Starting phenix.real_space_refine on Fri Jun 28 15:04:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5a_42981/06_2024/8v5a_42981.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5a_42981/06_2024/8v5a_42981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5a_42981/06_2024/8v5a_42981.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5a_42981/06_2024/8v5a_42981.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5a_42981/06_2024/8v5a_42981.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5a_42981/06_2024/8v5a_42981.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2628 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 8226 2.51 5 N 2232 2.21 5 O 2544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 45": "OE1" <-> "OE2" Residue "A ARG 47": "NH1" <-> "NH2" Residue "A ARG 73": "NH1" <-> "NH2" Residue "A ARG 77": "NH1" <-> "NH2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "A ARG 109": "NH1" <-> "NH2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A ARG 141": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A ASP 252": "OD1" <-> "OD2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ASP 268": "OD1" <-> "OD2" Residue "A ASP 270": "OD1" <-> "OD2" Residue "A ARG 281": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 306": "NH1" <-> "NH2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A ARG 375": "NH1" <-> "NH2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "A ARG 475": "NH1" <-> "NH2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "Y ARG 19": "NH1" <-> "NH2" Residue "Y ARG 38": "NH1" <-> "NH2" Residue "Y ARG 39": "NH1" <-> "NH2" Residue "Y ARG 43": "NH1" <-> "NH2" Residue "Y ARG 45": "NH1" <-> "NH2" Residue "Y ARG 66": "NH1" <-> "NH2" Residue "Y ARG 81": "NH1" <-> "NH2" Residue "B GLU 45": "OE1" <-> "OE2" Residue "B ARG 47": "NH1" <-> "NH2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B ARG 87": "NH1" <-> "NH2" Residue "B ARG 109": "NH1" <-> "NH2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B ASP 252": "OD1" <-> "OD2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ASP 268": "OD1" <-> "OD2" Residue "B ASP 270": "OD1" <-> "OD2" Residue "B ARG 281": "NH1" <-> "NH2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B GLU 416": "OE1" <-> "OE2" Residue "B ARG 475": "NH1" <-> "NH2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "W ARG 19": "NH1" <-> "NH2" Residue "W ARG 38": "NH1" <-> "NH2" Residue "W ARG 39": "NH1" <-> "NH2" Residue "W ARG 43": "NH1" <-> "NH2" Residue "W ARG 45": "NH1" <-> "NH2" Residue "W ARG 66": "NH1" <-> "NH2" Residue "W ARG 81": "NH1" <-> "NH2" Residue "C GLU 45": "OE1" <-> "OE2" Residue "C ARG 47": "NH1" <-> "NH2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 87": "NH1" <-> "NH2" Residue "C ARG 109": "NH1" <-> "NH2" Residue "C GLU 136": "OE1" <-> "OE2" Residue "C ARG 141": "NH1" <-> "NH2" Residue "C ARG 152": "NH1" <-> "NH2" Residue "C ARG 189": "NH1" <-> "NH2" Residue "C ARG 236": "NH1" <-> "NH2" Residue "C ASP 252": "OD1" <-> "OD2" Residue "C ARG 265": "NH1" <-> "NH2" Residue "C ASP 268": "OD1" <-> "OD2" Residue "C ASP 270": "OD1" <-> "OD2" Residue "C ARG 281": "NH1" <-> "NH2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C ARG 375": "NH1" <-> "NH2" Residue "C ARG 400": "NH1" <-> "NH2" Residue "C GLU 416": "OE1" <-> "OE2" Residue "C ARG 475": "NH1" <-> "NH2" Residue "C ARG 476": "NH1" <-> "NH2" Residue "U ARG 19": "NH1" <-> "NH2" Residue "U ARG 38": "NH1" <-> "NH2" Residue "U ARG 39": "NH1" <-> "NH2" Residue "U ARG 43": "NH1" <-> "NH2" Residue "U ARG 45": "NH1" <-> "NH2" Residue "U ARG 66": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 13056 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3476 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 19, 'TRANS': 430} Chain breaks: 2 Chain: "Y" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 876 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "B" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3476 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 19, 'TRANS': 430} Chain breaks: 2 Chain: "W" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 876 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "C" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3476 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 19, 'TRANS': 430} Chain breaks: 2 Chain: "U" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 876 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Time building chain proxies: 8.85, per 1000 atoms: 0.68 Number of scatterers: 13056 At special positions: 0 Unit cell: (125.55, 132.84, 132.84, 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 54 16.00 O 2544 8.00 N 2232 7.00 C 8226 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.02 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.04 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.02 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.04 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 340 " distance=2.02 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 392 " distance=2.04 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.95 Conformation dependent library (CDL) restraints added in 2.4 seconds 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3138 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 15 sheets defined 34.2% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 21 through 26 Processing helix chain 'A' and resid 64 through 89 removed outlier: 4.545A pdb=" N ARG A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Proline residue: A 81 - end of helix removed outlier: 3.712A pdb=" N LEU A 88 " --> pdb=" O ASP A 84 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET A 89 " --> pdb=" O GLY A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 138 Processing helix chain 'A' and resid 139 through 152 removed outlier: 4.568A pdb=" N ASP A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 182 through 190 removed outlier: 4.141A pdb=" N ALA A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 215 removed outlier: 4.445A pdb=" N ALA A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 224 Processing helix chain 'A' and resid 228 through 236 Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'A' and resid 253 through 262 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 351 through 357 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 452 through 487 Processing helix chain 'Y' and resid 86 through 90 Processing helix chain 'B' and resid 21 through 26 Processing helix chain 'B' and resid 64 through 89 removed outlier: 4.545A pdb=" N ARG B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Proline residue: B 81 - end of helix removed outlier: 3.712A pdb=" N LEU B 88 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET B 89 " --> pdb=" O GLY B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 138 Processing helix chain 'B' and resid 139 through 152 removed outlier: 4.568A pdb=" N ASP B 143 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 182 through 190 removed outlier: 4.142A pdb=" N ALA B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 215 removed outlier: 4.445A pdb=" N ALA B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 224 Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 238 through 244 Processing helix chain 'B' and resid 253 through 262 Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 351 through 357 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 452 through 487 Processing helix chain 'W' and resid 86 through 90 Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 64 through 89 removed outlier: 4.545A pdb=" N ARG C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU C 78 " --> pdb=" O LEU C 74 " (cutoff:3.500A) Proline residue: C 81 - end of helix removed outlier: 3.712A pdb=" N LEU C 88 " --> pdb=" O ASP C 84 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 Processing helix chain 'C' and resid 139 through 152 removed outlier: 4.568A pdb=" N ASP C 143 " --> pdb=" O GLN C 139 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 182 Processing helix chain 'C' and resid 182 through 190 removed outlier: 4.141A pdb=" N ALA C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 215 removed outlier: 4.446A pdb=" N ALA C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 224 Processing helix chain 'C' and resid 228 through 236 Processing helix chain 'C' and resid 238 through 244 Processing helix chain 'C' and resid 253 through 262 Processing helix chain 'C' and resid 328 through 331 Processing helix chain 'C' and resid 351 through 357 Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 452 through 487 Processing helix chain 'U' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 52 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 30 through 52 current: chain 'A' and resid 169 through 173 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 169 through 173 current: chain 'A' and resid 263 through 270 removed outlier: 7.304A pdb=" N VAL A 264 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ARG A 281 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL A 266 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLN A 279 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N HIS A 315 " --> pdb=" O ALA A 326 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 322 through 326 current: chain 'A' and resid 337 through 339 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 337 through 339 current: chain 'Y' and resid 46 through 52 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 57 through 59 current: chain 'Y' and resid 103 through 106 Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 93 removed outlier: 3.986A pdb=" N GLY A 116 " --> pdb=" O LEU B 426 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA4, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AA5, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA6, first strand: chain 'A' and resid 392 through 393 removed outlier: 7.232A pdb=" N LEU A 426 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE C 118 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASN A 428 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Y' and resid 2 through 5 removed outlier: 3.537A pdb=" N THR Y 77 " --> pdb=" O ASP Y 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 30 through 52 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 30 through 52 current: chain 'B' and resid 169 through 173 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 169 through 173 current: chain 'B' and resid 263 through 270 removed outlier: 7.303A pdb=" N VAL B 264 " --> pdb=" O ARG B 281 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ARG B 281 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL B 266 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN B 279 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N HIS B 315 " --> pdb=" O ALA B 326 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 322 through 326 current: chain 'B' and resid 337 through 339 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 337 through 339 current: chain 'W' and resid 46 through 52 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 57 through 59 current: chain 'W' and resid 103 through 106 Processing sheet with id=AA9, first strand: chain 'B' and resid 92 through 93 removed outlier: 4.035A pdb=" N GLY B 116 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 122 through 124 Processing sheet with id=AB2, first strand: chain 'B' and resid 301 through 303 Processing sheet with id=AB3, first strand: chain 'W' and resid 2 through 5 removed outlier: 3.537A pdb=" N THR W 77 " --> pdb=" O ASP W 72 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 30 through 52 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 30 through 52 current: chain 'C' and resid 169 through 173 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 169 through 173 current: chain 'C' and resid 263 through 270 removed outlier: 7.304A pdb=" N VAL C 264 " --> pdb=" O ARG C 281 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ARG C 281 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N VAL C 266 " --> pdb=" O GLN C 279 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN C 279 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N HIS C 315 " --> pdb=" O ALA C 326 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 322 through 326 current: chain 'C' and resid 337 through 339 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 337 through 339 current: chain 'U' and resid 46 through 52 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 57 through 59 current: chain 'U' and resid 103 through 106 Processing sheet with id=AB5, first strand: chain 'C' and resid 301 through 303 Processing sheet with id=AB6, first strand: chain 'U' and resid 2 through 5 removed outlier: 3.537A pdb=" N THR U 77 " --> pdb=" O ASP U 72 " (cutoff:3.500A) 523 hydrogen bonds defined for protein. 1425 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: 4.06 Time building geometry restraints manager: 5.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3593 1.33 - 1.45: 2143 1.45 - 1.57: 7440 1.57 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 13248 Sorted by residual: bond pdb=" CG1 ILE B 262 " pdb=" CD1 ILE B 262 " ideal model delta sigma weight residual 1.513 1.431 0.082 3.90e-02 6.57e+02 4.43e+00 bond pdb=" CG1 ILE C 262 " pdb=" CD1 ILE C 262 " ideal model delta sigma weight residual 1.513 1.431 0.082 3.90e-02 6.57e+02 4.42e+00 bond pdb=" CG1 ILE A 262 " pdb=" CD1 ILE A 262 " ideal model delta sigma weight residual 1.513 1.431 0.082 3.90e-02 6.57e+02 4.37e+00 bond pdb=" CB ARG B 365 " pdb=" CG ARG B 365 " ideal model delta sigma weight residual 1.520 1.457 0.063 3.00e-02 1.11e+03 4.36e+00 bond pdb=" CB ARG C 365 " pdb=" CG ARG C 365 " ideal model delta sigma weight residual 1.520 1.458 0.062 3.00e-02 1.11e+03 4.32e+00 ... (remaining 13243 not shown) Histogram of bond angle deviations from ideal: 97.28 - 104.63: 209 104.63 - 111.98: 6283 111.98 - 119.34: 4761 119.34 - 126.69: 6602 126.69 - 134.04: 112 Bond angle restraints: 17967 Sorted by residual: angle pdb=" N SER C 174 " pdb=" CA SER C 174 " pdb=" C SER C 174 " ideal model delta sigma weight residual 111.37 116.86 -5.49 1.64e+00 3.72e-01 1.12e+01 angle pdb=" N SER A 174 " pdb=" CA SER A 174 " pdb=" C SER A 174 " ideal model delta sigma weight residual 111.37 116.84 -5.47 1.64e+00 3.72e-01 1.11e+01 angle pdb=" N SER B 174 " pdb=" CA SER B 174 " pdb=" C SER B 174 " ideal model delta sigma weight residual 111.37 116.81 -5.44 1.64e+00 3.72e-01 1.10e+01 angle pdb=" CA PRO B 81 " pdb=" N PRO B 81 " pdb=" CD PRO B 81 " ideal model delta sigma weight residual 112.00 107.39 4.61 1.40e+00 5.10e-01 1.09e+01 angle pdb=" CA TYR W 59 " pdb=" CB TYR W 59 " pdb=" CG TYR W 59 " ideal model delta sigma weight residual 113.90 119.81 -5.91 1.80e+00 3.09e-01 1.08e+01 ... (remaining 17962 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 7506 17.54 - 35.08: 483 35.08 - 52.62: 90 52.62 - 70.16: 15 70.16 - 87.70: 18 Dihedral angle restraints: 8112 sinusoidal: 3225 harmonic: 4887 Sorted by residual: dihedral pdb=" CA LYS A 173 " pdb=" C LYS A 173 " pdb=" N SER A 174 " pdb=" CA SER A 174 " ideal model delta harmonic sigma weight residual 180.00 -152.63 -27.37 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA LYS C 173 " pdb=" C LYS C 173 " pdb=" N SER C 174 " pdb=" CA SER C 174 " ideal model delta harmonic sigma weight residual -180.00 -152.66 -27.34 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA LYS B 173 " pdb=" C LYS B 173 " pdb=" N SER B 174 " pdb=" CA SER B 174 " ideal model delta harmonic sigma weight residual -180.00 -152.70 -27.30 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 8109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1538 0.066 - 0.132: 541 0.132 - 0.198: 43 0.198 - 0.264: 5 0.264 - 0.330: 9 Chirality restraints: 2136 Sorted by residual: chirality pdb=" CG LEU U 4 " pdb=" CB LEU U 4 " pdb=" CD1 LEU U 4 " pdb=" CD2 LEU U 4 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CG LEU W 4 " pdb=" CB LEU W 4 " pdb=" CD1 LEU W 4 " pdb=" CD2 LEU W 4 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CG LEU Y 4 " pdb=" CB LEU Y 4 " pdb=" CD1 LEU Y 4 " pdb=" CD2 LEU Y 4 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 2133 not shown) Planarity restraints: 2307 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 80 " 0.073 5.00e-02 4.00e+02 1.10e-01 1.92e+01 pdb=" N PRO B 81 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO B 81 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 81 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 80 " -0.073 5.00e-02 4.00e+02 1.09e-01 1.92e+01 pdb=" N PRO C 81 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO C 81 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 81 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 80 " 0.073 5.00e-02 4.00e+02 1.09e-01 1.92e+01 pdb=" N PRO A 81 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " 0.060 5.00e-02 4.00e+02 ... (remaining 2304 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 219 2.66 - 3.22: 12827 3.22 - 3.78: 20017 3.78 - 4.34: 28149 4.34 - 4.90: 46614 Nonbonded interactions: 107826 Sorted by model distance: nonbonded pdb=" NE2 GLN A 139 " pdb=" O GLU Y 1 " model vdw 2.106 2.520 nonbonded pdb=" OE1 GLU C 136 " pdb=" OG SER U 99 " model vdw 2.219 2.440 nonbonded pdb=" OE1 GLU A 136 " pdb=" OG SER Y 99 " model vdw 2.242 2.440 nonbonded pdb=" NE2 GLN C 139 " pdb=" O GLU U 1 " model vdw 2.247 2.520 nonbonded pdb=" NE2 GLN B 139 " pdb=" O GLU W 1 " model vdw 2.261 2.520 ... (remaining 107821 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'U' selection = chain 'W' selection = chain 'Y' } 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: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 11.370 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 38.650 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 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 : 0.009 0.082 13248 Z= 0.557 Angle : 1.045 8.992 17967 Z= 0.579 Chirality : 0.064 0.330 2136 Planarity : 0.007 0.110 2307 Dihedral : 13.034 87.697 4920 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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 (0.20), residues: 1677 helix: -0.35 (0.22), residues: 492 sheet: -0.23 (0.25), residues: 393 loop : -0.42 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.005 TRP C 308 HIS 0.015 0.005 HIS C 350 PHE 0.024 0.004 PHE W 67 TYR 0.042 0.006 TYR A 438 ARG 0.016 0.003 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 1.582 Fit side-chains revert: symmetry clash REVERT: A 362 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7382 (mm110) REVERT: A 413 THR cc_start: 0.7865 (p) cc_final: 0.7643 (m) REVERT: Y 31 ILE cc_start: 0.8385 (mm) cc_final: 0.8166 (mp) REVERT: B 84 ASP cc_start: 0.6974 (m-30) cc_final: 0.6669 (m-30) REVERT: W 99 SER cc_start: 0.7601 (t) cc_final: 0.7085 (t) REVERT: C 148 LYS cc_start: 0.7388 (mttt) cc_final: 0.7174 (mmmm) REVERT: C 362 GLN cc_start: 0.7581 (mm-40) cc_final: 0.7369 (mm-40) REVERT: C 413 THR cc_start: 0.7945 (p) cc_final: 0.7653 (m) outliers start: 0 outliers final: 5 residues processed: 338 average time/residue: 1.2423 time to fit residues: 455.5257 Evaluate side-chains 325 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 320 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain C residue 218 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.9980 chunk 127 optimal weight: 0.4980 chunk 70 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 85 optimal weight: 0.3980 chunk 68 optimal weight: 0.9990 chunk 131 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 98 optimal weight: 0.0970 chunk 152 optimal weight: 0.7980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 ASN A 399 ASN Y 111 GLN ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 GLN B 229 GLN B 292 GLN ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 ASN B 407 GLN ** W 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN U 111 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13248 Z= 0.236 Angle : 0.632 7.511 17967 Z= 0.333 Chirality : 0.046 0.156 2136 Planarity : 0.005 0.071 2307 Dihedral : 5.432 29.837 1834 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.39 % Allowed : 9.54 % Favored : 88.07 % 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: 0.11 (0.21), residues: 1677 helix: 0.62 (0.23), residues: 495 sheet: -0.26 (0.24), residues: 411 loop : 0.08 (0.25), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 308 HIS 0.006 0.002 HIS B 350 PHE 0.012 0.002 PHE U 67 TYR 0.020 0.002 TYR C 48 ARG 0.006 0.001 ARG U 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 328 time to evaluate : 1.518 Fit side-chains REVERT: A 90 LYS cc_start: 0.5893 (mppt) cc_final: 0.5492 (mppt) REVERT: A 270 ASP cc_start: 0.6669 (t0) cc_final: 0.6463 (t0) REVERT: A 362 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7394 (mm110) REVERT: A 422 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7475 (mt) REVERT: B 353 GLU cc_start: 0.6468 (tp30) cc_final: 0.6190 (tp30) REVERT: C 362 GLN cc_start: 0.7526 (mm-40) cc_final: 0.7309 (mm-40) REVERT: C 413 THR cc_start: 0.8020 (p) cc_final: 0.7729 (m) outliers start: 35 outliers final: 17 residues processed: 334 average time/residue: 1.2913 time to fit residues: 466.7569 Evaluate side-chains 335 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 317 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain Y residue 27 SER Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain U residue 78 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 136 optimal weight: 0.5980 chunk 151 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS A 399 ASN ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN B 292 GLN ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 ASN W 111 GLN C 127 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 ASN C 292 GLN C 395 ASN C 399 ASN C 402 ASN U 103 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13248 Z= 0.306 Angle : 0.615 7.129 17967 Z= 0.319 Chirality : 0.046 0.141 2136 Planarity : 0.004 0.064 2307 Dihedral : 5.080 22.500 1826 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.52 % Allowed : 12.61 % Favored : 84.87 % 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: 0.14 (0.21), residues: 1677 helix: 0.93 (0.23), residues: 498 sheet: -0.56 (0.22), residues: 456 loop : 0.15 (0.26), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 106 HIS 0.004 0.002 HIS C 350 PHE 0.014 0.002 PHE C 427 TYR 0.019 0.002 TYR A 207 ARG 0.005 0.000 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 333 time to evaluate : 1.557 Fit side-chains REVERT: A 23 THR cc_start: 0.8026 (OUTLIER) cc_final: 0.7773 (m) REVERT: A 45 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6728 (mt-10) REVERT: A 270 ASP cc_start: 0.6840 (t0) cc_final: 0.6570 (t0) REVERT: A 422 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7552 (mt) REVERT: B 23 THR cc_start: 0.8252 (OUTLIER) cc_final: 0.7920 (m) REVERT: B 353 GLU cc_start: 0.6605 (tp30) cc_final: 0.6190 (tp30) REVERT: C 357 SER cc_start: 0.7393 (p) cc_final: 0.7135 (p) REVERT: C 413 THR cc_start: 0.8009 (p) cc_final: 0.7775 (m) REVERT: C 422 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7384 (mt) outliers start: 37 outliers final: 11 residues processed: 343 average time/residue: 1.3079 time to fit residues: 486.1263 Evaluate side-chains 342 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 327 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain U residue 78 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 72 optimal weight: 0.3980 chunk 102 optimal weight: 8.9990 chunk 153 optimal weight: 0.0980 chunk 162 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 145 optimal weight: 0.0970 chunk 43 optimal weight: 0.6980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 162 GLN ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS A 362 GLN A 407 GLN B 162 GLN ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 GLN C 127 GLN C 162 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN C 399 ASN U 103 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13248 Z= 0.196 Angle : 0.554 7.258 17967 Z= 0.285 Chirality : 0.043 0.131 2136 Planarity : 0.004 0.054 2307 Dihedral : 4.786 20.403 1824 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.73 % Allowed : 14.72 % Favored : 82.55 % 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: 0.20 (0.21), residues: 1677 helix: 1.09 (0.23), residues: 501 sheet: -0.52 (0.23), residues: 444 loop : 0.05 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 308 HIS 0.005 0.001 HIS C 350 PHE 0.008 0.001 PHE Y 67 TYR 0.020 0.002 TYR A 207 ARG 0.005 0.000 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 333 time to evaluate : 1.438 Fit side-chains revert: symmetry clash REVERT: A 23 THR cc_start: 0.7924 (OUTLIER) cc_final: 0.7717 (m) REVERT: A 270 ASP cc_start: 0.6839 (t0) cc_final: 0.6526 (t0) REVERT: A 362 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7343 (mm110) REVERT: A 375 ARG cc_start: 0.7432 (tpp-160) cc_final: 0.7149 (mpt180) REVERT: A 422 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7512 (mt) REVERT: B 21 ASP cc_start: 0.7272 (t0) cc_final: 0.7068 (t0) REVERT: B 23 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7875 (m) REVERT: B 281 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7567 (mtp85) REVERT: B 353 GLU cc_start: 0.6627 (tp30) cc_final: 0.6275 (tp30) REVERT: W 105 TYR cc_start: 0.8055 (m-80) cc_final: 0.7794 (m-80) REVERT: C 357 SER cc_start: 0.7328 (p) cc_final: 0.7112 (p) REVERT: C 413 THR cc_start: 0.8113 (p) cc_final: 0.7741 (m) REVERT: C 422 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7364 (mt) outliers start: 40 outliers final: 14 residues processed: 343 average time/residue: 1.2866 time to fit residues: 478.2501 Evaluate side-chains 338 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 319 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 399 ASN Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain U residue 78 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.6980 chunk 92 optimal weight: 0.0570 chunk 2 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 138 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 40 optimal weight: 0.2980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS A 395 ASN A 418 ASN ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 402 ASN C 127 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN U 103 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13248 Z= 0.236 Angle : 0.564 6.885 17967 Z= 0.289 Chirality : 0.044 0.163 2136 Planarity : 0.004 0.051 2307 Dihedral : 4.759 20.430 1824 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.20 % Allowed : 15.54 % Favored : 81.25 % 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: 0.21 (0.21), residues: 1677 helix: 1.18 (0.23), residues: 501 sheet: -0.56 (0.23), residues: 444 loop : 0.03 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 106 HIS 0.006 0.001 HIS C 350 PHE 0.010 0.001 PHE C 427 TYR 0.020 0.002 TYR A 207 ARG 0.004 0.000 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 330 time to evaluate : 1.519 Fit side-chains revert: symmetry clash REVERT: A 270 ASP cc_start: 0.6874 (t0) cc_final: 0.6556 (t0) REVERT: A 357 SER cc_start: 0.7639 (p) cc_final: 0.7366 (t) REVERT: A 375 ARG cc_start: 0.7472 (tpp-160) cc_final: 0.7193 (mpt180) REVERT: A 422 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7548 (mt) REVERT: B 23 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7856 (m) REVERT: B 281 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7513 (mtp85) REVERT: B 353 GLU cc_start: 0.6629 (tp30) cc_final: 0.6289 (tp30) REVERT: W 105 TYR cc_start: 0.8071 (m-80) cc_final: 0.7783 (m-80) REVERT: C 357 SER cc_start: 0.7428 (p) cc_final: 0.7224 (p) REVERT: C 413 THR cc_start: 0.8168 (p) cc_final: 0.7801 (m) REVERT: C 422 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7386 (mt) REVERT: C 462 LYS cc_start: 0.7534 (tppp) cc_final: 0.7310 (ttpp) outliers start: 47 outliers final: 19 residues processed: 346 average time/residue: 1.2482 time to fit residues: 468.2442 Evaluate side-chains 336 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 313 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 399 ASN Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain U residue 78 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 75 optimal weight: 0.0770 chunk 13 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS A 359 ASN ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 402 ASN C 70 GLN C 127 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN U 103 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13248 Z= 0.321 Angle : 0.595 10.934 17967 Z= 0.302 Chirality : 0.045 0.146 2136 Planarity : 0.004 0.052 2307 Dihedral : 4.867 20.431 1824 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.07 % Allowed : 16.22 % Favored : 80.71 % 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: 0.09 (0.21), residues: 1677 helix: 1.14 (0.23), residues: 501 sheet: -0.68 (0.23), residues: 444 loop : -0.05 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 106 HIS 0.010 0.002 HIS C 350 PHE 0.013 0.002 PHE C 427 TYR 0.022 0.002 TYR C 207 ARG 0.005 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 328 time to evaluate : 1.418 Fit side-chains REVERT: A 270 ASP cc_start: 0.6919 (t0) cc_final: 0.6562 (t0) REVERT: A 357 SER cc_start: 0.7610 (p) cc_final: 0.7352 (t) REVERT: A 362 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7372 (mm110) REVERT: A 375 ARG cc_start: 0.7513 (tpp-160) cc_final: 0.7227 (mpt180) REVERT: A 422 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7593 (mt) REVERT: B 23 THR cc_start: 0.8072 (OUTLIER) cc_final: 0.7824 (m) REVERT: B 281 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7564 (mtp85) REVERT: B 353 GLU cc_start: 0.6644 (tp30) cc_final: 0.6336 (tp30) REVERT: W 105 TYR cc_start: 0.8114 (m-80) cc_final: 0.7791 (m-80) REVERT: C 357 SER cc_start: 0.7484 (p) cc_final: 0.7264 (p) REVERT: C 413 THR cc_start: 0.8143 (p) cc_final: 0.7826 (m) REVERT: C 422 ILE cc_start: 0.7717 (OUTLIER) cc_final: 0.7432 (mt) REVERT: C 462 LYS cc_start: 0.7541 (tppp) cc_final: 0.7310 (ttpp) outliers start: 45 outliers final: 18 residues processed: 341 average time/residue: 1.2729 time to fit residues: 471.4640 Evaluate side-chains 335 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 313 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 399 ASN Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain U residue 78 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 92 optimal weight: 0.0470 chunk 118 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 161 optimal weight: 3.9990 chunk 101 optimal weight: 0.0970 chunk 98 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN A 407 GLN ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN B 359 ASN B 402 ASN C 127 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN C 402 ASN U 103 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13248 Z= 0.225 Angle : 0.567 7.974 17967 Z= 0.288 Chirality : 0.044 0.156 2136 Planarity : 0.004 0.051 2307 Dihedral : 4.718 20.220 1824 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.79 % Allowed : 17.11 % Favored : 80.10 % 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: 0.17 (0.21), residues: 1677 helix: 1.22 (0.23), residues: 504 sheet: -0.64 (0.23), residues: 429 loop : -0.02 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 106 HIS 0.009 0.001 HIS C 350 PHE 0.015 0.001 PHE Y 67 TYR 0.025 0.002 TYR A 207 ARG 0.005 0.000 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 319 time to evaluate : 1.520 Fit side-chains revert: symmetry clash REVERT: A 270 ASP cc_start: 0.6894 (t0) cc_final: 0.6562 (t0) REVERT: A 375 ARG cc_start: 0.7477 (tpp-160) cc_final: 0.7203 (mpt180) REVERT: A 422 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7565 (mt) REVERT: B 23 THR cc_start: 0.8039 (OUTLIER) cc_final: 0.7798 (m) REVERT: B 281 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7542 (mtp85) REVERT: B 353 GLU cc_start: 0.6651 (tp30) cc_final: 0.6362 (tp30) REVERT: W 105 TYR cc_start: 0.8068 (m-80) cc_final: 0.7818 (m-80) REVERT: C 357 SER cc_start: 0.7456 (p) cc_final: 0.7240 (p) REVERT: C 413 THR cc_start: 0.8164 (p) cc_final: 0.7828 (m) REVERT: C 422 ILE cc_start: 0.7717 (OUTLIER) cc_final: 0.7398 (mt) REVERT: C 462 LYS cc_start: 0.7530 (tppp) cc_final: 0.7302 (ttpp) outliers start: 41 outliers final: 22 residues processed: 332 average time/residue: 1.2736 time to fit residues: 458.4747 Evaluate side-chains 341 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 315 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 78 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 110 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 15 optimal weight: 0.0050 chunk 127 optimal weight: 2.9990 chunk 147 optimal weight: 0.0870 overall best weight: 0.4972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS A 359 ASN ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 ASN B 402 ASN C 292 GLN ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN U 103 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13248 Z= 0.245 Angle : 0.580 9.536 17967 Z= 0.291 Chirality : 0.044 0.129 2136 Planarity : 0.004 0.048 2307 Dihedral : 4.689 21.876 1824 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.59 % Allowed : 17.66 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.21), residues: 1677 helix: 1.21 (0.23), residues: 504 sheet: -0.65 (0.23), residues: 429 loop : 0.00 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 473 HIS 0.011 0.001 HIS C 350 PHE 0.022 0.001 PHE Y 67 TYR 0.027 0.002 TYR C 207 ARG 0.006 0.000 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 312 time to evaluate : 1.522 Fit side-chains revert: symmetry clash REVERT: A 231 ILE cc_start: 0.8334 (mt) cc_final: 0.8110 (mp) REVERT: A 270 ASP cc_start: 0.6881 (t0) cc_final: 0.6560 (t0) REVERT: A 375 ARG cc_start: 0.7481 (tpp-160) cc_final: 0.7220 (mpt180) REVERT: A 422 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7558 (mt) REVERT: B 23 THR cc_start: 0.8032 (OUTLIER) cc_final: 0.7794 (m) REVERT: B 231 ILE cc_start: 0.8489 (mt) cc_final: 0.8189 (mp) REVERT: B 281 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7521 (mtp85) REVERT: B 353 GLU cc_start: 0.6656 (tp30) cc_final: 0.6386 (tp30) REVERT: C 357 SER cc_start: 0.7471 (p) cc_final: 0.7256 (p) REVERT: C 419 THR cc_start: 0.7610 (OUTLIER) cc_final: 0.7271 (p) REVERT: C 422 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7393 (mt) REVERT: C 462 LYS cc_start: 0.7527 (tppp) cc_final: 0.7296 (ttpp) outliers start: 38 outliers final: 21 residues processed: 328 average time/residue: 1.2912 time to fit residues: 458.4464 Evaluate side-chains 339 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 313 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 78 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 136 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 159 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS A 359 ASN ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 ASN B 402 ASN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN U 103 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13248 Z= 0.317 Angle : 0.617 11.042 17967 Z= 0.309 Chirality : 0.046 0.164 2136 Planarity : 0.004 0.049 2307 Dihedral : 4.814 22.030 1824 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.66 % Allowed : 18.13 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.21), residues: 1677 helix: 1.12 (0.23), residues: 504 sheet: -0.80 (0.23), residues: 444 loop : 0.01 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 106 HIS 0.012 0.002 HIS C 350 PHE 0.024 0.002 PHE Y 67 TYR 0.032 0.002 TYR A 207 ARG 0.007 0.000 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 298 time to evaluate : 1.579 Fit side-chains revert: symmetry clash REVERT: A 22 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.8005 (mm) REVERT: A 231 ILE cc_start: 0.8320 (mt) cc_final: 0.8095 (mp) REVERT: A 270 ASP cc_start: 0.6888 (t0) cc_final: 0.6553 (t0) REVERT: A 357 SER cc_start: 0.7521 (p) cc_final: 0.7283 (t) REVERT: A 362 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7364 (mm110) REVERT: A 375 ARG cc_start: 0.7489 (tpp-160) cc_final: 0.7245 (mpt180) REVERT: A 393 THR cc_start: 0.7936 (p) cc_final: 0.7696 (p) REVERT: B 23 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7813 (m) REVERT: B 231 ILE cc_start: 0.8479 (mt) cc_final: 0.8182 (mp) REVERT: B 281 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7526 (mtp85) REVERT: B 353 GLU cc_start: 0.6688 (tp30) cc_final: 0.6415 (tp30) REVERT: B 397 ILE cc_start: 0.7512 (mm) cc_final: 0.7277 (mm) REVERT: C 156 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7793 (mtmm) REVERT: C 357 SER cc_start: 0.7473 (p) cc_final: 0.7264 (p) REVERT: C 397 ILE cc_start: 0.7491 (mm) cc_final: 0.7145 (mm) REVERT: C 419 THR cc_start: 0.7615 (OUTLIER) cc_final: 0.7219 (p) REVERT: C 422 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7425 (mt) REVERT: C 462 LYS cc_start: 0.7541 (tppp) cc_final: 0.7324 (ttpp) outliers start: 39 outliers final: 17 residues processed: 316 average time/residue: 1.2501 time to fit residues: 429.2515 Evaluate side-chains 320 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 297 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 386 ASN Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain C residue 156 LYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 110 optimal weight: 0.1980 chunk 167 optimal weight: 0.0470 chunk 154 optimal weight: 0.5980 chunk 133 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 105 optimal weight: 0.0970 chunk 141 optimal weight: 1.9990 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN A 407 GLN ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 359 ASN B 386 ASN B 402 ASN C 70 GLN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN U 103 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13248 Z= 0.204 Angle : 0.601 12.768 17967 Z= 0.298 Chirality : 0.044 0.163 2136 Planarity : 0.004 0.067 2307 Dihedral : 4.694 21.647 1824 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.70 % Allowed : 19.22 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.21), residues: 1677 helix: 1.23 (0.23), residues: 504 sheet: -0.72 (0.23), residues: 429 loop : 0.04 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 308 HIS 0.008 0.001 HIS C 350 PHE 0.020 0.001 PHE Y 67 TYR 0.029 0.002 TYR C 207 ARG 0.007 0.000 ARG B 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 311 time to evaluate : 1.450 Fit side-chains revert: symmetry clash REVERT: A 22 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7968 (mm) REVERT: A 231 ILE cc_start: 0.8258 (mt) cc_final: 0.8024 (mp) REVERT: A 270 ASP cc_start: 0.6859 (t0) cc_final: 0.6535 (t0) REVERT: B 23 THR cc_start: 0.8013 (OUTLIER) cc_final: 0.7776 (m) REVERT: B 38 MET cc_start: 0.7077 (ttp) cc_final: 0.6797 (ttp) REVERT: B 231 ILE cc_start: 0.8457 (mt) cc_final: 0.8139 (mp) REVERT: B 281 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7516 (mtp85) REVERT: C 156 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7792 (mtmm) REVERT: C 397 ILE cc_start: 0.7433 (mm) cc_final: 0.7120 (mm) REVERT: C 419 THR cc_start: 0.7606 (OUTLIER) cc_final: 0.7218 (p) REVERT: C 422 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7405 (mt) REVERT: C 462 LYS cc_start: 0.7527 (tppp) cc_final: 0.7300 (ttpp) REVERT: C 464 LYS cc_start: 0.8175 (mtpt) cc_final: 0.7945 (mtpt) outliers start: 25 outliers final: 14 residues processed: 323 average time/residue: 1.3179 time to fit residues: 461.3329 Evaluate side-chains 317 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 297 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 386 ASN Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain C residue 156 LYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 137 optimal weight: 0.0170 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN A 407 GLN ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN C 292 GLN ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN U 103 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.145085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.122371 restraints weight = 18016.496| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.08 r_work: 0.3409 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13248 Z= 0.263 Angle : 0.612 12.477 17967 Z= 0.305 Chirality : 0.045 0.162 2136 Planarity : 0.004 0.057 2307 Dihedral : 4.702 21.345 1824 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.84 % Allowed : 19.22 % Favored : 78.94 % 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: 0.19 (0.21), residues: 1677 helix: 1.24 (0.23), residues: 504 sheet: -0.71 (0.23), residues: 429 loop : 0.04 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 308 HIS 0.007 0.001 HIS A 350 PHE 0.017 0.001 PHE Y 67 TYR 0.031 0.002 TYR A 207 ARG 0.007 0.000 ARG B 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6864.39 seconds wall clock time: 119 minutes 32.04 seconds (7172.04 seconds total)