Starting phenix.real_space_refine on Tue Aug 6 02:50:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5a_42981/08_2024/8v5a_42981.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5a_42981/08_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_42981/08_2024/8v5a_42981.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5a_42981/08_2024/8v5a_42981.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5a_42981/08_2024/8v5a_42981.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5a_42981/08_2024/8v5a_42981.cif" } 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 7.87, per 1000 atoms: 0.60 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: 4.99 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: 1.64 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: 3.88 Time building geometry restraints manager: 5.46 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 3.120 nonbonded pdb=" OE1 GLU C 136 " pdb=" OG SER U 99 " model vdw 2.219 3.040 nonbonded pdb=" OE1 GLU A 136 " pdb=" OG SER Y 99 " model vdw 2.242 3.040 nonbonded pdb=" NE2 GLN C 139 " pdb=" O GLU U 1 " model vdw 2.247 3.120 nonbonded pdb=" NE2 GLN B 139 " pdb=" O GLU W 1 " model vdw 2.261 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 37.360 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.800 ------------------------------------------------------------------------------- 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 : 1.378 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: 1.2500 time to fit residues: 459.0331 Evaluate side-chains 325 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 320 time to evaluate : 1.518 ------------------------------------------------------------------------------- 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: 0.0970 chunk 127 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 85 optimal weight: 0.0980 chunk 68 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 98 optimal weight: 0.0870 chunk 152 optimal weight: 0.6980 overall best weight: 0.3156 ------------------------------------------------------------------------------- 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 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 ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN U 103 ASN U 111 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13248 Z= 0.209 Angle : 0.643 7.709 17967 Z= 0.340 Chirality : 0.046 0.158 2136 Planarity : 0.004 0.068 2307 Dihedral : 5.457 29.684 1834 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.45 % Allowed : 9.41 % Favored : 88.14 % 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: 0.03 (0.21), residues: 1677 helix: 0.56 (0.23), residues: 495 sheet: -0.43 (0.24), residues: 411 loop : 0.12 (0.25), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 308 HIS 0.006 0.001 HIS A 350 PHE 0.015 0.001 PHE U 67 TYR 0.021 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 376 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 340 time to evaluate : 1.324 Fit side-chains REVERT: A 90 LYS cc_start: 0.5896 (mppt) cc_final: 0.5493 (mppt) REVERT: A 362 GLN cc_start: 0.7582 (mm-40) cc_final: 0.7368 (mm110) REVERT: A 422 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7489 (mt) REVERT: B 353 GLU cc_start: 0.6453 (tp30) cc_final: 0.6153 (tp30) REVERT: C 24 LYS cc_start: 0.7615 (mtpt) cc_final: 0.7324 (mtpt) REVERT: C 362 GLN cc_start: 0.7526 (mm-40) cc_final: 0.7298 (mm-40) REVERT: C 413 THR cc_start: 0.8037 (p) cc_final: 0.7671 (m) outliers start: 36 outliers final: 17 residues processed: 346 average time/residue: 1.2955 time to fit residues: 485.1599 Evaluate side-chains 330 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 312 time to evaluate : 1.457 ------------------------------------------------------------------------------- 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 420 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 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 420 ILE Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain U residue 31 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: 1.9990 chunk 47 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 103 optimal weight: 0.1980 chunk 42 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 136 optimal weight: 0.3980 chunk 151 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 359 ASN A 395 ASN A 399 ASN Y 103 ASN B 272 ASN B 292 GLN B 350 HIS B 399 ASN ** W 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN C 180 ASN C 292 GLN C 395 ASN U 103 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.2068 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= 0.293 Angle : 0.625 7.328 17967 Z= 0.323 Chirality : 0.045 0.137 2136 Planarity : 0.004 0.063 2307 Dihedral : 5.081 22.298 1826 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.00 % Allowed : 12.75 % Favored : 84.25 % 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: 0.11 (0.21), residues: 1677 helix: 0.87 (0.23), residues: 501 sheet: -0.59 (0.23), residues: 414 loop : 0.10 (0.25), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP W 106 HIS 0.005 0.002 HIS C 350 PHE 0.013 0.002 PHE C 427 TYR 0.020 0.002 TYR A 207 ARG 0.006 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 385 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 341 time to evaluate : 1.459 Fit side-chains REVERT: A 362 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7382 (mm110) REVERT: A 422 ILE cc_start: 0.7846 (OUTLIER) cc_final: 0.7609 (mt) REVERT: B 281 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7545 (mtp85) REVERT: B 353 GLU cc_start: 0.6596 (tp30) cc_final: 0.6215 (tp30) REVERT: C 413 THR cc_start: 0.8023 (p) cc_final: 0.7746 (m) REVERT: C 422 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7426 (mt) outliers start: 44 outliers final: 17 residues processed: 350 average time/residue: 1.4083 time to fit residues: 532.8614 Evaluate side-chains 357 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 337 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Y residue 25 SER Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 226 ILE 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 413 THR Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain U residue 31 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: 0.9980 chunk 114 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 72 optimal weight: 0.0980 chunk 102 optimal weight: 20.0000 chunk 153 optimal weight: 0.9990 chunk 162 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 145 optimal weight: 0.1980 chunk 43 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 W 111 GLN C 26 GLN C 127 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN C 350 HIS 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: 0.6988 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13248 Z= 0.251 Angle : 0.582 7.627 17967 Z= 0.299 Chirality : 0.044 0.132 2136 Planarity : 0.004 0.055 2307 Dihedral : 4.899 21.204 1824 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.20 % Allowed : 15.20 % 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: 0.03 (0.21), residues: 1677 helix: 0.96 (0.23), residues: 501 sheet: -0.86 (0.23), residues: 447 loop : 0.14 (0.25), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 106 HIS 0.002 0.001 HIS A 315 PHE 0.011 0.001 PHE C 427 TYR 0.019 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 385 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 338 time to evaluate : 1.461 Fit side-chains REVERT: B 21 ASP cc_start: 0.7291 (t0) cc_final: 0.7075 (t0) REVERT: B 23 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7873 (m) REVERT: B 281 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7545 (mtp85) REVERT: B 353 GLU cc_start: 0.6637 (tp30) cc_final: 0.6295 (tp30) REVERT: C 375 ARG cc_start: 0.7630 (mmt-90) cc_final: 0.7426 (mpt180) REVERT: C 413 THR cc_start: 0.8048 (p) cc_final: 0.7738 (m) REVERT: C 422 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7441 (mt) REVERT: C 462 LYS cc_start: 0.7593 (tppp) cc_final: 0.7369 (ttpp) outliers start: 47 outliers final: 17 residues processed: 354 average time/residue: 1.2888 time to fit residues: 494.2823 Evaluate side-chains 352 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 332 time to evaluate : 1.488 ------------------------------------------------------------------------------- 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 420 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 226 ILE 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 W residue 25 SER 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 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: 0.8980 chunk 92 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 120 optimal weight: 0.0870 chunk 67 optimal weight: 0.7980 chunk 138 optimal weight: 0.0010 chunk 112 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 overall best weight: 0.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS A 359 ASN A 362 GLN A 395 ASN A 418 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 407 GLN C 127 GLN C 162 GLN C 272 ASN C 292 GLN C 399 ASN U 103 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13248 Z= 0.214 Angle : 0.566 7.058 17967 Z= 0.292 Chirality : 0.044 0.139 2136 Planarity : 0.004 0.050 2307 Dihedral : 4.793 20.759 1824 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.20 % Allowed : 16.56 % Favored : 80.23 % 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: 0.06 (0.21), residues: 1677 helix: 1.09 (0.23), residues: 501 sheet: -0.95 (0.23), residues: 447 loop : 0.15 (0.25), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 106 HIS 0.007 0.001 HIS C 350 PHE 0.009 0.001 PHE C 427 TYR 0.021 0.002 TYR A 207 ARG 0.004 0.000 ARG C 375 *********************** 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 379 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 332 time to evaluate : 1.491 Fit side-chains revert: symmetry clash REVERT: A 362 GLN cc_start: 0.7665 (mm-40) cc_final: 0.7365 (mm110) REVERT: B 21 ASP cc_start: 0.7239 (t0) cc_final: 0.7036 (t0) REVERT: B 23 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7837 (m) REVERT: B 281 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7428 (mtp85) REVERT: B 353 GLU cc_start: 0.6617 (tp30) cc_final: 0.6313 (tp30) REVERT: B 365 ARG cc_start: 0.8156 (mtp180) cc_final: 0.7892 (mtp180) REVERT: W 105 TYR cc_start: 0.8151 (m-80) cc_final: 0.7858 (m-80) REVERT: C 422 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7402 (mt) REVERT: C 462 LYS cc_start: 0.7581 (tppp) cc_final: 0.7369 (ttpp) outliers start: 47 outliers final: 20 residues processed: 347 average time/residue: 1.2994 time to fit residues: 488.0963 Evaluate side-chains 344 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 321 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 296 VAL 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 420 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 328 VAL Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain W residue 25 SER Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain W residue 53 SER 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 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: 1.9990 chunk 146 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 359 ASN B 407 GLN C 127 GLN 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13248 Z= 0.323 Angle : 0.596 6.812 17967 Z= 0.307 Chirality : 0.046 0.224 2136 Planarity : 0.004 0.051 2307 Dihedral : 4.894 24.044 1824 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.54 % Allowed : 16.84 % Favored : 79.62 % 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: -0.03 (0.21), residues: 1677 helix: 1.05 (0.23), residues: 501 sheet: -1.10 (0.22), residues: 477 loop : 0.21 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 106 HIS 0.010 0.001 HIS C 350 PHE 0.013 0.002 PHE C 427 TYR 0.023 0.002 TYR C 207 ARG 0.006 0.000 ARG A 375 *********************** 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: 52 poor density : 321 time to evaluate : 1.441 Fit side-chains revert: symmetry clash REVERT: A 375 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7225 (mpt180) REVERT: B 23 THR cc_start: 0.8083 (OUTLIER) cc_final: 0.7832 (m) REVERT: B 281 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7515 (mtp85) REVERT: B 353 GLU cc_start: 0.6656 (tp30) cc_final: 0.6378 (tp30) REVERT: B 375 ARG cc_start: 0.7601 (mpt180) cc_final: 0.7398 (mpt180) REVERT: W 105 TYR cc_start: 0.8166 (m-80) cc_final: 0.7820 (m-80) REVERT: C 375 ARG cc_start: 0.7602 (mpt180) cc_final: 0.7258 (mpt180) REVERT: C 422 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7432 (mt) REVERT: C 462 LYS cc_start: 0.7547 (tppp) cc_final: 0.7294 (ttpp) outliers start: 52 outliers final: 24 residues processed: 341 average time/residue: 1.2771 time to fit residues: 472.8109 Evaluate side-chains 345 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 317 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain B residue 23 THR 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 360 ILE Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain W residue 25 SER 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 46 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 262 ILE 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 31 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: 3.9990 chunk 18 optimal weight: 0.3980 chunk 92 optimal weight: 0.6980 chunk 118 optimal weight: 0.2980 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 90 optimal weight: 0.1980 chunk 161 optimal weight: 0.0270 chunk 101 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 overall best weight: 0.3238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS A 362 GLN A 407 GLN A 461 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 ASN C 127 GLN C 292 GLN C 399 ASN U 103 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13248 Z= 0.198 Angle : 0.560 7.243 17967 Z= 0.287 Chirality : 0.043 0.134 2136 Planarity : 0.004 0.047 2307 Dihedral : 4.710 22.181 1824 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.34 % Allowed : 18.00 % Favored : 78.66 % 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: 0.05 (0.21), residues: 1677 helix: 1.21 (0.23), residues: 501 sheet: -1.14 (0.22), residues: 477 loop : 0.25 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 308 HIS 0.010 0.001 HIS C 350 PHE 0.013 0.001 PHE Y 67 TYR 0.027 0.002 TYR A 207 ARG 0.007 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 374 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 325 time to evaluate : 1.552 Fit side-chains revert: symmetry clash REVERT: A 362 GLN cc_start: 0.7636 (mm-40) cc_final: 0.7362 (mm110) REVERT: B 23 THR cc_start: 0.8021 (OUTLIER) cc_final: 0.7783 (m) REVERT: B 231 ILE cc_start: 0.8527 (mt) cc_final: 0.8242 (mp) REVERT: B 281 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7441 (mtp85) REVERT: B 353 GLU cc_start: 0.6631 (tp30) cc_final: 0.6374 (tp30) REVERT: W 105 TYR cc_start: 0.8165 (m-80) cc_final: 0.7843 (m-80) REVERT: C 375 ARG cc_start: 0.7563 (mpt180) cc_final: 0.7240 (mpt180) REVERT: C 422 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7411 (mt) REVERT: C 462 LYS cc_start: 0.7511 (tppp) cc_final: 0.7295 (ttpp) REVERT: C 471 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7644 (mtpt) outliers start: 49 outliers final: 22 residues processed: 341 average time/residue: 1.2965 time to fit residues: 478.6174 Evaluate side-chains 340 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 314 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 30 THR 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 284 LEU 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 420 ILE Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain W residue 25 SER 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 422 ILE Chi-restraints excluded: chain C residue 471 LYS 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: 3.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 102 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 127 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS A 359 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 359 ASN B 386 ASN B 407 GLN B 418 ASN C 127 GLN C 292 GLN C 399 ASN U 103 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13248 Z= 0.274 Angle : 0.594 9.598 17967 Z= 0.301 Chirality : 0.045 0.144 2136 Planarity : 0.004 0.047 2307 Dihedral : 4.745 21.937 1824 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.73 % Allowed : 18.88 % Favored : 78.39 % 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: 0.02 (0.21), residues: 1677 helix: 1.23 (0.23), residues: 501 sheet: -1.17 (0.22), residues: 477 loop : 0.22 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 106 HIS 0.011 0.001 HIS C 350 PHE 0.019 0.002 PHE Y 67 TYR 0.028 0.002 TYR C 207 ARG 0.004 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 351 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 311 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 393 THR cc_start: 0.7911 (p) cc_final: 0.7631 (p) REVERT: B 23 THR cc_start: 0.8027 (OUTLIER) cc_final: 0.7786 (m) REVERT: B 231 ILE cc_start: 0.8506 (mt) cc_final: 0.8222 (mp) REVERT: B 281 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7465 (mtp85) REVERT: W 105 TYR cc_start: 0.8175 (m-80) cc_final: 0.7863 (m-80) REVERT: C 422 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7401 (mt) REVERT: C 462 LYS cc_start: 0.7556 (tppp) cc_final: 0.7314 (ttpp) outliers start: 40 outliers final: 21 residues processed: 328 average time/residue: 1.2913 time to fit residues: 459.4949 Evaluate side-chains 332 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 308 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 284 LEU 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 360 ILE Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain W residue 25 SER 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 422 ILE Chi-restraints excluded: chain U residue 78 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.52 > 50: distance: 121 - 183: 33.061 distance: 148 - 152: 18.428 distance: 152 - 153: 15.604 distance: 153 - 154: 28.334 distance: 153 - 156: 35.280 distance: 154 - 155: 43.694 distance: 154 - 158: 18.433 distance: 156 - 157: 25.321 distance: 159 - 162: 27.488 distance: 160 - 161: 40.227 distance: 160 - 170: 8.361 distance: 162 - 163: 26.004 distance: 163 - 164: 9.429 distance: 163 - 165: 4.322 distance: 164 - 166: 14.181 distance: 165 - 167: 13.001 distance: 166 - 168: 12.877 distance: 167 - 168: 15.525 distance: 168 - 169: 31.660 distance: 170 - 171: 49.247 distance: 171 - 172: 31.067 distance: 171 - 174: 8.254 distance: 172 - 173: 11.689 distance: 172 - 178: 33.945 distance: 174 - 175: 54.466 distance: 174 - 176: 56.919 distance: 175 - 177: 49.117 distance: 178 - 179: 43.927 distance: 179 - 180: 43.411 distance: 179 - 182: 15.569 distance: 180 - 181: 18.449 distance: 180 - 184: 38.996 distance: 182 - 183: 37.151 distance: 184 - 185: 30.290 distance: 184 - 190: 13.547 distance: 185 - 186: 35.008 distance: 185 - 188: 43.503 distance: 186 - 187: 22.419 distance: 186 - 191: 31.378 distance: 188 - 189: 37.744 distance: 189 - 190: 10.041 distance: 191 - 192: 26.843 distance: 192 - 193: 47.128 distance: 193 - 194: 14.087 distance: 193 - 197: 9.307 distance: 195 - 196: 39.871 distance: 197 - 198: 15.378 distance: 198 - 199: 28.573 distance: 198 - 201: 13.993 distance: 199 - 200: 12.844 distance: 199 - 205: 42.474 distance: 201 - 202: 20.155 distance: 202 - 203: 32.620 distance: 202 - 204: 25.213 distance: 205 - 206: 20.647 distance: 205 - 211: 32.526 distance: 206 - 207: 19.615 distance: 206 - 209: 19.868 distance: 207 - 208: 19.268 distance: 207 - 212: 28.273 distance: 209 - 210: 29.780 distance: 210 - 211: 25.313 distance: 212 - 213: 45.892 distance: 213 - 214: 33.593 distance: 214 - 215: 53.552 distance: 214 - 216: 14.751 distance: 216 - 217: 12.578 distance: 217 - 218: 12.580 distance: 217 - 220: 28.165 distance: 218 - 219: 20.804 distance: 218 - 227: 27.217 distance: 220 - 221: 42.730 distance: 221 - 222: 14.772 distance: 221 - 223: 27.040 distance: 222 - 224: 27.180 distance: 223 - 225: 18.431 distance: 224 - 226: 8.248 distance: 225 - 226: 29.640