8945 (mm) REVERT: B 491 PHE cc_start: 0.7670 (t80) cc_final: 0.7393 (t80) REVERT: C 453 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8949 (mm) REVERT: C 491 PHE cc_start: 0.7676 (t80) cc_final: 0.7404 (t80) REVERT: D 453 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8927 (mm) REVERT: D 491 PHE cc_start: 0.7668 (t80) cc_final: 0.7393 (t80) outliers start: 74 outliers final: 57 residues processed: 324 average time/residue: 0.2683 time to fit residues: 143.7746 Evaluate side-chains 295 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 233 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 223 TRP Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 251 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 122 optimal weight: 7.9990 chunk 158 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20976 Z= 0.191 Angle : 0.524 11.656 28456 Z= 0.255 Chirality : 0.036 0.121 3188 Planarity : 0.003 0.043 3540 Dihedral : 3.427 13.840 2756 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.21 % Allowed : 23.96 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.36 (0.17), residues: 2488 helix: 2.02 (0.14), residues: 1436 sheet: -0.94 (0.53), residues: 64 loop : -0.65 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 676 HIS 0.001 0.000 HIS A 165 PHE 0.007 0.001 PHE C 311 TYR 0.012 0.001 TYR C 98 ARG 0.001 0.000 ARG D 517 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 245 time to evaluate : 2.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 GLU cc_start: 0.8168 (tt0) cc_final: 0.7808 (tt0) REVERT: A 453 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8889 (mm) REVERT: A 491 PHE cc_start: 0.7700 (t80) cc_final: 0.7461 (t80) REVERT: A 614 GLU cc_start: 0.6989 (pp20) cc_final: 0.6458 (pp20) REVERT: B 277 MET cc_start: 0.7420 (mtm) cc_final: 0.7206 (mtt) REVERT: B 345 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8296 (pp) REVERT: B 453 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8950 (mm) REVERT: B 491 PHE cc_start: 0.7693 (t80) cc_final: 0.7425 (t80) REVERT: B 492 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6936 (ttt) REVERT: C 453 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8957 (mm) REVERT: C 491 PHE cc_start: 0.7689 (t80) cc_final: 0.7422 (t80) REVERT: C 492 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.7003 (ttt) REVERT: D 277 MET cc_start: 0.7425 (mtm) cc_final: 0.7210 (mtt) REVERT: D 453 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8939 (mm) REVERT: D 491 PHE cc_start: 0.7678 (t80) cc_final: 0.7411 (t80) REVERT: D 492 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.7008 (ttt) outliers start: 71 outliers final: 58 residues processed: 305 average time/residue: 0.2914 time to fit residues: 148.0744 Evaluate side-chains 299 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 233 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.3980 chunk 61 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 200 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 205 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 175 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.123190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.102900 restraints weight = 29466.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.105199 restraints weight = 19408.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.106784 restraints weight = 14712.496| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20976 Z= 0.149 Angle : 0.503 11.599 28456 Z= 0.245 Chirality : 0.035 0.124 3188 Planarity : 0.003 0.043 3540 Dihedral : 3.312 13.136 2756 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.89 % Allowed : 24.64 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.48 (0.17), residues: 2488 helix: 2.13 (0.14), residues: 1436 sheet: -0.87 (0.53), residues: 64 loop : -0.62 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 676 HIS 0.003 0.000 HIS D 269 PHE 0.007 0.001 PHE A 311 TYR 0.013 0.001 TYR C 98 ARG 0.001 0.000 ARG A 280 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3463.30 seconds wall clock time: 69 minutes 12.38 seconds (4152.38 seconds total)