Starting phenix.real_space_refine on Thu Feb 22 18:55:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k59_22678/02_2024/7k59_22678.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k59_22678/02_2024/7k59_22678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k59_22678/02_2024/7k59_22678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k59_22678/02_2024/7k59_22678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k59_22678/02_2024/7k59_22678.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k59_22678/02_2024/7k59_22678.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.091 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 186 5.16 5 C 22044 2.51 5 N 6180 2.21 5 O 6642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 29": "OD1" <-> "OD2" Residue "A GLU 30": "OE1" <-> "OE2" Residue "A ASP 55": "OD1" <-> "OD2" Residue "A ASP 79": "OD1" <-> "OD2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A ASP 304": "OD1" <-> "OD2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A ASP 410": "OD1" <-> "OD2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A ASP 564": "OD1" <-> "OD2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A ASP 630": "OD1" <-> "OD2" Residue "A GLU 650": "OE1" <-> "OE2" Residue "A GLU 724": "OE1" <-> "OE2" Residue "A ASP 749": "OD1" <-> "OD2" Residue "B ASP 29": "OD1" <-> "OD2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B ASP 55": "OD1" <-> "OD2" Residue "B ASP 79": "OD1" <-> "OD2" Residue "B ASP 98": "OD1" <-> "OD2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B ASP 304": "OD1" <-> "OD2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B ASP 368": "OD1" <-> "OD2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B ASP 410": "OD1" <-> "OD2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B ASP 564": "OD1" <-> "OD2" Residue "B ARG 625": "NH1" <-> "NH2" Residue "B ASP 630": "OD1" <-> "OD2" Residue "B GLU 650": "OE1" <-> "OE2" Residue "B GLU 724": "OE1" <-> "OE2" Residue "B ASP 749": "OD1" <-> "OD2" Residue "C ASP 29": "OD1" <-> "OD2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C ASP 55": "OD1" <-> "OD2" Residue "C ASP 79": "OD1" <-> "OD2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C GLU 192": "OE1" <-> "OE2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C ASP 304": "OD1" <-> "OD2" Residue "C GLU 321": "OE1" <-> "OE2" Residue "C ASP 368": "OD1" <-> "OD2" Residue "C GLU 379": "OE1" <-> "OE2" Residue "C ASP 410": "OD1" <-> "OD2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C ASP 564": "OD1" <-> "OD2" Residue "C ARG 625": "NH1" <-> "NH2" Residue "C ASP 630": "OD1" <-> "OD2" Residue "C GLU 650": "OE1" <-> "OE2" Residue "C GLU 724": "OE1" <-> "OE2" Residue "C ASP 749": "OD1" <-> "OD2" Residue "D ASP 29": "OD1" <-> "OD2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D ASP 55": "OD1" <-> "OD2" Residue "D ASP 79": "OD1" <-> "OD2" Residue "D ASP 98": "OD1" <-> "OD2" Residue "D GLU 132": "OE1" <-> "OE2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "D ASP 304": "OD1" <-> "OD2" Residue "D GLU 321": "OE1" <-> "OE2" Residue "D ASP 368": "OD1" <-> "OD2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "D ASP 410": "OD1" <-> "OD2" Residue "D ARG 453": "NH1" <-> "NH2" Residue "D ASP 564": "OD1" <-> "OD2" Residue "D ARG 625": "NH1" <-> "NH2" Residue "D ASP 630": "OD1" <-> "OD2" Residue "D GLU 650": "OE1" <-> "OE2" Residue "D GLU 724": "OE1" <-> "OE2" Residue "D ASP 749": "OD1" <-> "OD2" Residue "D PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 29": "OD1" <-> "OD2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E ASP 55": "OD1" <-> "OD2" Residue "E ASP 79": "OD1" <-> "OD2" Residue "E ASP 98": "OD1" <-> "OD2" Residue "E GLU 132": "OE1" <-> "OE2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "E GLU 192": "OE1" <-> "OE2" Residue "E GLU 218": "OE1" <-> "OE2" Residue "E ASP 304": "OD1" <-> "OD2" Residue "E GLU 321": "OE1" <-> "OE2" Residue "E ASP 368": "OD1" <-> "OD2" Residue "E GLU 379": "OE1" <-> "OE2" Residue "E ASP 410": "OD1" <-> "OD2" Residue "E ARG 453": "NH1" <-> "NH2" Residue "E ASP 564": "OD1" <-> "OD2" Residue "E ARG 625": "NH1" <-> "NH2" Residue "E ASP 630": "OD1" <-> "OD2" Residue "E GLU 650": "OE1" <-> "OE2" Residue "E GLU 724": "OE1" <-> "OE2" Residue "E ASP 749": "OD1" <-> "OD2" Residue "F ASP 29": "OD1" <-> "OD2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "F ASP 55": "OD1" <-> "OD2" Residue "F ASP 79": "OD1" <-> "OD2" Residue "F ASP 98": "OD1" <-> "OD2" Residue "F GLU 132": "OE1" <-> "OE2" Residue "F GLU 185": "OE1" <-> "OE2" Residue "F GLU 187": "OE1" <-> "OE2" Residue "F GLU 192": "OE1" <-> "OE2" Residue "F GLU 218": "OE1" <-> "OE2" Residue "F ASP 304": "OD1" <-> "OD2" Residue "F GLU 321": "OE1" <-> "OE2" Residue "F ASP 368": "OD1" <-> "OD2" Residue "F GLU 379": "OE1" <-> "OE2" Residue "F ASP 410": "OD1" <-> "OD2" Residue "F ARG 453": "NH1" <-> "NH2" Residue "F ASP 564": "OD1" <-> "OD2" Residue "F ARG 625": "NH1" <-> "NH2" Residue "F ASP 630": "OD1" <-> "OD2" Residue "F GLU 650": "OE1" <-> "OE2" Residue "F GLU 724": "OE1" <-> "OE2" Residue "F ASP 749": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 35052 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5842 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 698} Chain breaks: 1 Chain: "B" Number of atoms: 5842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5842 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 698} Chain breaks: 1 Chain: "C" Number of atoms: 5842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5842 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 698} Chain breaks: 1 Chain: "D" Number of atoms: 5842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5842 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 698} Chain breaks: 1 Chain: "E" Number of atoms: 5842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5842 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 698} Chain breaks: 1 Chain: "F" Number of atoms: 5842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5842 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 698} Chain breaks: 1 Time building chain proxies: 17.77, per 1000 atoms: 0.51 Number of scatterers: 35052 At special positions: 0 Unit cell: (181.643, 172.328, 119.543, 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 186 16.00 O 6642 8.00 N 6180 7.00 C 22044 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: 12.54 Conformation dependent library (CDL) restraints added in 6.4 seconds 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8364 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 30 sheets defined 42.0% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.69 Creating SS restraints... Processing helix chain 'A' and resid 61 through 65 removed outlier: 4.119A pdb=" N ARG A 64 " --> pdb=" O GLY A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 92 Processing helix chain 'A' and resid 135 through 140 removed outlier: 4.410A pdb=" N LEU A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 196 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 209 through 226 removed outlier: 4.655A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 234 removed outlier: 4.179A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 261 Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.531A pdb=" N ILE A 274 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 306 through 309 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 319 through 334 Processing helix chain 'A' and resid 354 through 358 removed outlier: 3.619A pdb=" N ARG A 358 " --> pdb=" O PRO A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 383 removed outlier: 3.671A pdb=" N LEU A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 402 removed outlier: 3.535A pdb=" N GLU A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.521A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 removed outlier: 3.510A pdb=" N ILE A 479 " --> pdb=" O TRP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 499 removed outlier: 4.720A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 501 through 506 removed outlier: 4.090A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 removed outlier: 4.226A pdb=" N ALA A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.683A pdb=" N THR A 549 " --> pdb=" O PRO A 545 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TRP A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 569 removed outlier: 3.711A pdb=" N ALA A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 609 removed outlier: 3.581A pdb=" N GLU A 607 " --> pdb=" O GLN A 603 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.620A pdb=" N ARG A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 660 Processing helix chain 'A' and resid 672 through 677 Processing helix chain 'A' and resid 686 through 711 removed outlier: 3.692A pdb=" N ILE A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N CYS A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLN A 692 " --> pdb=" O THR A 688 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N CYS A 695 " --> pdb=" O CYS A 691 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 701 " --> pdb=" O LEU A 697 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 709 " --> pdb=" O SER A 705 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 removed outlier: 4.137A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'A' and resid 751 through 762 removed outlier: 3.612A pdb=" N TYR A 755 " --> pdb=" O ASP A 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 removed outlier: 4.119A pdb=" N ARG B 64 " --> pdb=" O GLY B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 135 through 140 removed outlier: 4.409A pdb=" N LEU B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 196 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.655A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 234 removed outlier: 4.179A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 261 Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.531A pdb=" N ILE B 274 " --> pdb=" O GLY B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 296 Processing helix chain 'B' and resid 306 through 309 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 319 through 334 Processing helix chain 'B' and resid 354 through 358 removed outlier: 3.617A pdb=" N ARG B 358 " --> pdb=" O PRO B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 383 removed outlier: 3.672A pdb=" N LEU B 381 " --> pdb=" O ARG B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 402 removed outlier: 3.534A pdb=" N GLU B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 Processing helix chain 'B' and resid 448 through 459 removed outlier: 3.521A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 459 " --> pdb=" O ALA B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 removed outlier: 3.510A pdb=" N ILE B 479 " --> pdb=" O TRP B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 499 removed outlier: 4.721A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 501 through 506 removed outlier: 4.089A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 535 removed outlier: 4.226A pdb=" N ALA B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 removed outlier: 3.681A pdb=" N THR B 549 " --> pdb=" O PRO B 545 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TRP B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY B 553 " --> pdb=" O THR B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 569 removed outlier: 3.710A pdb=" N ALA B 566 " --> pdb=" O ILE B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 609 removed outlier: 3.580A pdb=" N GLU B 607 " --> pdb=" O GLN B 603 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.620A pdb=" N ARG B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 660 Processing helix chain 'B' and resid 672 through 677 Processing helix chain 'B' and resid 686 through 711 removed outlier: 3.692A pdb=" N ILE B 690 " --> pdb=" O ASP B 686 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N CYS B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN B 692 " --> pdb=" O THR B 688 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N CYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU B 701 " --> pdb=" O LEU B 697 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG B 709 " --> pdb=" O SER B 705 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 710 " --> pdb=" O GLU B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 740 removed outlier: 4.138A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 743 No H-bonds generated for 'chain 'B' and resid 741 through 743' Processing helix chain 'B' and resid 751 through 762 removed outlier: 3.612A pdb=" N TYR B 755 " --> pdb=" O ASP B 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 65 removed outlier: 4.119A pdb=" N ARG C 64 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 135 through 140 removed outlier: 4.410A pdb=" N LEU C 140 " --> pdb=" O LYS C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 209 through 226 removed outlier: 4.655A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 234 removed outlier: 4.179A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS C 231 " --> pdb=" O PRO C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 261 Processing helix chain 'C' and resid 271 through 275 removed outlier: 3.532A pdb=" N ILE C 274 " --> pdb=" O GLY C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 306 through 309 Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 319 through 334 Processing helix chain 'C' and resid 354 through 358 removed outlier: 3.618A pdb=" N ARG C 358 " --> pdb=" O PRO C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 383 removed outlier: 3.670A pdb=" N LEU C 381 " --> pdb=" O ARG C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 402 removed outlier: 3.534A pdb=" N GLU C 402 " --> pdb=" O GLN C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 425 Processing helix chain 'C' and resid 448 through 459 removed outlier: 3.521A pdb=" N PHE C 452 " --> pdb=" O THR C 448 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER C 459 " --> pdb=" O ALA C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 removed outlier: 3.509A pdb=" N ILE C 479 " --> pdb=" O TRP C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 499 removed outlier: 4.721A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 501 through 506 removed outlier: 4.088A pdb=" N PHE C 506 " --> pdb=" O LYS C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 535 removed outlier: 4.226A pdb=" N ALA C 530 " --> pdb=" O LEU C 526 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE C 531 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 removed outlier: 3.682A pdb=" N THR C 549 " --> pdb=" O PRO C 545 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TRP C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY C 553 " --> pdb=" O THR C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 569 removed outlier: 3.710A pdb=" N ALA C 566 " --> pdb=" O ILE C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 609 removed outlier: 3.581A pdb=" N GLU C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.620A pdb=" N ARG C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 660 Processing helix chain 'C' and resid 672 through 677 Processing helix chain 'C' and resid 686 through 711 removed outlier: 3.692A pdb=" N ILE C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N CYS C 691 " --> pdb=" O LEU C 687 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN C 692 " --> pdb=" O THR C 688 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N CYS C 695 " --> pdb=" O CYS C 691 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU C 701 " --> pdb=" O LEU C 697 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG C 708 " --> pdb=" O GLU C 704 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG C 709 " --> pdb=" O SER C 705 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU C 710 " --> pdb=" O GLU C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 740 removed outlier: 4.138A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 743 No H-bonds generated for 'chain 'C' and resid 741 through 743' Processing helix chain 'C' and resid 751 through 762 removed outlier: 3.611A pdb=" N TYR C 755 " --> pdb=" O ASP C 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 65 removed outlier: 4.119A pdb=" N ARG D 64 " --> pdb=" O GLY D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'D' and resid 135 through 140 removed outlier: 4.410A pdb=" N LEU D 140 " --> pdb=" O LYS D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 196 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 209 through 226 removed outlier: 4.656A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 234 removed outlier: 4.179A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 271 through 275 removed outlier: 3.531A pdb=" N ILE D 274 " --> pdb=" O GLY D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 296 Processing helix chain 'D' and resid 306 through 309 Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 319 through 334 Processing helix chain 'D' and resid 354 through 358 removed outlier: 3.618A pdb=" N ARG D 358 " --> pdb=" O PRO D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 383 removed outlier: 3.671A pdb=" N LEU D 381 " --> pdb=" O ARG D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 402 removed outlier: 3.534A pdb=" N GLU D 402 " --> pdb=" O GLN D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 425 Processing helix chain 'D' and resid 448 through 459 removed outlier: 3.521A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER D 459 " --> pdb=" O ALA D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 removed outlier: 3.510A pdb=" N ILE D 479 " --> pdb=" O TRP D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 499 removed outlier: 4.721A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 501 through 506 removed outlier: 4.089A pdb=" N PHE D 506 " --> pdb=" O LYS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 535 removed outlier: 4.226A pdb=" N ALA D 530 " --> pdb=" O LEU D 526 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE D 531 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 553 removed outlier: 3.682A pdb=" N THR D 549 " --> pdb=" O PRO D 545 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TRP D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY D 553 " --> pdb=" O THR D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 569 removed outlier: 3.711A pdb=" N ALA D 566 " --> pdb=" O ILE D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 609 removed outlier: 3.581A pdb=" N GLU D 607 " --> pdb=" O GLN D 603 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP D 609 " --> pdb=" O LEU D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.620A pdb=" N ARG D 635 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 660 Processing helix chain 'D' and resid 672 through 677 Processing helix chain 'D' and resid 686 through 711 removed outlier: 3.692A pdb=" N ILE D 690 " --> pdb=" O ASP D 686 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N CYS D 691 " --> pdb=" O LEU D 687 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLN D 692 " --> pdb=" O THR D 688 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N CYS D 695 " --> pdb=" O CYS D 691 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU D 701 " --> pdb=" O LEU D 697 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG D 708 " --> pdb=" O GLU D 704 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG D 709 " --> pdb=" O SER D 705 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU D 710 " --> pdb=" O GLU D 706 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 740 removed outlier: 4.137A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 743 No H-bonds generated for 'chain 'D' and resid 741 through 743' Processing helix chain 'D' and resid 751 through 762 removed outlier: 3.611A pdb=" N TYR D 755 " --> pdb=" O ASP D 751 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 65 removed outlier: 4.118A pdb=" N ARG E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 135 through 140 removed outlier: 4.410A pdb=" N LEU E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 196 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.656A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 234 removed outlier: 4.179A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 261 Processing helix chain 'E' and resid 271 through 275 removed outlier: 3.531A pdb=" N ILE E 274 " --> pdb=" O GLY E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 296 Processing helix chain 'E' and resid 306 through 309 Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 319 through 334 Processing helix chain 'E' and resid 354 through 358 removed outlier: 3.618A pdb=" N ARG E 358 " --> pdb=" O PRO E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 383 removed outlier: 3.671A pdb=" N LEU E 381 " --> pdb=" O ARG E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 402 removed outlier: 3.535A pdb=" N GLU E 402 " --> pdb=" O GLN E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 425 Processing helix chain 'E' and resid 448 through 459 removed outlier: 3.522A pdb=" N PHE E 452 " --> pdb=" O THR E 448 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER E 459 " --> pdb=" O ALA E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 removed outlier: 3.509A pdb=" N ILE E 479 " --> pdb=" O TRP E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 482 through 499 removed outlier: 4.720A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 501 through 506 removed outlier: 4.089A pdb=" N PHE E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 535 removed outlier: 4.226A pdb=" N ALA E 530 " --> pdb=" O LEU E 526 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE E 531 " --> pdb=" O LEU E 527 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 553 removed outlier: 3.681A pdb=" N THR E 549 " --> pdb=" O PRO E 545 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TRP E 551 " --> pdb=" O LEU E 547 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY E 553 " --> pdb=" O THR E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 569 removed outlier: 3.710A pdb=" N ALA E 566 " --> pdb=" O ILE E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 609 removed outlier: 3.581A pdb=" N GLU E 607 " --> pdb=" O GLN E 603 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP E 609 " --> pdb=" O LEU E 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.621A pdb=" N ARG E 635 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 660 Processing helix chain 'E' and resid 672 through 677 Processing helix chain 'E' and resid 686 through 711 removed outlier: 3.692A pdb=" N ILE E 690 " --> pdb=" O ASP E 686 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N CYS E 691 " --> pdb=" O LEU E 687 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLN E 692 " --> pdb=" O THR E 688 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N CYS E 695 " --> pdb=" O CYS E 691 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU E 701 " --> pdb=" O LEU E 697 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG E 708 " --> pdb=" O GLU E 704 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG E 709 " --> pdb=" O SER E 705 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU E 710 " --> pdb=" O GLU E 706 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 740 removed outlier: 4.137A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 743 No H-bonds generated for 'chain 'E' and resid 741 through 743' Processing helix chain 'E' and resid 751 through 762 removed outlier: 3.611A pdb=" N TYR E 755 " --> pdb=" O ASP E 751 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 65 removed outlier: 4.119A pdb=" N ARG F 64 " --> pdb=" O GLY F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 92 Processing helix chain 'F' and resid 135 through 140 removed outlier: 4.410A pdb=" N LEU F 140 " --> pdb=" O LYS F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 196 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 209 through 226 removed outlier: 4.655A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 234 removed outlier: 4.180A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS F 231 " --> pdb=" O PRO F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 261 Processing helix chain 'F' and resid 271 through 275 removed outlier: 3.532A pdb=" N ILE F 274 " --> pdb=" O GLY F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 296 Processing helix chain 'F' and resid 306 through 309 Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 319 through 334 Processing helix chain 'F' and resid 354 through 358 removed outlier: 3.619A pdb=" N ARG F 358 " --> pdb=" O PRO F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 383 removed outlier: 3.671A pdb=" N LEU F 381 " --> pdb=" O ARG F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 402 removed outlier: 3.534A pdb=" N GLU F 402 " --> pdb=" O GLN F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 425 Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.521A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER F 459 " --> pdb=" O ALA F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 removed outlier: 3.510A pdb=" N ILE F 479 " --> pdb=" O TRP F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 499 removed outlier: 4.721A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 501 through 506 removed outlier: 4.089A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 535 removed outlier: 4.226A pdb=" N ALA F 530 " --> pdb=" O LEU F 526 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE F 531 " --> pdb=" O LEU F 527 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 553 removed outlier: 3.682A pdb=" N THR F 549 " --> pdb=" O PRO F 545 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TRP F 551 " --> pdb=" O LEU F 547 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY F 553 " --> pdb=" O THR F 549 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 569 removed outlier: 3.711A pdb=" N ALA F 566 " --> pdb=" O ILE F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 600 through 609 removed outlier: 3.581A pdb=" N GLU F 607 " --> pdb=" O GLN F 603 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP F 609 " --> pdb=" O LEU F 605 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.620A pdb=" N ARG F 635 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 660 Processing helix chain 'F' and resid 672 through 677 Processing helix chain 'F' and resid 686 through 711 removed outlier: 3.693A pdb=" N ILE F 690 " --> pdb=" O ASP F 686 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N CYS F 691 " --> pdb=" O LEU F 687 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLN F 692 " --> pdb=" O THR F 688 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N CYS F 695 " --> pdb=" O CYS F 691 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU F 701 " --> pdb=" O LEU F 697 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU F 706 " --> pdb=" O SER F 702 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG F 708 " --> pdb=" O GLU F 704 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG F 709 " --> pdb=" O SER F 705 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU F 710 " --> pdb=" O GLU F 706 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 740 removed outlier: 4.137A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 743 No H-bonds generated for 'chain 'F' and resid 741 through 743' Processing helix chain 'F' and resid 751 through 762 removed outlier: 3.610A pdb=" N TYR F 755 " --> pdb=" O ASP F 751 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 42 removed outlier: 3.505A pdb=" N ALA A 67 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A 101 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA3, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA4, first strand: chain 'A' and resid 266 through 269 removed outlier: 3.671A pdb=" N ASP A 304 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 342 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 301 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET A 344 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 573 through 575 removed outlier: 6.486A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 514 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 643 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A 517 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 38 through 42 removed outlier: 3.504A pdb=" N ALA B 67 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER B 101 " --> pdb=" O LYS B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AA8, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AA9, first strand: chain 'B' and resid 266 through 269 removed outlier: 3.670A pdb=" N ASP B 304 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE B 342 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 301 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET B 344 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 573 through 575 removed outlier: 6.486A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 514 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B 643 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR B 517 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 38 through 42 removed outlier: 3.505A pdb=" N ALA C 67 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AB4, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AB5, first strand: chain 'C' and resid 266 through 269 removed outlier: 3.670A pdb=" N ASP C 304 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE C 342 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 301 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET C 344 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 573 through 575 removed outlier: 6.486A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 514 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE C 643 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR C 517 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 38 through 42 removed outlier: 3.505A pdb=" N ALA D 67 " --> pdb=" O LEU D 59 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AB9, first strand: chain 'D' and resid 153 through 155 Processing sheet with id=AC1, first strand: chain 'D' and resid 266 through 269 removed outlier: 3.671A pdb=" N ASP D 304 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE D 342 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE D 301 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET D 344 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 573 through 575 removed outlier: 6.486A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D 514 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE D 643 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR D 517 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 38 through 42 removed outlier: 3.505A pdb=" N ALA E 67 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 145 through 147 Processing sheet with id=AC5, first strand: chain 'E' and resid 153 through 155 Processing sheet with id=AC6, first strand: chain 'E' and resid 266 through 269 removed outlier: 3.670A pdb=" N ASP E 304 " --> pdb=" O ILE E 269 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE E 342 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE E 301 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET E 344 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 573 through 575 removed outlier: 6.487A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL E 514 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE E 643 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR E 517 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 38 through 42 removed outlier: 3.504A pdb=" N ALA F 67 " --> pdb=" O LEU F 59 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER F 101 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 145 through 147 Processing sheet with id=AD1, first strand: chain 'F' and resid 153 through 155 Processing sheet with id=AD2, first strand: chain 'F' and resid 266 through 269 removed outlier: 3.671A pdb=" N ASP F 304 " --> pdb=" O ILE F 269 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE F 342 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE F 301 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET F 344 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 573 through 575 removed outlier: 6.486A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL F 514 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE F 643 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR F 517 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1098 hydrogen bonds defined for protein. 3096 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: 11.89 Time building geometry restraints manager: 13.61 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: 11924 1.34 - 1.46: 6187 1.46 - 1.58: 17227 1.58 - 1.70: 2 1.70 - 1.82: 300 Bond restraints: 35640 Sorted by residual: bond pdb=" CB VAL A 514 " pdb=" CG1 VAL A 514 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.39e+00 bond pdb=" CB VAL D 514 " pdb=" CG1 VAL D 514 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.37e+00 bond pdb=" CB VAL C 514 " pdb=" CG1 VAL C 514 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.36e+00 bond pdb=" CB VAL F 514 " pdb=" CG1 VAL F 514 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.35e+00 bond pdb=" CB VAL E 514 " pdb=" CG1 VAL E 514 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.31e+00 ... (remaining 35635 not shown) Histogram of bond angle deviations from ideal: 99.57 - 106.74: 1325 106.74 - 113.90: 20144 113.90 - 121.06: 16665 121.06 - 128.22: 9767 128.22 - 135.39: 225 Bond angle restraints: 48126 Sorted by residual: angle pdb=" CB GLU B 546 " pdb=" CG GLU B 546 " pdb=" CD GLU B 546 " ideal model delta sigma weight residual 112.60 122.00 -9.40 1.70e+00 3.46e-01 3.06e+01 angle pdb=" CB GLU C 546 " pdb=" CG GLU C 546 " pdb=" CD GLU C 546 " ideal model delta sigma weight residual 112.60 121.99 -9.39 1.70e+00 3.46e-01 3.05e+01 angle pdb=" CB GLU A 546 " pdb=" CG GLU A 546 " pdb=" CD GLU A 546 " ideal model delta sigma weight residual 112.60 121.98 -9.38 1.70e+00 3.46e-01 3.04e+01 angle pdb=" CB GLU D 546 " pdb=" CG GLU D 546 " pdb=" CD GLU D 546 " ideal model delta sigma weight residual 112.60 121.98 -9.38 1.70e+00 3.46e-01 3.04e+01 angle pdb=" CB GLU E 546 " pdb=" CG GLU E 546 " pdb=" CD GLU E 546 " ideal model delta sigma weight residual 112.60 121.97 -9.37 1.70e+00 3.46e-01 3.04e+01 ... (remaining 48121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 19347 17.22 - 34.44: 2268 34.44 - 51.66: 423 51.66 - 68.87: 138 68.87 - 86.09: 48 Dihedral angle restraints: 22224 sinusoidal: 9360 harmonic: 12864 Sorted by residual: dihedral pdb=" CA PHE F 506 " pdb=" C PHE F 506 " pdb=" N GLY F 507 " pdb=" CA GLY F 507 " ideal model delta harmonic sigma weight residual 180.00 153.27 26.73 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA PHE A 506 " pdb=" C PHE A 506 " pdb=" N GLY A 507 " pdb=" CA GLY A 507 " ideal model delta harmonic sigma weight residual 180.00 153.28 26.72 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA PHE C 506 " pdb=" C PHE C 506 " pdb=" N GLY C 507 " pdb=" CA GLY C 507 " ideal model delta harmonic sigma weight residual 180.00 153.29 26.71 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 22221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4114 0.066 - 0.132: 1032 0.132 - 0.198: 224 0.198 - 0.264: 30 0.264 - 0.330: 6 Chirality restraints: 5406 Sorted by residual: chirality pdb=" CB ILE C 114 " pdb=" CA ILE C 114 " pdb=" CG1 ILE C 114 " pdb=" CG2 ILE C 114 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB ILE F 114 " pdb=" CA ILE F 114 " pdb=" CG1 ILE F 114 " pdb=" CG2 ILE F 114 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CB ILE D 114 " pdb=" CA ILE D 114 " pdb=" CG1 ILE D 114 " pdb=" CG2 ILE D 114 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 5403 not shown) Planarity restraints: 6390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 122 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.55e+00 pdb=" C THR E 122 " 0.051 2.00e-02 2.50e+03 pdb=" O THR E 122 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL E 123 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 122 " -0.015 2.00e-02 2.50e+03 2.90e-02 8.44e+00 pdb=" C THR F 122 " 0.050 2.00e-02 2.50e+03 pdb=" O THR F 122 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL F 123 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 122 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.42e+00 pdb=" C THR B 122 " -0.050 2.00e-02 2.50e+03 pdb=" O THR B 122 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL B 123 " 0.017 2.00e-02 2.50e+03 ... (remaining 6387 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3649 2.74 - 3.28: 33927 3.28 - 3.82: 56495 3.82 - 4.36: 63706 4.36 - 4.90: 105050 Nonbonded interactions: 262827 Sorted by model distance: nonbonded pdb=" OG SER D 276 " pdb=" OG SER E 326 " model vdw 2.198 2.440 nonbonded pdb=" O THR A 122 " pdb=" OG1 THR A 122 " model vdw 2.210 2.440 nonbonded pdb=" O THR F 122 " pdb=" OG1 THR F 122 " model vdw 2.211 2.440 nonbonded pdb=" O THR E 122 " pdb=" OG1 THR E 122 " model vdw 2.211 2.440 nonbonded pdb=" O THR D 122 " pdb=" OG1 THR D 122 " model vdw 2.211 2.440 ... (remaining 262822 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' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 0.040 Extract box with map and model: 5.860 Check model and map are aligned: 0.490 Set scattering table: 0.320 Process input model: 85.530 Find NCS groups from input model: 2.240 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 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 : 0.006 0.077 35640 Z= 0.414 Angle : 1.078 12.875 48126 Z= 0.569 Chirality : 0.061 0.330 5406 Planarity : 0.008 0.066 6390 Dihedral : 15.769 86.094 13860 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.19 % Allowed : 6.79 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -4.45 (0.10), residues: 4422 helix: -3.19 (0.09), residues: 1602 sheet: -2.97 (0.19), residues: 558 loop : -2.74 (0.11), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 476 HIS 0.009 0.002 HIS E 404 PHE 0.035 0.003 PHE F 552 TYR 0.018 0.002 TYR F 173 ARG 0.008 0.001 ARG B 465 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 477 time to evaluate : 3.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.1151 (mmp) cc_final: 0.0276 (tpt) REVERT: A 47 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.6925 (p0) REVERT: A 80 GLU cc_start: 0.4169 (OUTLIER) cc_final: 0.3960 (tp30) REVERT: A 114 ILE cc_start: 0.5048 (OUTLIER) cc_final: 0.4733 (mt) REVERT: A 639 LEU cc_start: 0.9362 (mt) cc_final: 0.9025 (mp) REVERT: A 640 ASP cc_start: 0.8444 (p0) cc_final: 0.7872 (p0) REVERT: A 687 LEU cc_start: 0.9338 (pt) cc_final: 0.9051 (mp) REVERT: B 32 ILE cc_start: 0.5824 (OUTLIER) cc_final: 0.5581 (mp) REVERT: B 46 MET cc_start: 0.1256 (mmp) cc_final: 0.0308 (tpt) REVERT: B 47 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7214 (p0) REVERT: B 114 ILE cc_start: 0.4839 (OUTLIER) cc_final: 0.4602 (mt) REVERT: B 242 LEU cc_start: 0.9410 (mt) cc_final: 0.8429 (tt) REVERT: B 604 ILE cc_start: 0.9674 (mt) cc_final: 0.9446 (mm) REVERT: B 620 ILE cc_start: 0.9467 (pt) cc_final: 0.9235 (tp) REVERT: B 639 LEU cc_start: 0.9101 (mt) cc_final: 0.8661 (mp) REVERT: B 640 ASP cc_start: 0.8336 (p0) cc_final: 0.7864 (p0) REVERT: B 687 LEU cc_start: 0.9007 (pt) cc_final: 0.8789 (mp) REVERT: B 764 GLN cc_start: 0.7319 (tt0) cc_final: 0.6452 (tp40) REVERT: C 32 ILE cc_start: 0.4499 (OUTLIER) cc_final: 0.4083 (mp) REVERT: C 46 MET cc_start: -0.0833 (mmp) cc_final: -0.1369 (tpt) REVERT: C 47 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6509 (p0) REVERT: C 114 ILE cc_start: 0.5465 (OUTLIER) cc_final: 0.5230 (mt) REVERT: C 242 LEU cc_start: 0.9651 (mt) cc_final: 0.9106 (tt) REVERT: C 332 MET cc_start: 0.8975 (tpp) cc_final: 0.8640 (tpp) REVERT: C 639 LEU cc_start: 0.9162 (mt) cc_final: 0.8829 (mp) REVERT: C 640 ASP cc_start: 0.8151 (p0) cc_final: 0.7590 (p0) REVERT: C 661 LEU cc_start: 0.9186 (mt) cc_final: 0.8961 (pp) REVERT: C 687 LEU cc_start: 0.9133 (pt) cc_final: 0.8901 (mp) REVERT: C 764 GLN cc_start: 0.7233 (tt0) cc_final: 0.7016 (tt0) REVERT: D 46 MET cc_start: 0.1152 (mmp) cc_final: 0.0138 (tpt) REVERT: D 47 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6891 (p0) REVERT: D 307 ASP cc_start: 0.9269 (p0) cc_final: 0.8735 (m-30) REVERT: D 353 ILE cc_start: 0.9334 (mt) cc_final: 0.8939 (mp) REVERT: D 464 LEU cc_start: 0.7986 (tt) cc_final: 0.7722 (tp) REVERT: D 639 LEU cc_start: 0.9372 (mt) cc_final: 0.9000 (mp) REVERT: D 640 ASP cc_start: 0.8441 (p0) cc_final: 0.7922 (p0) REVERT: D 687 LEU cc_start: 0.9280 (pt) cc_final: 0.9037 (mp) REVERT: E 32 ILE cc_start: 0.5599 (OUTLIER) cc_final: 0.5327 (mp) REVERT: E 46 MET cc_start: 0.0572 (mmp) cc_final: -0.0384 (tpt) REVERT: E 47 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7382 (p0) REVERT: E 604 ILE cc_start: 0.9635 (mt) cc_final: 0.9426 (mm) REVERT: E 620 ILE cc_start: 0.9483 (pt) cc_final: 0.9248 (tp) REVERT: E 639 LEU cc_start: 0.9132 (mt) cc_final: 0.8685 (mp) REVERT: E 640 ASP cc_start: 0.8314 (p0) cc_final: 0.7925 (p0) REVERT: F 46 MET cc_start: -0.0479 (mmp) cc_final: -0.0832 (tpt) REVERT: F 47 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6704 (p0) REVERT: F 219 MET cc_start: 0.8553 (mtt) cc_final: 0.8319 (mmm) REVERT: F 332 MET cc_start: 0.8914 (tpp) cc_final: 0.8637 (tpp) REVERT: F 640 ASP cc_start: 0.8167 (p0) cc_final: 0.7720 (p0) REVERT: F 651 LYS cc_start: 0.9520 (mttt) cc_final: 0.9319 (ptmm) REVERT: F 661 LEU cc_start: 0.9210 (mt) cc_final: 0.9002 (pp) REVERT: F 687 LEU cc_start: 0.9133 (pt) cc_final: 0.8913 (mp) outliers start: 84 outliers final: 16 residues processed: 555 average time/residue: 0.5186 time to fit residues: 445.5399 Evaluate side-chains 280 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 251 time to evaluate : 3.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 5.9990 chunk 336 optimal weight: 0.0670 chunk 186 optimal weight: 7.9990 chunk 114 optimal weight: 0.0470 chunk 227 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 chunk 348 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 211 optimal weight: 2.9990 chunk 259 optimal weight: 0.9980 chunk 403 optimal weight: 7.9990 overall best weight: 1.2220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 ASN A 285 ASN A 384 HIS A 401 ASN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN B 215 GLN B 285 ASN B 384 HIS B 401 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN C 90 ASN C 91 ASN C 199 ASN C 285 ASN C 384 HIS C 401 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN D 90 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN D 285 ASN D 337 GLN D 384 HIS D 401 ASN ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN ** D 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN E 285 ASN E 337 GLN E 384 HIS E 401 ASN ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN E 750 ASN ** E 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 ASN F 91 ASN F 199 ASN F 215 GLN F 285 ASN F 337 GLN F 384 HIS F 401 ASN ** F 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35640 Z= 0.192 Angle : 0.644 10.345 48126 Z= 0.320 Chirality : 0.044 0.174 5406 Planarity : 0.004 0.050 6390 Dihedral : 5.140 19.806 4842 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.39 % Allowed : 4.94 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -2.87 (0.11), residues: 4422 helix: -1.43 (0.12), residues: 1632 sheet: -2.62 (0.19), residues: 564 loop : -2.02 (0.12), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 454 HIS 0.002 0.001 HIS C 404 PHE 0.019 0.001 PHE E 363 TYR 0.019 0.002 TYR D 244 ARG 0.007 0.000 ARG D 365 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 305 time to evaluate : 4.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.1422 (mmp) cc_final: 0.0447 (tpt) REVERT: A 639 LEU cc_start: 0.9259 (mt) cc_final: 0.8727 (mp) REVERT: A 687 LEU cc_start: 0.9215 (pt) cc_final: 0.8909 (mp) REVERT: B 46 MET cc_start: 0.1671 (mmp) cc_final: 0.0451 (tpt) REVERT: B 242 LEU cc_start: 0.9513 (mt) cc_final: 0.9083 (tt) REVERT: B 508 MET cc_start: 0.8092 (tpp) cc_final: 0.7660 (tpp) REVERT: B 639 LEU cc_start: 0.9124 (mt) cc_final: 0.8552 (mp) REVERT: B 640 ASP cc_start: 0.8182 (p0) cc_final: 0.7833 (p0) REVERT: B 687 LEU cc_start: 0.8750 (pt) cc_final: 0.8448 (mp) REVERT: B 764 GLN cc_start: 0.7347 (tt0) cc_final: 0.6536 (tp40) REVERT: C 46 MET cc_start: -0.0640 (mmp) cc_final: -0.1497 (tpt) REVERT: C 242 LEU cc_start: 0.9559 (mt) cc_final: 0.9240 (tt) REVERT: C 332 MET cc_start: 0.8947 (tpp) cc_final: 0.8668 (tpp) REVERT: C 639 LEU cc_start: 0.9175 (mt) cc_final: 0.8604 (mp) REVERT: C 640 ASP cc_start: 0.7856 (p0) cc_final: 0.7474 (p0) REVERT: C 687 LEU cc_start: 0.9088 (pt) cc_final: 0.8814 (mp) REVERT: C 764 GLN cc_start: 0.7348 (tt0) cc_final: 0.7056 (tt0) REVERT: D 46 MET cc_start: 0.1877 (mmp) cc_final: 0.0931 (tpt) REVERT: D 307 ASP cc_start: 0.9281 (p0) cc_final: 0.8808 (m-30) REVERT: D 464 LEU cc_start: 0.7581 (tt) cc_final: 0.7337 (tp) REVERT: D 687 LEU cc_start: 0.9149 (pt) cc_final: 0.8892 (mp) REVERT: E 46 MET cc_start: 0.0681 (mmp) cc_final: -0.0518 (tpt) REVERT: E 332 MET cc_start: 0.8969 (ttt) cc_final: 0.8623 (tmm) REVERT: E 639 LEU cc_start: 0.9019 (mt) cc_final: 0.8510 (mp) REVERT: E 640 ASP cc_start: 0.8214 (p0) cc_final: 0.7882 (p0) REVERT: E 740 MET cc_start: 0.9048 (tpp) cc_final: 0.8809 (tpp) REVERT: F 46 MET cc_start: -0.0134 (mmp) cc_final: -0.0860 (tpt) REVERT: F 508 MET cc_start: 0.8305 (tpt) cc_final: 0.8094 (tpt) REVERT: F 547 LEU cc_start: 0.9635 (tp) cc_final: 0.9191 (tp) REVERT: F 640 ASP cc_start: 0.7866 (p0) cc_final: 0.7504 (p0) REVERT: F 687 LEU cc_start: 0.9125 (pt) cc_final: 0.8838 (mp) outliers start: 15 outliers final: 0 residues processed: 320 average time/residue: 0.4346 time to fit residues: 233.9513 Evaluate side-chains 206 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 4.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 0.3980 chunk 125 optimal weight: 3.9990 chunk 335 optimal weight: 0.7980 chunk 274 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 403 optimal weight: 5.9990 chunk 436 optimal weight: 2.9990 chunk 359 optimal weight: 4.9990 chunk 400 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 324 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 ASN ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN B 401 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 ASN C 401 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN C 750 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN ** D 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 ASN E 337 GLN E 401 ASN ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 660 ASN ** E 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 GLN F 401 ASN ** F 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 750 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 35640 Z= 0.171 Angle : 0.599 9.790 48126 Z= 0.296 Chirality : 0.044 0.168 5406 Planarity : 0.004 0.054 6390 Dihedral : 4.737 23.458 4842 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.16 % Allowed : 5.20 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -2.08 (0.12), residues: 4422 helix: -0.74 (0.13), residues: 1644 sheet: -2.27 (0.19), residues: 570 loop : -1.55 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 551 HIS 0.003 0.001 HIS D 404 PHE 0.024 0.001 PHE A 363 TYR 0.011 0.001 TYR C 203 ARG 0.013 0.000 ARG B 560 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 254 time to evaluate : 4.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.1639 (mmp) cc_final: 0.0604 (tpt) REVERT: A 343 VAL cc_start: 0.9332 (t) cc_final: 0.9127 (m) REVERT: A 639 LEU cc_start: 0.9295 (mt) cc_final: 0.8884 (mp) REVERT: A 687 LEU cc_start: 0.9247 (pt) cc_final: 0.9014 (mp) REVERT: A 740 MET cc_start: 0.9065 (tpp) cc_final: 0.8511 (tpp) REVERT: B 46 MET cc_start: 0.1786 (mmp) cc_final: 0.0507 (tpt) REVERT: B 242 LEU cc_start: 0.9660 (mt) cc_final: 0.9185 (tp) REVERT: B 275 MET cc_start: 0.8953 (mmm) cc_final: 0.8394 (mmm) REVERT: B 508 MET cc_start: 0.8357 (tpp) cc_final: 0.8020 (tpp) REVERT: B 550 MET cc_start: 0.9086 (mtm) cc_final: 0.8781 (mtt) REVERT: B 639 LEU cc_start: 0.8981 (mt) cc_final: 0.8276 (mp) REVERT: B 640 ASP cc_start: 0.8015 (p0) cc_final: 0.7752 (p0) REVERT: B 687 LEU cc_start: 0.8910 (pt) cc_final: 0.8666 (mp) REVERT: B 764 GLN cc_start: 0.7120 (tt0) cc_final: 0.6403 (tp40) REVERT: C 46 MET cc_start: -0.0460 (mmp) cc_final: -0.1397 (tpt) REVERT: C 242 LEU cc_start: 0.9611 (mt) cc_final: 0.9306 (tp) REVERT: C 344 MET cc_start: 0.8774 (mtp) cc_final: 0.8501 (mtt) REVERT: C 639 LEU cc_start: 0.9048 (mt) cc_final: 0.8603 (mp) REVERT: C 687 LEU cc_start: 0.9142 (pt) cc_final: 0.8868 (mp) REVERT: C 740 MET cc_start: 0.9402 (tpp) cc_final: 0.9073 (tpp) REVERT: C 764 GLN cc_start: 0.7312 (tt0) cc_final: 0.6919 (tt0) REVERT: D 46 MET cc_start: 0.1889 (mmp) cc_final: 0.0846 (tpt) REVERT: D 275 MET cc_start: 0.8921 (mmm) cc_final: 0.8465 (mmm) REVERT: D 307 ASP cc_start: 0.9284 (p0) cc_final: 0.8812 (m-30) REVERT: D 464 LEU cc_start: 0.7542 (tt) cc_final: 0.7221 (tp) REVERT: D 639 LEU cc_start: 0.9217 (mt) cc_final: 0.8692 (mp) REVERT: D 687 LEU cc_start: 0.9244 (pt) cc_final: 0.9038 (mp) REVERT: D 740 MET cc_start: 0.9166 (tpp) cc_final: 0.8663 (tpp) REVERT: E 46 MET cc_start: 0.0771 (mmp) cc_final: -0.0464 (tpt) REVERT: E 242 LEU cc_start: 0.9485 (mt) cc_final: 0.9062 (tp) REVERT: E 508 MET cc_start: 0.8503 (mmm) cc_final: 0.8244 (tpp) REVERT: E 639 LEU cc_start: 0.9043 (mt) cc_final: 0.8361 (mp) REVERT: E 640 ASP cc_start: 0.8003 (p0) cc_final: 0.7736 (p0) REVERT: E 740 MET cc_start: 0.9191 (tpp) cc_final: 0.8903 (tpp) REVERT: F 46 MET cc_start: -0.0010 (mmp) cc_final: -0.0876 (tpt) REVERT: F 242 LEU cc_start: 0.9587 (mt) cc_final: 0.9309 (tp) REVERT: F 332 MET cc_start: 0.9144 (ttt) cc_final: 0.8782 (tmm) REVERT: F 687 LEU cc_start: 0.9180 (pt) cc_final: 0.8920 (mp) REVERT: F 740 MET cc_start: 0.9388 (tpp) cc_final: 0.9081 (tpp) outliers start: 6 outliers final: 0 residues processed: 260 average time/residue: 0.4284 time to fit residues: 191.1872 Evaluate side-chains 215 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 4.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 0.8980 chunk 303 optimal weight: 0.9980 chunk 209 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 192 optimal weight: 4.9990 chunk 271 optimal weight: 1.9990 chunk 405 optimal weight: 9.9990 chunk 429 optimal weight: 5.9990 chunk 211 optimal weight: 10.0000 chunk 384 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 35640 Z= 0.283 Angle : 0.649 9.851 48126 Z= 0.329 Chirality : 0.045 0.162 5406 Planarity : 0.004 0.042 6390 Dihedral : 4.752 21.053 4842 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.16 % Allowed : 4.60 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.69 (0.12), residues: 4422 helix: -0.46 (0.13), residues: 1644 sheet: -2.21 (0.19), residues: 576 loop : -1.24 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 551 HIS 0.008 0.002 HIS F 183 PHE 0.018 0.002 PHE A 363 TYR 0.007 0.001 TYR C 203 ARG 0.012 0.001 ARG D 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 226 time to evaluate : 4.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.1847 (mmp) cc_final: 0.0671 (tpt) REVERT: A 740 MET cc_start: 0.9318 (tpp) cc_final: 0.8820 (tpp) REVERT: B 46 MET cc_start: 0.1821 (mmp) cc_final: 0.0539 (tpt) REVERT: B 242 LEU cc_start: 0.9668 (mt) cc_final: 0.9100 (tp) REVERT: B 344 MET cc_start: 0.8694 (mtp) cc_final: 0.8476 (mtp) REVERT: B 508 MET cc_start: 0.8519 (tpp) cc_final: 0.8246 (tpp) REVERT: B 550 MET cc_start: 0.9022 (mtm) cc_final: 0.8573 (mtt) REVERT: B 639 LEU cc_start: 0.9040 (mt) cc_final: 0.8501 (mp) REVERT: B 764 GLN cc_start: 0.7416 (tt0) cc_final: 0.6443 (tp40) REVERT: C 46 MET cc_start: -0.0136 (mmp) cc_final: -0.1091 (tpt) REVERT: C 242 LEU cc_start: 0.9607 (mt) cc_final: 0.9099 (tt) REVERT: C 639 LEU cc_start: 0.9141 (mt) cc_final: 0.8675 (mp) REVERT: C 687 LEU cc_start: 0.9353 (pt) cc_final: 0.9118 (mp) REVERT: C 740 MET cc_start: 0.9509 (tpp) cc_final: 0.9259 (tpp) REVERT: D 46 MET cc_start: 0.2041 (mmp) cc_final: 0.0824 (tpt) REVERT: D 275 MET cc_start: 0.8892 (mmm) cc_final: 0.8436 (mmm) REVERT: D 464 LEU cc_start: 0.7507 (tt) cc_final: 0.7249 (tp) REVERT: D 639 LEU cc_start: 0.9240 (mt) cc_final: 0.8639 (mp) REVERT: D 687 LEU cc_start: 0.9283 (pt) cc_final: 0.9053 (mp) REVERT: D 740 MET cc_start: 0.9314 (tpp) cc_final: 0.8847 (tpp) REVERT: E 46 MET cc_start: 0.0853 (mmp) cc_final: -0.0453 (tpt) REVERT: E 242 LEU cc_start: 0.9517 (mt) cc_final: 0.9033 (tp) REVERT: E 508 MET cc_start: 0.8621 (mmm) cc_final: 0.8397 (tpp) REVERT: E 639 LEU cc_start: 0.9069 (mt) cc_final: 0.8413 (mp) REVERT: E 740 MET cc_start: 0.9325 (tpp) cc_final: 0.9024 (tpp) REVERT: F 46 MET cc_start: 0.0032 (mmp) cc_final: -0.0797 (tpt) REVERT: F 242 LEU cc_start: 0.9607 (mt) cc_final: 0.9125 (tt) REVERT: F 687 LEU cc_start: 0.9379 (pt) cc_final: 0.9127 (mp) REVERT: F 740 MET cc_start: 0.9514 (tpp) cc_final: 0.9196 (tpp) REVERT: F 764 GLN cc_start: 0.6914 (tt0) cc_final: 0.6226 (tp40) outliers start: 6 outliers final: 0 residues processed: 232 average time/residue: 0.4329 time to fit residues: 170.8023 Evaluate side-chains 191 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 4.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 3.9990 chunk 243 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 319 optimal weight: 0.5980 chunk 177 optimal weight: 0.9990 chunk 366 optimal weight: 5.9990 chunk 296 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 219 optimal weight: 1.9990 chunk 385 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 HIS ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN D 384 HIS ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 HIS ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 384 HIS ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35640 Z= 0.186 Angle : 0.592 10.585 48126 Z= 0.291 Chirality : 0.044 0.179 5406 Planarity : 0.004 0.042 6390 Dihedral : 4.576 19.690 4842 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.41 (0.13), residues: 4422 helix: -0.22 (0.13), residues: 1650 sheet: -2.05 (0.20), residues: 576 loop : -1.09 (0.13), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 551 HIS 0.007 0.001 HIS A 384 PHE 0.014 0.001 PHE E 552 TYR 0.008 0.001 TYR C 244 ARG 0.010 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 4.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.1860 (mmp) cc_final: 0.0668 (tpt) REVERT: A 332 MET cc_start: 0.9274 (ppp) cc_final: 0.9022 (ppp) REVERT: A 411 LEU cc_start: 0.9351 (mt) cc_final: 0.9124 (pp) REVERT: A 687 LEU cc_start: 0.9280 (pt) cc_final: 0.9049 (mp) REVERT: A 740 MET cc_start: 0.9299 (tpp) cc_final: 0.8758 (tpp) REVERT: B 46 MET cc_start: 0.1808 (mmp) cc_final: 0.0516 (tpt) REVERT: B 242 LEU cc_start: 0.9658 (mt) cc_final: 0.9089 (tp) REVERT: B 344 MET cc_start: 0.8707 (mtp) cc_final: 0.8452 (mtp) REVERT: B 550 MET cc_start: 0.8992 (mtm) cc_final: 0.8626 (mtt) REVERT: B 639 LEU cc_start: 0.8884 (mt) cc_final: 0.8185 (mp) REVERT: C 46 MET cc_start: -0.0092 (mmp) cc_final: -0.1055 (tpt) REVERT: C 242 LEU cc_start: 0.9576 (mt) cc_final: 0.9187 (tp) REVERT: C 639 LEU cc_start: 0.9068 (mt) cc_final: 0.8615 (mp) REVERT: C 687 LEU cc_start: 0.9335 (pt) cc_final: 0.9112 (mp) REVERT: C 740 MET cc_start: 0.9455 (tpp) cc_final: 0.9144 (tpp) REVERT: D 46 MET cc_start: 0.2042 (mmp) cc_final: 0.0816 (tpt) REVERT: D 242 LEU cc_start: 0.9534 (mt) cc_final: 0.9024 (tt) REVERT: D 275 MET cc_start: 0.8966 (mmm) cc_final: 0.8764 (mmm) REVERT: D 332 MET cc_start: 0.9260 (ppp) cc_final: 0.9018 (ppp) REVERT: D 464 LEU cc_start: 0.7270 (tt) cc_final: 0.6836 (tp) REVERT: D 639 LEU cc_start: 0.9193 (mt) cc_final: 0.8609 (mp) REVERT: D 687 LEU cc_start: 0.9263 (pt) cc_final: 0.9024 (mp) REVERT: D 740 MET cc_start: 0.9279 (tpp) cc_final: 0.8908 (tpp) REVERT: E 46 MET cc_start: 0.0841 (mmp) cc_final: -0.0469 (tpt) REVERT: E 242 LEU cc_start: 0.9610 (mt) cc_final: 0.9078 (tp) REVERT: E 508 MET cc_start: 0.8655 (mmm) cc_final: 0.8272 (tpp) REVERT: E 639 LEU cc_start: 0.8964 (mt) cc_final: 0.8301 (mp) REVERT: E 740 MET cc_start: 0.9325 (tpp) cc_final: 0.8999 (tpp) REVERT: F 46 MET cc_start: 0.0037 (mmp) cc_final: -0.0801 (tpt) REVERT: F 242 LEU cc_start: 0.9616 (mt) cc_final: 0.9179 (tp) REVERT: F 687 LEU cc_start: 0.9385 (pt) cc_final: 0.9172 (mp) REVERT: F 740 MET cc_start: 0.9435 (tpp) cc_final: 0.9161 (tpp) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.4125 time to fit residues: 169.6819 Evaluate side-chains 198 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 4.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 4.9990 chunk 386 optimal weight: 0.0070 chunk 84 optimal weight: 0.2980 chunk 251 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 429 optimal weight: 2.9990 chunk 356 optimal weight: 0.9990 chunk 198 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 overall best weight: 1.6604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN D 103 GLN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 35640 Z= 0.194 Angle : 0.595 9.743 48126 Z= 0.296 Chirality : 0.044 0.161 5406 Planarity : 0.004 0.040 6390 Dihedral : 4.492 18.880 4842 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.25 (0.13), residues: 4422 helix: -0.15 (0.13), residues: 1650 sheet: -1.89 (0.21), residues: 516 loop : -1.02 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 551 HIS 0.004 0.001 HIS D 384 PHE 0.021 0.001 PHE B 563 TYR 0.007 0.001 TYR C 244 ARG 0.007 0.000 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 4.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.1872 (mmp) cc_final: 0.0684 (tpt) REVERT: A 411 LEU cc_start: 0.9344 (mt) cc_final: 0.9089 (pp) REVERT: A 460 ASN cc_start: 0.8605 (p0) cc_final: 0.8249 (p0) REVERT: A 740 MET cc_start: 0.9297 (tpp) cc_final: 0.8885 (tpp) REVERT: B 46 MET cc_start: 0.1544 (mmp) cc_final: 0.0446 (tpt) REVERT: B 242 LEU cc_start: 0.9665 (mt) cc_final: 0.9074 (tp) REVERT: B 550 MET cc_start: 0.9009 (mtm) cc_final: 0.8596 (mtt) REVERT: C 46 MET cc_start: -0.0048 (mmp) cc_final: -0.1024 (tpt) REVERT: C 242 LEU cc_start: 0.9591 (mt) cc_final: 0.9193 (tp) REVERT: C 332 MET cc_start: 0.9320 (tmm) cc_final: 0.9112 (tmm) REVERT: C 639 LEU cc_start: 0.9085 (mt) cc_final: 0.8732 (mp) REVERT: C 687 LEU cc_start: 0.9337 (pt) cc_final: 0.9091 (mp) REVERT: C 740 MET cc_start: 0.9440 (tpp) cc_final: 0.9126 (tpp) REVERT: C 757 MET cc_start: 0.8023 (mmp) cc_final: 0.7713 (mmp) REVERT: D 46 MET cc_start: 0.1593 (mmp) cc_final: 0.0285 (tpt) REVERT: D 242 LEU cc_start: 0.9567 (mt) cc_final: 0.8982 (tt) REVERT: D 460 ASN cc_start: 0.8509 (p0) cc_final: 0.8095 (p0) REVERT: D 464 LEU cc_start: 0.7557 (tt) cc_final: 0.7116 (tp) REVERT: D 639 LEU cc_start: 0.9164 (mt) cc_final: 0.8594 (mp) REVERT: D 740 MET cc_start: 0.9301 (tpp) cc_final: 0.8929 (tpp) REVERT: E 46 MET cc_start: 0.0705 (mmp) cc_final: -0.0563 (tpt) REVERT: E 242 LEU cc_start: 0.9613 (mt) cc_final: 0.9057 (tp) REVERT: E 508 MET cc_start: 0.8606 (mmm) cc_final: 0.8239 (tpp) REVERT: E 639 LEU cc_start: 0.8840 (mt) cc_final: 0.8090 (mp) REVERT: F 46 MET cc_start: 0.0073 (mmp) cc_final: -0.0775 (tpt) REVERT: F 242 LEU cc_start: 0.9618 (mt) cc_final: 0.9172 (tp) REVERT: F 687 LEU cc_start: 0.9376 (pt) cc_final: 0.9103 (mp) REVERT: F 740 MET cc_start: 0.9382 (tpp) cc_final: 0.9076 (tpp) REVERT: F 757 MET cc_start: 0.8145 (mmp) cc_final: 0.7864 (mmp) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.4415 time to fit residues: 165.7128 Evaluate side-chains 188 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 4.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 chunk 244 optimal weight: 0.4980 chunk 313 optimal weight: 1.9990 chunk 243 optimal weight: 4.9990 chunk 361 optimal weight: 1.9990 chunk 239 optimal weight: 0.6980 chunk 427 optimal weight: 0.8980 chunk 267 optimal weight: 4.9990 chunk 260 optimal weight: 5.9990 chunk 197 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN ** F 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 35640 Z= 0.150 Angle : 0.581 10.029 48126 Z= 0.281 Chirality : 0.044 0.202 5406 Planarity : 0.003 0.043 6390 Dihedral : 4.340 19.327 4842 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.12 (0.13), residues: 4422 helix: -0.06 (0.13), residues: 1686 sheet: -1.62 (0.22), residues: 504 loop : -0.99 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 476 HIS 0.003 0.001 HIS A 404 PHE 0.011 0.001 PHE C 552 TYR 0.008 0.001 TYR C 244 ARG 0.005 0.000 ARG F 560 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 4.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.1813 (mmp) cc_final: 0.0616 (tpt) REVERT: A 242 LEU cc_start: 0.9512 (mt) cc_final: 0.9078 (tp) REVERT: A 411 LEU cc_start: 0.9320 (mt) cc_final: 0.9119 (pp) REVERT: A 460 ASN cc_start: 0.8607 (p0) cc_final: 0.8214 (p0) REVERT: A 740 MET cc_start: 0.9321 (tpp) cc_final: 0.9064 (tpp) REVERT: B 46 MET cc_start: 0.1521 (mmp) cc_final: 0.0402 (tpt) REVERT: B 242 LEU cc_start: 0.9650 (mt) cc_final: 0.9055 (tp) REVERT: B 550 MET cc_start: 0.8901 (mtm) cc_final: 0.8419 (mtt) REVERT: B 740 MET cc_start: 0.7125 (ptt) cc_final: 0.6900 (tpp) REVERT: C 46 MET cc_start: -0.0081 (mmp) cc_final: -0.1054 (tpt) REVERT: C 242 LEU cc_start: 0.9613 (mt) cc_final: 0.9315 (tp) REVERT: C 639 LEU cc_start: 0.8891 (mt) cc_final: 0.8512 (mp) REVERT: C 740 MET cc_start: 0.9372 (tpp) cc_final: 0.9022 (tpp) REVERT: C 757 MET cc_start: 0.7941 (mmp) cc_final: 0.7631 (mmp) REVERT: D 46 MET cc_start: 0.1563 (mmp) cc_final: 0.0262 (tpt) REVERT: D 242 LEU cc_start: 0.9485 (mt) cc_final: 0.8899 (tt) REVERT: D 639 LEU cc_start: 0.9127 (mt) cc_final: 0.8571 (mp) REVERT: D 740 MET cc_start: 0.9308 (tpp) cc_final: 0.9045 (tpp) REVERT: E 46 MET cc_start: 0.0675 (mmp) cc_final: -0.0598 (tpt) REVERT: E 242 LEU cc_start: 0.9538 (mt) cc_final: 0.8981 (tp) REVERT: E 508 MET cc_start: 0.8564 (mmm) cc_final: 0.7974 (tpp) REVERT: E 639 LEU cc_start: 0.8752 (mt) cc_final: 0.8020 (mp) REVERT: F 46 MET cc_start: 0.0038 (mmp) cc_final: -0.0804 (tpt) REVERT: F 242 LEU cc_start: 0.9605 (mt) cc_final: 0.9236 (tp) REVERT: F 420 LEU cc_start: 0.9289 (tt) cc_final: 0.9077 (mm) REVERT: F 460 ASN cc_start: 0.8443 (p0) cc_final: 0.8208 (p0) REVERT: F 740 MET cc_start: 0.9357 (tpp) cc_final: 0.9046 (tpp) REVERT: F 757 MET cc_start: 0.8138 (mmp) cc_final: 0.7793 (mmp) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.4603 time to fit residues: 175.4492 Evaluate side-chains 193 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 4.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 9.9990 chunk 170 optimal weight: 0.2980 chunk 255 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 272 optimal weight: 8.9990 chunk 291 optimal weight: 0.5980 chunk 211 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 336 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 533 ASN ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN D 533 ASN ** D 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN ** F 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 35640 Z= 0.155 Angle : 0.577 9.811 48126 Z= 0.280 Chirality : 0.043 0.197 5406 Planarity : 0.003 0.041 6390 Dihedral : 4.260 19.386 4842 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.92 (0.13), residues: 4422 helix: 0.15 (0.13), residues: 1656 sheet: -1.69 (0.21), residues: 516 loop : -0.85 (0.14), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 476 HIS 0.003 0.001 HIS D 406 PHE 0.012 0.001 PHE C 506 TYR 0.008 0.001 TYR D 244 ARG 0.003 0.000 ARG F 465 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 4.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.1816 (mmp) cc_final: 0.0633 (tpt) REVERT: A 242 LEU cc_start: 0.9526 (mt) cc_final: 0.9088 (tp) REVERT: A 411 LEU cc_start: 0.9331 (mt) cc_final: 0.9125 (pp) REVERT: A 460 ASN cc_start: 0.8572 (p0) cc_final: 0.8237 (p0) REVERT: A 740 MET cc_start: 0.9264 (tpp) cc_final: 0.9056 (tpp) REVERT: A 757 MET cc_start: 0.8005 (mmp) cc_final: 0.7545 (ptp) REVERT: B 46 MET cc_start: 0.1512 (mmp) cc_final: 0.0403 (tpt) REVERT: B 242 LEU cc_start: 0.9645 (mt) cc_final: 0.9052 (tp) REVERT: B 550 MET cc_start: 0.8914 (mtm) cc_final: 0.8476 (mtt) REVERT: B 740 MET cc_start: 0.7094 (ptt) cc_final: 0.6876 (tpp) REVERT: C 46 MET cc_start: -0.0071 (mmp) cc_final: -0.1057 (tpt) REVERT: C 242 LEU cc_start: 0.9610 (mt) cc_final: 0.9325 (tp) REVERT: C 460 ASN cc_start: 0.8478 (p0) cc_final: 0.8276 (p0) REVERT: C 508 MET cc_start: 0.8530 (tpp) cc_final: 0.8328 (tpp) REVERT: C 639 LEU cc_start: 0.8905 (mt) cc_final: 0.8517 (mp) REVERT: C 740 MET cc_start: 0.9368 (tpp) cc_final: 0.9018 (tpp) REVERT: C 757 MET cc_start: 0.7930 (mmp) cc_final: 0.7623 (mmp) REVERT: D 46 MET cc_start: 0.1574 (mmp) cc_final: 0.0260 (tpt) REVERT: D 242 LEU cc_start: 0.9499 (mt) cc_final: 0.8910 (tt) REVERT: D 639 LEU cc_start: 0.9144 (mt) cc_final: 0.8586 (mp) REVERT: D 740 MET cc_start: 0.9293 (tpp) cc_final: 0.9044 (tpp) REVERT: D 757 MET cc_start: 0.8032 (mmp) cc_final: 0.7544 (ptp) REVERT: E 46 MET cc_start: 0.0665 (mmp) cc_final: -0.0614 (tpt) REVERT: E 242 LEU cc_start: 0.9611 (mt) cc_final: 0.9029 (tp) REVERT: E 508 MET cc_start: 0.8555 (mmm) cc_final: 0.7988 (tpp) REVERT: E 639 LEU cc_start: 0.8779 (mt) cc_final: 0.8047 (mp) REVERT: F 46 MET cc_start: 0.0153 (mmp) cc_final: -0.0820 (tpt) REVERT: F 242 LEU cc_start: 0.9619 (mt) cc_final: 0.9276 (tp) REVERT: F 420 LEU cc_start: 0.9292 (tt) cc_final: 0.9062 (mm) REVERT: F 740 MET cc_start: 0.9348 (tpp) cc_final: 0.9050 (tpp) REVERT: F 757 MET cc_start: 0.8114 (mmp) cc_final: 0.7779 (mmp) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.4514 time to fit residues: 166.8774 Evaluate side-chains 189 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 4.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 0.8980 chunk 409 optimal weight: 0.6980 chunk 374 optimal weight: 5.9990 chunk 398 optimal weight: 0.9990 chunk 240 optimal weight: 8.9990 chunk 173 optimal weight: 8.9990 chunk 313 optimal weight: 0.0070 chunk 122 optimal weight: 3.9990 chunk 360 optimal weight: 10.0000 chunk 377 optimal weight: 6.9990 chunk 397 optimal weight: 0.5980 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 35640 Z= 0.142 Angle : 0.580 9.941 48126 Z= 0.279 Chirality : 0.043 0.167 5406 Planarity : 0.003 0.042 6390 Dihedral : 4.158 19.527 4842 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.91 (0.13), residues: 4422 helix: 0.09 (0.13), residues: 1692 sheet: -1.45 (0.22), residues: 504 loop : -0.87 (0.14), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 476 HIS 0.002 0.001 HIS F 735 PHE 0.009 0.001 PHE C 771 TYR 0.010 0.001 TYR D 244 ARG 0.003 0.000 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 4.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.1798 (mmp) cc_final: 0.0614 (tpt) REVERT: A 242 LEU cc_start: 0.9490 (mt) cc_final: 0.9036 (tp) REVERT: A 411 LEU cc_start: 0.9319 (mt) cc_final: 0.9115 (pp) REVERT: A 740 MET cc_start: 0.9286 (tpp) cc_final: 0.9080 (tpp) REVERT: A 757 MET cc_start: 0.8194 (mmp) cc_final: 0.7770 (ptp) REVERT: B 46 MET cc_start: 0.1499 (mmp) cc_final: 0.0366 (tpt) REVERT: B 242 LEU cc_start: 0.9646 (mt) cc_final: 0.9062 (tp) REVERT: B 550 MET cc_start: 0.8936 (mtm) cc_final: 0.8462 (mtt) REVERT: B 606 THR cc_start: 0.9538 (t) cc_final: 0.9310 (p) REVERT: B 740 MET cc_start: 0.6825 (ptt) cc_final: 0.6498 (tpp) REVERT: C 46 MET cc_start: -0.0095 (mmp) cc_final: -0.1074 (tpt) REVERT: C 242 LEU cc_start: 0.9611 (mt) cc_final: 0.9321 (tp) REVERT: C 740 MET cc_start: 0.9356 (tpp) cc_final: 0.9020 (tpp) REVERT: C 757 MET cc_start: 0.8064 (mmp) cc_final: 0.7787 (mmp) REVERT: D 46 MET cc_start: 0.1563 (mmp) cc_final: 0.0304 (tpt) REVERT: D 242 LEU cc_start: 0.9494 (mt) cc_final: 0.8925 (tt) REVERT: D 639 LEU cc_start: 0.9077 (mt) cc_final: 0.8573 (mp) REVERT: D 740 MET cc_start: 0.9258 (tpp) cc_final: 0.9045 (tpp) REVERT: D 757 MET cc_start: 0.8120 (mmp) cc_final: 0.7648 (ptp) REVERT: E 46 MET cc_start: 0.0734 (mmp) cc_final: -0.0591 (tpt) REVERT: E 508 MET cc_start: 0.8530 (mmm) cc_final: 0.7950 (tpp) REVERT: E 639 LEU cc_start: 0.8750 (mt) cc_final: 0.8037 (mp) REVERT: F 46 MET cc_start: 0.0133 (mmp) cc_final: -0.0837 (tpt) REVERT: F 242 LEU cc_start: 0.9599 (mt) cc_final: 0.9275 (tp) REVERT: F 344 MET cc_start: 0.8960 (mtt) cc_final: 0.8735 (mtp) REVERT: F 420 LEU cc_start: 0.9285 (tt) cc_final: 0.9048 (mm) REVERT: F 460 ASN cc_start: 0.8303 (p0) cc_final: 0.8019 (p0) REVERT: F 740 MET cc_start: 0.9335 (tpp) cc_final: 0.9044 (tpp) REVERT: F 757 MET cc_start: 0.8067 (mmp) cc_final: 0.7754 (mmp) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.4540 time to fit residues: 175.4119 Evaluate side-chains 188 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 4.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 4.9990 chunk 421 optimal weight: 6.9990 chunk 257 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 chunk 293 optimal weight: 8.9990 chunk 442 optimal weight: 6.9990 chunk 407 optimal weight: 6.9990 chunk 352 optimal weight: 2.9990 chunk 36 optimal weight: 0.0470 chunk 272 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 340 HIS ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN B 340 HIS ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 340 HIS ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN D 340 HIS ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN E 340 HIS ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN F 340 HIS ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 35640 Z= 0.338 Angle : 0.692 9.424 48126 Z= 0.351 Chirality : 0.045 0.183 5406 Planarity : 0.004 0.041 6390 Dihedral : 4.556 18.901 4842 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.15 (0.12), residues: 4422 helix: -0.12 (0.12), residues: 1674 sheet: -1.74 (0.21), residues: 516 loop : -0.94 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 476 HIS 0.009 0.002 HIS A 404 PHE 0.016 0.002 PHE D 768 TYR 0.009 0.001 TYR F 495 ARG 0.012 0.001 ARG F 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 4.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.2118 (mmp) cc_final: 0.0877 (tpt) REVERT: B 46 MET cc_start: 0.1617 (mmp) cc_final: 0.0501 (tpt) REVERT: B 508 MET cc_start: 0.8073 (tpp) cc_final: 0.7702 (tpp) REVERT: B 550 MET cc_start: 0.9012 (mtm) cc_final: 0.8701 (mtt) REVERT: C 46 MET cc_start: -0.0036 (mmp) cc_final: -0.0854 (tpt) REVERT: C 740 MET cc_start: 0.9481 (tpp) cc_final: 0.9194 (tpp) REVERT: C 757 MET cc_start: 0.8242 (mmp) cc_final: 0.7859 (mmp) REVERT: D 46 MET cc_start: 0.1771 (mmp) cc_final: 0.0521 (tpt) REVERT: D 242 LEU cc_start: 0.9540 (mt) cc_final: 0.9068 (tp) REVERT: E 46 MET cc_start: 0.1018 (mmp) cc_final: -0.0247 (tpt) REVERT: E 508 MET cc_start: 0.8503 (mmm) cc_final: 0.8160 (tpp) REVERT: E 692 GLN cc_start: 0.9383 (mt0) cc_final: 0.9084 (tm-30) REVERT: F 46 MET cc_start: 0.0273 (mmp) cc_final: -0.0746 (tpt) REVERT: F 460 ASN cc_start: 0.8462 (p0) cc_final: 0.8250 (p0) REVERT: F 740 MET cc_start: 0.9444 (tpp) cc_final: 0.8936 (tpp) REVERT: F 757 MET cc_start: 0.8294 (mmp) cc_final: 0.7908 (mmp) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.4588 time to fit residues: 157.0507 Evaluate side-chains 178 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 4.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 0.7980 chunk 375 optimal weight: 50.0000 chunk 107 optimal weight: 0.8980 chunk 324 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 97 optimal weight: 0.3980 chunk 352 optimal weight: 0.6980 chunk 147 optimal weight: 0.9990 chunk 362 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.090084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.057276 restraints weight = 165075.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.058432 restraints weight = 110586.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.059161 restraints weight = 84207.831| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 35640 Z= 0.151 Angle : 0.597 9.602 48126 Z= 0.289 Chirality : 0.044 0.164 5406 Planarity : 0.004 0.041 6390 Dihedral : 4.293 19.108 4842 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.84 (0.13), residues: 4422 helix: 0.21 (0.13), residues: 1656 sheet: -1.37 (0.21), residues: 498 loop : -0.88 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 476 HIS 0.004 0.001 HIS D 406 PHE 0.010 0.001 PHE E 230 TYR 0.009 0.001 TYR D 244 ARG 0.005 0.000 ARG F 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5633.65 seconds wall clock time: 104 minutes 33.03 seconds (6273.03 seconds total)