Starting phenix.real_space_refine on Sun Mar 17 16:53:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxg_27055/03_2024/8cxg_27055.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxg_27055/03_2024/8cxg_27055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxg_27055/03_2024/8cxg_27055.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxg_27055/03_2024/8cxg_27055.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxg_27055/03_2024/8cxg_27055.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxg_27055/03_2024/8cxg_27055.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 115 5.16 5 C 11636 2.51 5 N 3149 2.21 5 O 3481 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L ARG 24": "NH1" <-> "NH2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A ARG 73": "NH1" <-> "NH2" Residue "A ARG 94": "NH1" <-> "NH2" Residue "A PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A ARG 292": "NH1" <-> "NH2" Residue "A ARG 299": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 402": "NH1" <-> "NH2" Residue "A PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 10": "NH1" <-> "NH2" Residue "D GLU 21": "OE1" <-> "OE2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "D GLU 24": "OE1" <-> "OE2" Residue "D ARG 31": "NH1" <-> "NH2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "l ARG 54": "NH1" <-> "NH2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B ARG 94": "NH1" <-> "NH2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B GLU 244": "OE1" <-> "OE2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B ARG 299": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 402": "NH1" <-> "NH2" Residue "E ARG 10": "NH1" <-> "NH2" Residue "E GLU 21": "OE1" <-> "OE2" Residue "E ARG 23": "NH1" <-> "NH2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "E ARG 31": "NH1" <-> "NH2" Residue "E ARG 38": "NH1" <-> "NH2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C ARG 94": "NH1" <-> "NH2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C GLU 216": "OE1" <-> "OE2" Residue "C GLU 244": "OE1" <-> "OE2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "C ARG 299": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 402": "NH1" <-> "NH2" Residue "F ARG 10": "NH1" <-> "NH2" Residue "F GLU 21": "OE1" <-> "OE2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 31": "NH1" <-> "NH2" Residue "F ARG 38": "NH1" <-> "NH2" Residue "1 TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 24": "NH1" <-> "NH2" Residue "2 ARG 61": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18381 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 933 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "L" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 852 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "A" Number of atoms: 3721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3721 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 16, 'TRANS': 475} Chain breaks: 1 Chain: "D" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "h" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 933 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "l" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 852 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "B" Number of atoms: 3721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3721 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 16, 'TRANS': 475} Chain breaks: 1 Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3790 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 16, 'TRANS': 484} Chain: "F" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "1" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 933 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "2" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 846 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Time building chain proxies: 10.16, per 1000 atoms: 0.55 Number of scatterers: 18381 At special positions: 0 Unit cell: (107.06, 207.76, 115.54, 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 115 16.00 O 3481 8.00 N 3149 7.00 C 11636 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=2.08 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 339 " distance=1.72 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 96 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 30 " distance=2.51 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 121 " distance=1.75 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 105 " distance=2.08 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 116 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 291 " distance=2.02 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=1.38 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=1.18 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS C 105 " distance=2.79 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 190 " - pdb=" SG CYS C 291 " distance=2.02 Simple disulfide: pdb=" SG CYS C 308 " - pdb=" SG CYS C 339 " distance=1.24 Simple disulfide: pdb=" SG CYS 1 22 " - pdb=" SG CYS 1 96 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 23 " - pdb=" SG CYS 2 88 " distance=2.04 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: 6.67 Conformation dependent library (CDL) restraints added in 3.4 seconds 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4328 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 31 sheets defined 20.9% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.576A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 87 removed outlier: 3.634A pdb=" N SER A 86 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP A 87 " --> pdb=" O LYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 269 removed outlier: 3.696A pdb=" N HIS A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 425 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 437 through 457 Processing helix chain 'A' and resid 461 through 479 Processing helix chain 'A' and resid 483 through 499 removed outlier: 3.504A pdb=" N LEU A 498 " --> pdb=" O VAL A 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 11 removed outlier: 4.018A pdb=" N THR D 9 " --> pdb=" O SER D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 39 Processing helix chain 'D' and resid 40 through 53 removed outlier: 3.968A pdb=" N LEU D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 71 Processing helix chain 'h' and resid 28 through 30 No H-bonds generated for 'chain 'h' and resid 28 through 30' Processing helix chain 'h' and resid 87 through 91 Processing helix chain 'l' and resid 79 through 83 removed outlier: 3.621A pdb=" N PHE l 83 " --> pdb=" O PRO l 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 87 removed outlier: 3.811A pdb=" N SER B 86 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP B 87 " --> pdb=" O LYS B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 196 removed outlier: 4.601A pdb=" N LEU B 196 " --> pdb=" O PRO B 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 192 through 196' Processing helix chain 'B' and resid 263 through 269 Processing helix chain 'B' and resid 405 through 425 Processing helix chain 'B' and resid 425 through 430 Processing helix chain 'B' and resid 437 through 457 Processing helix chain 'B' and resid 463 through 479 Processing helix chain 'B' and resid 482 through 500 Processing helix chain 'E' and resid 6 through 11 removed outlier: 3.847A pdb=" N THR E 9 " --> pdb=" O SER E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 39 Processing helix chain 'E' and resid 40 through 53 removed outlier: 3.956A pdb=" N LEU E 44 " --> pdb=" O PRO E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 74 Proline residue: E 72 - end of helix Processing helix chain 'C' and resid 82 through 87 removed outlier: 3.594A pdb=" N SER C 86 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP C 87 " --> pdb=" O LYS C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 269 Processing helix chain 'C' and resid 405 through 425 Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 437 through 457 Processing helix chain 'C' and resid 463 through 479 Processing helix chain 'C' and resid 483 through 500 removed outlier: 3.695A pdb=" N GLY C 493 " --> pdb=" O LEU C 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 11 removed outlier: 3.889A pdb=" N THR F 9 " --> pdb=" O SER F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 39 removed outlier: 3.919A pdb=" N HIS F 28 " --> pdb=" O GLU F 24 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU F 29 " --> pdb=" O TYR F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 53 Processing helix chain 'F' and resid 56 through 74 Proline residue: F 72 - end of helix Processing helix chain '1' and resid 28 through 30 No H-bonds generated for 'chain '1' and resid 28 through 30' Processing helix chain '1' and resid 87 through 91 Processing helix chain '2' and resid 79 through 83 removed outlier: 3.517A pdb=" N PHE 2 83 " --> pdb=" O PRO 2 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 60 current: chain 'H' and resid 110 through 112 Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.608A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 41 through 50 current: chain 'A' and resid 126 through 129 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 126 through 129 current: chain 'A' and resid 164 through 169 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 164 through 169 current: chain 'A' and resid 210 through 214 removed outlier: 4.021A pdb=" N HIS A 210 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 21 through 26 removed outlier: 4.561A pdb=" N LYS A 290 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 63 through 65 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 63 through 65 current: chain 'A' and resid 113 through 121 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 243 through 248 removed outlier: 3.751A pdb=" N ARG A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 312 through 320 removed outlier: 6.724A pdb=" N THR A 315 " --> pdb=" O GLN A 331 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLN A 331 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE A 317 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU A 329 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 339 through 340 Processing sheet with id=AB2, first strand: chain 'A' and resid 353 through 355 removed outlier: 4.843A pdb=" N THR A 353 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL A 347 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N MET A 345 " --> pdb=" O VAL A 355 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'h' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'h' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'h' and resid 11 through 12 current: chain 'h' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'h' and resid 58 through 60 current: chain 'h' and resid 110 through 112 Processing sheet with id=AB5, first strand: chain 'l' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'l' and resid 10 through 13 removed outlier: 6.660A pdb=" N LEU l 33 " --> pdb=" O TYR l 49 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TYR l 49 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TRP l 35 " --> pdb=" O LEU l 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.587A pdb=" N ASP B 10 " --> pdb=" O THR B 32 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 41 through 51 current: chain 'B' and resid 110 through 129 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 110 through 129 current: chain 'B' and resid 164 through 169 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 164 through 169 current: chain 'B' and resid 210 through 214 removed outlier: 4.515A pdb=" N HIS B 210 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 21 through 26 removed outlier: 4.638A pdb=" N LYS B 290 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASP B 296 " --> pdb=" O SER B 185 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N SER B 185 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 243 through 247 Processing sheet with id=AC1, first strand: chain 'B' and resid 312 through 314 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 312 through 314 current: chain 'B' and resid 326 through 332 Processing sheet with id=AC2, first strand: chain 'B' and resid 339 through 340 Processing sheet with id=AC3, first strand: chain 'B' and resid 343 through 346 Processing sheet with id=AC4, first strand: chain 'C' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 41 through 50 current: chain 'C' and resid 112 through 129 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 112 through 129 current: chain 'C' and resid 164 through 169 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 164 through 169 current: chain 'C' and resid 210 through 214 removed outlier: 3.951A pdb=" N HIS C 210 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 20 through 26 removed outlier: 4.605A pdb=" N LYS C 290 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASP C 296 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N SER C 185 " --> pdb=" O ASP C 296 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 243 through 246 Processing sheet with id=AC7, first strand: chain 'C' and resid 312 through 314 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 312 through 314 current: chain 'C' and resid 326 through 332 Processing sheet with id=AC8, first strand: chain 'C' and resid 339 through 340 Processing sheet with id=AC9, first strand: chain 'C' and resid 343 through 346 removed outlier: 3.774A pdb=" N ILE C 389 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 396 " --> pdb=" O ILE C 389 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '1' and resid 3 through 7 removed outlier: 3.577A pdb=" N LEU 1 20 " --> pdb=" O PHE 1 81 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '1' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 11 through 12 current: chain '1' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 58 through 60 current: chain '1' and resid 110 through 112 Processing sheet with id=AD3, first strand: chain '2' and resid 4 through 6 Processing sheet with id=AD4, first strand: chain '2' and resid 10 through 13 removed outlier: 6.502A pdb=" N LEU 2 33 " --> pdb=" O TYR 2 49 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR 2 49 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP 2 35 " --> pdb=" O LEU 2 47 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1650 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.80 Time building geometry restraints manager: 7.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2975 1.29 - 1.43: 5117 1.43 - 1.57: 10529 1.57 - 1.72: 0 1.72 - 1.86: 179 Bond restraints: 18800 Sorted by residual: bond pdb=" CA CYS A 121 " pdb=" C CYS A 121 " ideal model delta sigma weight residual 1.522 1.408 0.114 1.20e-02 6.94e+03 9.05e+01 bond pdb=" C VAL A 243 " pdb=" O VAL A 243 " ideal model delta sigma weight residual 1.236 1.145 0.091 1.04e-02 9.25e+03 7.60e+01 bond pdb=" CA VAL A 243 " pdb=" CB VAL A 243 " ideal model delta sigma weight residual 1.541 1.459 0.082 1.28e-02 6.10e+03 4.15e+01 bond pdb=" CA PHE B 198 " pdb=" C PHE B 198 " ideal model delta sigma weight residual 1.524 1.444 0.080 1.29e-02 6.01e+03 3.87e+01 bond pdb=" CA THR C 126 " pdb=" C THR C 126 " ideal model delta sigma weight residual 1.521 1.444 0.077 1.24e-02 6.50e+03 3.82e+01 ... (remaining 18795 not shown) Histogram of bond angle deviations from ideal: 95.40 - 104.37: 317 104.37 - 113.34: 10602 113.34 - 122.31: 11232 122.31 - 131.28: 3279 131.28 - 140.25: 61 Bond angle restraints: 25491 Sorted by residual: angle pdb=" N LEU C 242 " pdb=" CA LEU C 242 " pdb=" C LEU C 242 " ideal model delta sigma weight residual 113.17 100.84 12.33 1.26e+00 6.30e-01 9.58e+01 angle pdb=" N ASN B 237 " pdb=" CA ASN B 237 " pdb=" C ASN B 237 " ideal model delta sigma weight residual 111.36 121.20 -9.84 1.09e+00 8.42e-01 8.15e+01 angle pdb=" N PRO l 95 " pdb=" CA PRO l 95 " pdb=" C PRO l 95 " ideal model delta sigma weight residual 110.70 121.59 -10.89 1.22e+00 6.72e-01 7.97e+01 angle pdb=" N SER B 433 " pdb=" CA SER B 433 " pdb=" C SER B 433 " ideal model delta sigma weight residual 110.70 124.32 -13.62 1.55e+00 4.16e-01 7.72e+01 angle pdb=" CA GLY B 195 " pdb=" C GLY B 195 " pdb=" N LEU B 196 " ideal model delta sigma weight residual 117.04 125.73 -8.69 9.90e-01 1.02e+00 7.70e+01 ... (remaining 25486 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 10279 17.75 - 35.50: 620 35.50 - 53.25: 136 53.25 - 71.00: 38 71.00 - 88.75: 8 Dihedral angle restraints: 11081 sinusoidal: 4278 harmonic: 6803 Sorted by residual: dihedral pdb=" CB CYS A 308 " pdb=" SG CYS A 308 " pdb=" SG CYS A 339 " pdb=" CB CYS A 339 " ideal model delta sinusoidal sigma weight residual -86.00 -174.75 88.75 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS C 3 " pdb=" SG CYS C 3 " pdb=" SG CYS C 30 " pdb=" CB CYS C 30 " ideal model delta sinusoidal sigma weight residual -86.00 -156.44 70.44 1 1.00e+01 1.00e-02 6.39e+01 dihedral pdb=" CB CYS A 3 " pdb=" SG CYS A 3 " pdb=" SG CYS A 30 " pdb=" CB CYS A 30 " ideal model delta sinusoidal sigma weight residual -86.00 -149.85 63.85 1 1.00e+01 1.00e-02 5.37e+01 ... (remaining 11078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2748 0.123 - 0.246: 80 0.246 - 0.369: 10 0.369 - 0.492: 6 0.492 - 0.615: 4 Chirality restraints: 2848 Sorted by residual: chirality pdb=" CA LYS B 123 " pdb=" N LYS B 123 " pdb=" C LYS B 123 " pdb=" CB LYS B 123 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.62 2.00e-01 2.50e+01 9.46e+00 chirality pdb=" CA MET C 349 " pdb=" N MET C 349 " pdb=" C MET C 349 " pdb=" CB MET C 349 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.76e+00 chirality pdb=" CA LYS A 123 " pdb=" N LYS A 123 " pdb=" C LYS A 123 " pdb=" CB LYS A 123 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.58e+00 ... (remaining 2845 not shown) Planarity restraints: 3232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 238 " -0.028 2.00e-02 2.50e+03 5.76e-02 3.32e+01 pdb=" C ASN A 238 " 0.100 2.00e-02 2.50e+03 pdb=" O ASN A 238 " -0.038 2.00e-02 2.50e+03 pdb=" N LYS A 239 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 121 " 0.022 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C CYS B 121 " -0.078 2.00e-02 2.50e+03 pdb=" O CYS B 121 " 0.029 2.00e-02 2.50e+03 pdb=" N SER B 122 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 359 " 0.024 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C ILE B 359 " -0.076 2.00e-02 2.50e+03 pdb=" O ILE B 359 " 0.026 2.00e-02 2.50e+03 pdb=" N THR B 360 " 0.026 2.00e-02 2.50e+03 ... (remaining 3229 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.84: 25 1.84 - 2.61: 390 2.61 - 3.37: 23228 3.37 - 4.14: 44280 4.14 - 4.90: 79722 Nonbonded interactions: 147645 Sorted by model distance: nonbonded pdb=" NH2 ARG C 2 " pdb=" OE1 GLU C 44 " model vdw 1.081 2.520 nonbonded pdb=" CG2 ILE 2 29 " pdb=" NE2 GLN 2 90 " model vdw 1.189 3.540 nonbonded pdb=" CZ ARG C 2 " pdb=" OE1 GLU C 44 " model vdw 1.192 3.270 nonbonded pdb=" CG PRO C 224 " pdb=" CD1 LEU C 242 " model vdw 1.266 3.860 nonbonded pdb=" O GLY B 104 " pdb=" CE2 PHE 2 32 " model vdw 1.284 3.340 ... (remaining 147640 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 '1' selection = chain 'H' selection = chain 'h' } ncs_group { reference = chain '2' selection = (chain 'L' and resid 1 through 108) selection = (chain 'l' and resid 1 through 108) } ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 1 through 150 or resid 160 through 501)) } ncs_group { reference = 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.480 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 48.620 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.140 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 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 : 0.008 0.121 18800 Z= 0.546 Angle : 0.961 15.253 25491 Z= 0.595 Chirality : 0.061 0.615 2848 Planarity : 0.006 0.088 3232 Dihedral : 12.574 85.278 6687 Min Nonbonded Distance : 1.081 Molprobity Statistics. All-atom Clashscore : 28.53 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.77 % Favored : 90.81 % Rotamer: Outliers : 2.73 % Allowed : 8.04 % Favored : 89.23 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.16), residues: 2371 helix: -0.76 (0.23), residues: 421 sheet: -0.34 (0.18), residues: 767 loop : -2.50 (0.15), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 101 HIS 0.005 0.001 HIS C 288 PHE 0.015 0.002 PHE F 42 TYR 0.024 0.002 TYR E 25 ARG 0.006 0.001 ARG C 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 410 time to evaluate : 2.291 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: H 34 MET cc_start: 0.9321 (mmm) cc_final: 0.8978 (mmm) REVERT: H 57 SER cc_start: 0.7649 (t) cc_final: 0.7390 (p) REVERT: H 97 VAL cc_start: 0.9267 (OUTLIER) cc_final: 0.8749 (m) REVERT: B 466 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7697 (tt) REVERT: C 349 MET cc_start: 0.6014 (mmm) cc_final: 0.4935 (ptp) REVERT: C 460 MET cc_start: 0.7468 (ptp) cc_final: 0.7185 (ptp) REVERT: 1 109 MET cc_start: 0.0576 (mtp) cc_final: -0.2075 (mtm) outliers start: 54 outliers final: 19 residues processed: 456 average time/residue: 0.2775 time to fit residues: 196.6301 Evaluate side-chains 332 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 311 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain 2 residue 94 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 198 optimal weight: 8.9990 chunk 178 optimal weight: 3.9990 chunk 98 optimal weight: 20.0000 chunk 60 optimal weight: 0.0670 chunk 120 optimal weight: 1.9990 chunk 95 optimal weight: 50.0000 chunk 184 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 213 optimal weight: 220.0000 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN L 42 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN A 148 HIS A 163 ASN ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 GLN A 399 HIS A 478 ASN ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN D 17 GLN h 39 GLN l 42 GLN l 90 GLN B 52 ASN B 77 GLN B 85 GLN B 103 ASN B 148 HIS ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 HIS C 103 ASN C 163 ASN C 350 GLN C 447 GLN C 478 ASN ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 39 GLN 2 42 GLN ** 2 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 18800 Z= 0.253 Angle : 0.696 17.369 25491 Z= 0.359 Chirality : 0.045 0.267 2848 Planarity : 0.006 0.128 3232 Dihedral : 6.422 59.791 2616 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.94 % Favored : 90.93 % Rotamer: Outliers : 3.64 % Allowed : 14.76 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.17), residues: 2371 helix: 0.01 (0.24), residues: 436 sheet: -0.00 (0.18), residues: 828 loop : -2.10 (0.17), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 400 HIS 0.008 0.001 HIS B 288 PHE 0.015 0.002 PHE F 42 TYR 0.013 0.001 TYR H 105 ARG 0.008 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 336 time to evaluate : 1.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 97 VAL cc_start: 0.9210 (OUTLIER) cc_final: 0.8997 (m) REVERT: H 116 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8710 (p) REVERT: A 487 MET cc_start: 0.5044 (mmm) cc_final: 0.4678 (mmp) REVERT: D 25 TYR cc_start: 0.6856 (OUTLIER) cc_final: 0.4968 (p90) REVERT: B 125 MET cc_start: 0.6988 (ptp) cc_final: 0.6763 (ptp) REVERT: C 491 LEU cc_start: 0.4735 (mt) cc_final: 0.3706 (mt) REVERT: 1 109 MET cc_start: 0.0311 (mtp) cc_final: -0.2286 (mtm) outliers start: 72 outliers final: 38 residues processed: 382 average time/residue: 0.2472 time to fit residues: 152.1860 Evaluate side-chains 338 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 297 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 33 SER Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 55 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 118 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 213 optimal weight: 320.0000 chunk 230 optimal weight: 40.0000 chunk 190 optimal weight: 20.0000 chunk 212 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 171 optimal weight: 20.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 ASN ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 HIS B 85 GLN B 288 HIS ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 HIS ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 HIS C 235 HIS C 478 ASN ** 2 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 18800 Z= 0.436 Angle : 0.743 19.448 25491 Z= 0.384 Chirality : 0.046 0.276 2848 Planarity : 0.006 0.116 3232 Dihedral : 5.985 56.593 2594 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.66 % Favored : 90.26 % Rotamer: Outliers : 5.66 % Allowed : 15.67 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.17), residues: 2371 helix: 0.28 (0.25), residues: 435 sheet: 0.29 (0.19), residues: 812 loop : -1.95 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 400 HIS 0.006 0.001 HIS C 288 PHE 0.017 0.002 PHE A 431 TYR 0.014 0.002 TYR C 202 ARG 0.007 0.000 ARG E 31 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 298 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 57 SER cc_start: 0.9067 (p) cc_final: 0.8866 (p) REVERT: H 105 TYR cc_start: 0.9111 (m-80) cc_final: 0.8886 (m-80) REVERT: 1 109 MET cc_start: 0.0457 (mtp) cc_final: -0.2027 (mtm) outliers start: 112 outliers final: 71 residues processed: 374 average time/residue: 0.2553 time to fit residues: 152.9707 Evaluate side-chains 356 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 285 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 33 SER Chi-restraints excluded: chain h residue 63 SER Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 94 TRP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 288 HIS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 27 HIS Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 253 GLN Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain 1 residue 35 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 211 optimal weight: 8.9990 chunk 160 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 214 optimal weight: 0.0980 chunk 227 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 GLN B 85 GLN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 18800 Z= 0.266 Angle : 0.646 12.208 25491 Z= 0.335 Chirality : 0.044 0.257 2848 Planarity : 0.005 0.095 3232 Dihedral : 5.675 59.081 2591 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.36 % Favored : 90.55 % Rotamer: Outliers : 4.90 % Allowed : 17.49 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.17), residues: 2371 helix: 0.47 (0.26), residues: 435 sheet: 0.52 (0.19), residues: 798 loop : -1.78 (0.17), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 400 HIS 0.006 0.001 HIS C 288 PHE 0.014 0.001 PHE F 42 TYR 0.019 0.001 TYR A 61 ARG 0.005 0.000 ARG E 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 309 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 95 TYR cc_start: 0.8956 (m-80) cc_final: 0.8665 (m-80) REVERT: H 107 TYR cc_start: 0.9485 (p90) cc_final: 0.9238 (p90) REVERT: H 116 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8657 (p) REVERT: L 94 TRP cc_start: 0.7675 (OUTLIER) cc_final: 0.5727 (t60) REVERT: D 25 TYR cc_start: 0.6738 (OUTLIER) cc_final: 0.4938 (p90) REVERT: h 80 TYR cc_start: 0.9069 (m-80) cc_final: 0.8821 (m-80) REVERT: B 197 ASP cc_start: 0.6035 (p0) cc_final: 0.5754 (p0) REVERT: C 253 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7532 (tt0) REVERT: 1 109 MET cc_start: 0.0325 (mtp) cc_final: -0.2649 (mtm) outliers start: 97 outliers final: 61 residues processed: 374 average time/residue: 0.2384 time to fit residues: 143.5746 Evaluate side-chains 358 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 293 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 33 SER Chi-restraints excluded: chain h residue 35 HIS Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain h residue 63 SER Chi-restraints excluded: chain h residue 71 SER Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 94 TRP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 27 HIS Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 253 GLN Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain 1 residue 35 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 189 optimal weight: 30.0000 chunk 128 optimal weight: 9.9990 chunk 3 optimal weight: 50.0000 chunk 169 optimal weight: 5.9990 chunk 93 optimal weight: 40.0000 chunk 193 optimal weight: 20.0000 chunk 157 optimal weight: 20.0000 chunk 0 optimal weight: 60.0000 chunk 115 optimal weight: 0.0040 chunk 203 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 overall best weight: 5.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 GLN B 85 GLN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 18800 Z= 0.293 Angle : 0.645 13.293 25491 Z= 0.334 Chirality : 0.044 0.271 2848 Planarity : 0.005 0.091 3232 Dihedral : 5.549 58.203 2590 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.41 % Favored : 90.51 % Rotamer: Outliers : 5.41 % Allowed : 18.15 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.18), residues: 2371 helix: 0.69 (0.27), residues: 423 sheet: 0.59 (0.19), residues: 795 loop : -1.65 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 101 HIS 0.006 0.001 HIS C 288 PHE 0.014 0.001 PHE F 42 TYR 0.016 0.001 TYR H 105 ARG 0.004 0.000 ARG F 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 303 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 95 TYR cc_start: 0.8949 (m-80) cc_final: 0.8677 (m-80) REVERT: H 107 TYR cc_start: 0.9505 (p90) cc_final: 0.9234 (p90) REVERT: H 116 THR cc_start: 0.9024 (OUTLIER) cc_final: 0.8565 (p) REVERT: L 94 TRP cc_start: 0.7636 (OUTLIER) cc_final: 0.5594 (t60) REVERT: D 25 TYR cc_start: 0.6735 (OUTLIER) cc_final: 0.4937 (p90) REVERT: D 74 TYR cc_start: 0.4443 (OUTLIER) cc_final: 0.3296 (m-80) REVERT: h 80 TYR cc_start: 0.9109 (m-80) cc_final: 0.8810 (m-80) REVERT: l 91 ARG cc_start: 0.8871 (mmt90) cc_final: 0.8596 (mtt180) REVERT: B 140 MET cc_start: 0.7258 (mmm) cc_final: 0.6954 (mmm) REVERT: B 197 ASP cc_start: 0.6187 (p0) cc_final: 0.5945 (p0) REVERT: B 433 SER cc_start: 0.7530 (t) cc_final: 0.7294 (p) REVERT: C 295 MET cc_start: 0.6193 (ptp) cc_final: 0.5957 (ptp) REVERT: C 349 MET cc_start: 0.4134 (ptp) cc_final: 0.3564 (ptm) REVERT: 1 109 MET cc_start: 0.0609 (mtp) cc_final: -0.2511 (mtm) outliers start: 107 outliers final: 77 residues processed: 369 average time/residue: 0.2463 time to fit residues: 145.7207 Evaluate side-chains 375 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 294 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 33 SER Chi-restraints excluded: chain h residue 35 HIS Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 71 SER Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 94 TRP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 288 HIS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 253 GLN Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 70 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 76 optimal weight: 20.0000 chunk 204 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 227 optimal weight: 40.0000 chunk 188 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 GLN B 85 GLN B 163 ASN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 18800 Z= 0.416 Angle : 0.704 16.094 25491 Z= 0.363 Chirality : 0.046 0.283 2848 Planarity : 0.005 0.091 3232 Dihedral : 5.777 59.252 2590 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.12 % Favored : 89.79 % Rotamer: Outliers : 5.86 % Allowed : 18.50 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.18), residues: 2371 helix: 0.68 (0.27), residues: 424 sheet: 0.57 (0.19), residues: 796 loop : -1.67 (0.18), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP 2 94 HIS 0.006 0.001 HIS C 288 PHE 0.015 0.001 PHE A 431 TYR 0.019 0.001 TYR H 105 ARG 0.003 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 288 time to evaluate : 2.246 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: H 95 TYR cc_start: 0.9015 (m-80) cc_final: 0.8747 (m-80) REVERT: H 107 TYR cc_start: 0.9524 (p90) cc_final: 0.9249 (p90) REVERT: H 116 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8583 (p) REVERT: L 94 TRP cc_start: 0.7726 (OUTLIER) cc_final: 0.5705 (t60) REVERT: D 25 TYR cc_start: 0.7210 (OUTLIER) cc_final: 0.5169 (p90) REVERT: D 74 TYR cc_start: 0.4840 (OUTLIER) cc_final: 0.3204 (m-80) REVERT: B 140 MET cc_start: 0.7298 (mmm) cc_final: 0.6990 (mmm) REVERT: B 433 SER cc_start: 0.7890 (t) cc_final: 0.7604 (p) REVERT: E 69 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.8036 (mp) REVERT: 1 109 MET cc_start: 0.0259 (mtp) cc_final: -0.2289 (mtt) outliers start: 116 outliers final: 90 residues processed: 364 average time/residue: 0.2534 time to fit residues: 147.6465 Evaluate side-chains 377 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 282 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 35 HIS Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 71 SER Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain h residue 101 SER Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 26 SER Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 63 SER Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 94 TRP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 288 HIS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 27 HIS Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 253 GLN Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain 1 residue 35 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 219 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 166 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 191 optimal weight: 0.5980 chunk 126 optimal weight: 9.9990 chunk 226 optimal weight: 0.0980 chunk 141 optimal weight: 7.9990 chunk 138 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 GLN B 85 GLN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 18800 Z= 0.235 Angle : 0.631 11.242 25491 Z= 0.324 Chirality : 0.043 0.223 2848 Planarity : 0.005 0.092 3232 Dihedral : 5.521 56.880 2590 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.62 % Favored : 90.30 % Rotamer: Outliers : 5.01 % Allowed : 19.36 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.18), residues: 2371 helix: 0.80 (0.27), residues: 421 sheet: 0.66 (0.19), residues: 811 loop : -1.58 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 101 HIS 0.006 0.001 HIS C 288 PHE 0.014 0.001 PHE F 42 TYR 0.016 0.001 TYR A 61 ARG 0.005 0.000 ARG l 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 297 time to evaluate : 2.092 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: H 95 TYR cc_start: 0.8968 (m-80) cc_final: 0.8710 (m-80) REVERT: L 94 TRP cc_start: 0.7537 (OUTLIER) cc_final: 0.5346 (t60) REVERT: A 317 ILE cc_start: 0.6915 (OUTLIER) cc_final: 0.6502 (pt) REVERT: D 25 TYR cc_start: 0.6566 (OUTLIER) cc_final: 0.4849 (p90) REVERT: D 74 TYR cc_start: 0.4720 (OUTLIER) cc_final: 0.3176 (m-80) REVERT: h 80 TYR cc_start: 0.9102 (m-80) cc_final: 0.8849 (m-80) REVERT: B 140 MET cc_start: 0.7195 (mmm) cc_final: 0.6874 (mmm) REVERT: B 433 SER cc_start: 0.7903 (t) cc_final: 0.7639 (p) REVERT: C 349 MET cc_start: 0.4525 (ptp) cc_final: 0.3813 (ptm) REVERT: 1 109 MET cc_start: 0.0388 (mtp) cc_final: -0.2173 (mtt) outliers start: 99 outliers final: 75 residues processed: 360 average time/residue: 0.2553 time to fit residues: 147.1224 Evaluate side-chains 374 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 295 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 35 HIS Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 94 TRP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 288 HIS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain 1 residue 35 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 140 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 chunk 135 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 43 optimal weight: 0.0770 chunk 144 optimal weight: 20.0000 chunk 154 optimal weight: 30.0000 chunk 111 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 178 optimal weight: 9.9990 overall best weight: 6.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 GLN B 85 GLN B 288 HIS ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 18800 Z= 0.351 Angle : 0.676 12.730 25491 Z= 0.348 Chirality : 0.045 0.232 2848 Planarity : 0.005 0.092 3232 Dihedral : 5.582 58.347 2589 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.42 % Favored : 89.50 % Rotamer: Outliers : 5.41 % Allowed : 19.36 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.18), residues: 2371 helix: 0.73 (0.27), residues: 424 sheet: 0.67 (0.19), residues: 811 loop : -1.58 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 101 HIS 0.006 0.001 HIS C 288 PHE 0.014 0.001 PHE A 431 TYR 0.034 0.001 TYR H 105 ARG 0.007 0.000 ARG l 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 294 time to evaluate : 2.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 95 TYR cc_start: 0.8995 (m-80) cc_final: 0.8757 (m-80) REVERT: L 94 TRP cc_start: 0.7530 (OUTLIER) cc_final: 0.4194 (m-10) REVERT: A 317 ILE cc_start: 0.7303 (OUTLIER) cc_final: 0.6918 (pt) REVERT: D 25 TYR cc_start: 0.6649 (OUTLIER) cc_final: 0.4827 (p90) REVERT: D 74 TYR cc_start: 0.4831 (OUTLIER) cc_final: 0.3190 (m-80) REVERT: h 80 TYR cc_start: 0.9120 (m-80) cc_final: 0.8808 (m-80) REVERT: B 140 MET cc_start: 0.7246 (mmm) cc_final: 0.6963 (mmm) REVERT: B 433 SER cc_start: 0.7993 (t) cc_final: 0.7719 (p) REVERT: C 151 MET cc_start: 0.5442 (mmm) cc_final: 0.5134 (mmt) REVERT: 1 109 MET cc_start: 0.0527 (mtp) cc_final: -0.2508 (mpp) outliers start: 107 outliers final: 82 residues processed: 362 average time/residue: 0.2409 time to fit residues: 141.2200 Evaluate side-chains 376 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 290 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 35 HIS Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 63 SER Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 94 TRP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 288 HIS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain 1 residue 35 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 206 optimal weight: 9.9990 chunk 216 optimal weight: 50.0000 chunk 197 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 91 optimal weight: 50.0000 chunk 165 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 190 optimal weight: 7.9990 chunk 199 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 GLN B 85 GLN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 18800 Z= 0.341 Angle : 0.673 13.189 25491 Z= 0.347 Chirality : 0.045 0.229 2848 Planarity : 0.005 0.093 3232 Dihedral : 5.590 58.212 2589 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.78 % Favored : 90.13 % Rotamer: Outliers : 5.11 % Allowed : 20.17 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.18), residues: 2371 helix: 0.72 (0.27), residues: 424 sheet: 0.68 (0.19), residues: 810 loop : -1.57 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 101 HIS 0.007 0.001 HIS B 288 PHE 0.014 0.001 PHE A 431 TYR 0.030 0.001 TYR H 105 ARG 0.004 0.000 ARG F 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 293 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 95 TYR cc_start: 0.9004 (m-80) cc_final: 0.8769 (m-80) REVERT: L 94 TRP cc_start: 0.7461 (OUTLIER) cc_final: 0.4075 (m-10) REVERT: A 317 ILE cc_start: 0.7425 (OUTLIER) cc_final: 0.7044 (pt) REVERT: D 25 TYR cc_start: 0.6619 (OUTLIER) cc_final: 0.4779 (p90) REVERT: D 74 TYR cc_start: 0.4870 (OUTLIER) cc_final: 0.3229 (m-80) REVERT: h 80 TYR cc_start: 0.9110 (m-80) cc_final: 0.8804 (m-80) REVERT: B 140 MET cc_start: 0.7248 (mmm) cc_final: 0.6950 (mmm) REVERT: B 433 SER cc_start: 0.8067 (t) cc_final: 0.7780 (p) REVERT: 1 109 MET cc_start: 0.0634 (mtp) cc_final: -0.2439 (mpp) outliers start: 101 outliers final: 88 residues processed: 355 average time/residue: 0.2487 time to fit residues: 141.4123 Evaluate side-chains 382 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 290 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 35 HIS Chi-restraints excluded: chain h residue 63 SER Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain l residue 26 SER Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 63 SER Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 94 TRP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 288 HIS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain 1 residue 35 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 138 optimal weight: 8.9990 chunk 223 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 105 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 234 optimal weight: 50.0000 chunk 215 optimal weight: 40.0000 chunk 186 optimal weight: 8.9990 chunk 19 optimal weight: 50.0000 chunk 144 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 GLN B 85 GLN B 134 ASN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 18800 Z= 0.413 Angle : 0.707 13.679 25491 Z= 0.366 Chirality : 0.046 0.234 2848 Planarity : 0.005 0.093 3232 Dihedral : 5.744 59.959 2589 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.33 % Favored : 89.58 % Rotamer: Outliers : 4.95 % Allowed : 20.42 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.18), residues: 2371 helix: 0.73 (0.27), residues: 424 sheet: 0.71 (0.19), residues: 791 loop : -1.64 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP B 101 HIS 0.007 0.001 HIS C 288 PHE 0.015 0.001 PHE B 497 TYR 0.029 0.002 TYR H 105 ARG 0.005 0.000 ARG l 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 287 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 ILE cc_start: 0.7607 (OUTLIER) cc_final: 0.7261 (pt) REVERT: D 25 TYR cc_start: 0.6667 (OUTLIER) cc_final: 0.4582 (p90) REVERT: D 74 TYR cc_start: 0.4822 (OUTLIER) cc_final: 0.3135 (m-80) REVERT: h 80 TYR cc_start: 0.9106 (m-80) cc_final: 0.8807 (m-80) REVERT: B 140 MET cc_start: 0.7255 (mmm) cc_final: 0.6970 (mmm) REVERT: B 433 SER cc_start: 0.8060 (t) cc_final: 0.7772 (p) REVERT: C 151 MET cc_start: 0.5402 (mmm) cc_final: 0.5001 (mmt) REVERT: 1 109 MET cc_start: 0.0802 (mtp) cc_final: -0.2220 (mpp) outliers start: 98 outliers final: 90 residues processed: 349 average time/residue: 0.2618 time to fit residues: 146.2991 Evaluate side-chains 376 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 283 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 63 SER Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 26 SER Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 63 SER Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 94 TRP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 288 HIS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain 1 residue 35 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 148 optimal weight: 5.9990 chunk 198 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 171 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 186 optimal weight: 8.9990 chunk 78 optimal weight: 80.0000 chunk 191 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.155465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.116427 restraints weight = 37335.559| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.11 r_work: 0.2999 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.282 18800 Z= 0.427 Angle : 0.863 59.197 25491 Z= 0.478 Chirality : 0.047 0.759 2848 Planarity : 0.006 0.106 3232 Dihedral : 5.742 59.987 2589 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.38 % Favored : 89.54 % Rotamer: Outliers : 5.06 % Allowed : 20.63 % Favored : 74.32 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.18), residues: 2371 helix: 0.74 (0.27), residues: 424 sheet: 0.66 (0.19), residues: 809 loop : -1.61 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 101 HIS 0.016 0.001 HIS B 210 PHE 0.015 0.001 PHE A 431 TYR 0.021 0.001 TYR C 202 ARG 0.004 0.000 ARG F 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4043.84 seconds wall clock time: 74 minutes 24.10 seconds (4464.10 seconds total)