Starting phenix.real_space_refine on Fri Feb 23 06:49:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3n_13181/02_2024/7p3n_13181_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3n_13181/02_2024/7p3n_13181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3n_13181/02_2024/7p3n_13181.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3n_13181/02_2024/7p3n_13181.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3n_13181/02_2024/7p3n_13181_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3n_13181/02_2024/7p3n_13181_updated.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 4 5.21 5 S 147 5.16 5 C 23633 2.51 5 N 6307 2.21 5 O 7012 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 52": "OE1" <-> "OE2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "B GLU 8": "OE1" <-> "OE2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B GLU 461": "OE1" <-> "OE2" Residue "B ARG 477": "NH1" <-> "NH2" Residue "B GLU 498": "OE1" <-> "OE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C GLU 332": "OE1" <-> "OE2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C GLU 461": "OE1" <-> "OE2" Residue "C GLU 479": "OE1" <-> "OE2" Residue "D ARG 5": "NH1" <-> "NH2" Residue "D ARG 20": "NH1" <-> "NH2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D ARG 181": "NH1" <-> "NH2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "D GLU 357": "OE1" <-> "OE2" Residue "D GLU 386": "OE1" <-> "OE2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "E ARG 20": "NH1" <-> "NH2" Residue "E GLU 180": "OE1" <-> "OE2" Residue "E ARG 217": "NH1" <-> "NH2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E GLU 232": "OE1" <-> "OE2" Residue "E ARG 240": "NH1" <-> "NH2" Residue "E TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 258": "OE1" <-> "OE2" Residue "E ARG 371": "NH1" <-> "NH2" Residue "E GLU 427": "OE1" <-> "OE2" Residue "E GLU 439": "OE1" <-> "OE2" Residue "F GLU 59": "OE1" <-> "OE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "F GLU 232": "OE1" <-> "OE2" Residue "F ARG 251": "NH1" <-> "NH2" Residue "F GLU 285": "OE1" <-> "OE2" Residue "F ARG 363": "NH1" <-> "NH2" Residue "F GLU 374": "OE1" <-> "OE2" Residue "F GLU 389": "OE1" <-> "OE2" Residue "F GLU 413": "OE1" <-> "OE2" Residue "H GLU 36": "OE1" <-> "OE2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 43": "OE1" <-> "OE2" Residue "Q GLU 36": "OE1" <-> "OE2" Residue "S GLU 2": "OE1" <-> "OE2" Residue "a GLU 87": "OE1" <-> "OE2" Residue "a ARG 182": "NH1" <-> "NH2" Residue "a ARG 224": "NH1" <-> "NH2" Residue "a GLU 240": "OE1" <-> "OE2" Residue "b ARG 38": "NH1" <-> "NH2" Residue "b ARG 91": "NH1" <-> "NH2" Residue "b GLU 97": "OE1" <-> "OE2" Residue "b GLU 112": "OE1" <-> "OE2" Residue "b GLU 143": "OE1" <-> "OE2" Residue "d GLU 98": "OE1" <-> "OE2" Residue "d GLU 121": "OE1" <-> "OE2" Residue "d GLU 131": "OE1" <-> "OE2" Residue "e ARG 51": "NH1" <-> "NH2" Residue "e GLU 60": "OE1" <-> "OE2" Residue "e ARG 85": "NH1" <-> "NH2" Residue "g GLU 62": "OE1" <-> "OE2" Residue "g ARG 66": "NH1" <-> "NH2" Residue "g GLU 108": "OE1" <-> "OE2" Residue "g GLU 164": "OE1" <-> "OE2" Residue "g GLU 196": "OE1" <-> "OE2" Residue "g ARG 224": "NH1" <-> "NH2" Residue "g GLU 227": "OE1" <-> "OE2" Residue "g GLU 281": "OE1" <-> "OE2" Residue "p GLU 77": "OE1" <-> "OE2" Residue "p ARG 121": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 37114 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3875 Classifications: {'peptide': 512} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "B" Number of atoms: 3892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3892 Classifications: {'peptide': 514} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 495} Chain: "C" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3821 Classifications: {'peptide': 506} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 488} Chain: "D" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3533 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 441} Chain: "E" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 440} Chain: "F" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 440} Chain: "G" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 577 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "H" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "J" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "K" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 577 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "L" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 577 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "O" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "P" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "Q" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "R" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "S" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 577 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2104 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 15, 'TRANS': 261} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 58 Chain: "b" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1112 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain: "d" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1347 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "e" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1010 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "g" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2243 Classifications: {'peptide': 288} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 279} Chain: "p" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1185 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.74, per 1000 atoms: 0.50 Number of scatterers: 37114 At special positions: 0 Unit cell: (135.15, 138.55, 239.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 147 16.00 P 11 15.00 Mg 4 11.99 O 7012 8.00 N 6307 7.00 C 23633 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.75 Conformation dependent library (CDL) restraints added in 7.6 seconds 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8914 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 178 helices and 25 sheets defined 54.6% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.99 Creating SS restraints... Processing helix chain 'A' and resid 4 through 14 Processing helix chain 'A' and resid 18 through 25 removed outlier: 3.660A pdb=" N THR A 25 " --> pdb=" O ASP A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 176 through 187 removed outlier: 3.705A pdb=" N ASP A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 233 through 252 Proline residue: A 240 - end of helix removed outlier: 3.727A pdb=" N PHE A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 277 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 289 through 301 removed outlier: 4.093A pdb=" N GLU A 300 " --> pdb=" O ARG A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 313 Processing helix chain 'A' and resid 341 through 349 removed outlier: 3.841A pdb=" N SER A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 385 through 403 removed outlier: 4.720A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLY A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.953A pdb=" N GLN A 409 " --> pdb=" O ALA A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 432 Processing helix chain 'A' and resid 442 through 453 Processing helix chain 'A' and resid 463 through 479 removed outlier: 3.666A pdb=" N VAL A 466 " --> pdb=" O LYS A 463 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP A 467 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 477 " --> pdb=" O ALA A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 490 Processing helix chain 'A' and resid 495 through 510 Processing helix chain 'B' and resid 10 through 18 Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 137 through 139 No H-bonds generated for 'chain 'B' and resid 137 through 139' Processing helix chain 'B' and resid 154 through 157 No H-bonds generated for 'chain 'B' and resid 154 through 157' Processing helix chain 'B' and resid 176 through 190 removed outlier: 3.530A pdb=" N ALA B 180 " --> pdb=" O LYS B 176 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASN B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 233 through 253 Proline residue: B 240 - end of helix removed outlier: 3.657A pdb=" N PHE B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 277 Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 289 through 301 removed outlier: 3.600A pdb=" N PHE B 292 " --> pdb=" O GLY B 289 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG B 297 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU B 300 " --> pdb=" O ARG B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 313 Processing helix chain 'B' and resid 341 through 347 Processing helix chain 'B' and resid 358 through 361 No H-bonds generated for 'chain 'B' and resid 358 through 361' Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 385 through 407 removed outlier: 4.110A pdb=" N GLY B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLY B 393 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ALA B 406 " --> pdb=" O ARG B 402 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N PHE B 407 " --> pdb=" O GLU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 429 Processing helix chain 'B' and resid 442 through 453 Processing helix chain 'B' and resid 462 through 479 removed outlier: 4.868A pdb=" N VAL B 466 " --> pdb=" O LYS B 463 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B 475 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 490 Processing helix chain 'B' and resid 495 through 511 Processing helix chain 'C' and resid 7 through 17 Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 137 through 139 No H-bonds generated for 'chain 'C' and resid 137 through 139' Processing helix chain 'C' and resid 153 through 157 Processing helix chain 'C' and resid 177 through 190 removed outlier: 3.636A pdb=" N LYS C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ASN C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER C 190 " --> pdb=" O ALA C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 233 through 253 Proline residue: C 240 - end of helix removed outlier: 3.589A pdb=" N TYR C 249 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE C 250 " --> pdb=" O MET C 246 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 277 Processing helix chain 'C' and resid 284 through 286 No H-bonds generated for 'chain 'C' and resid 284 through 286' Processing helix chain 'C' and resid 289 through 301 removed outlier: 4.255A pdb=" N ARG C 297 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU C 300 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 313 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 341 through 347 Processing helix chain 'C' and resid 358 through 362 Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 394 through 409 removed outlier: 3.730A pdb=" N GLN C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 431 Processing helix chain 'C' and resid 442 through 453 Processing helix chain 'C' and resid 463 through 479 removed outlier: 3.797A pdb=" N VAL C 466 " --> pdb=" O LYS C 463 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER C 478 " --> pdb=" O TYR C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 490 Processing helix chain 'C' and resid 495 through 509 Processing helix chain 'D' and resid 80 through 82 No H-bonds generated for 'chain 'D' and resid 80 through 82' Processing helix chain 'D' and resid 130 through 135 Processing helix chain 'D' and resid 154 through 168 Processing helix chain 'D' and resid 182 through 194 Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 212 through 231 removed outlier: 4.733A pdb=" N ALA D 219 " --> pdb=" O ARG D 215 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU D 220 " --> pdb=" O LEU D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 262 Processing helix chain 'D' and resid 274 through 285 removed outlier: 4.231A pdb=" N ALA D 277 " --> pdb=" O PRO D 274 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLU D 285 " --> pdb=" O VAL D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 306 No H-bonds generated for 'chain 'D' and resid 304 through 306' Processing helix chain 'D' and resid 311 through 318 removed outlier: 3.614A pdb=" N ALA D 318 " --> pdb=" O ALA D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 332 Processing helix chain 'D' and resid 351 through 354 No H-bonds generated for 'chain 'D' and resid 351 through 354' Processing helix chain 'D' and resid 356 through 382 removed outlier: 4.119A pdb=" N ASP D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE D 378 " --> pdb=" O GLU D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 386 No H-bonds generated for 'chain 'D' and resid 384 through 386' Processing helix chain 'D' and resid 389 through 405 Processing helix chain 'D' and resid 410 through 415 removed outlier: 3.514A pdb=" N VAL D 414 " --> pdb=" O HIS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 437 Processing helix chain 'D' and resid 445 through 448 Processing helix chain 'D' and resid 454 through 463 Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'E' and resid 115 through 117 No H-bonds generated for 'chain 'E' and resid 115 through 117' Processing helix chain 'E' and resid 130 through 135 Processing helix chain 'E' and resid 154 through 168 removed outlier: 3.568A pdb=" N MET E 158 " --> pdb=" O LYS E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 194 Processing helix chain 'E' and resid 212 through 216 Processing helix chain 'E' and resid 219 through 231 Processing helix chain 'E' and resid 249 through 260 Processing helix chain 'E' and resid 274 through 285 removed outlier: 4.074A pdb=" N ALA E 277 " --> pdb=" O PRO E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 311 through 319 removed outlier: 3.796A pdb=" N ALA E 318 " --> pdb=" O ALA E 314 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N HIS E 319 " --> pdb=" O THR E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 332 Processing helix chain 'E' and resid 351 through 354 No H-bonds generated for 'chain 'E' and resid 351 through 354' Processing helix chain 'E' and resid 356 through 381 removed outlier: 4.368A pdb=" N ASP E 377 " --> pdb=" O LYS E 373 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE E 378 " --> pdb=" O GLU E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 386 No H-bonds generated for 'chain 'E' and resid 384 through 386' Processing helix chain 'E' and resid 389 through 405 Processing helix chain 'E' and resid 412 through 414 No H-bonds generated for 'chain 'E' and resid 412 through 414' Processing helix chain 'E' and resid 425 through 436 Processing helix chain 'E' and resid 445 through 448 Processing helix chain 'E' and resid 454 through 463 Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'F' and resid 130 through 135 Processing helix chain 'F' and resid 154 through 168 Processing helix chain 'F' and resid 182 through 195 Processing helix chain 'F' and resid 197 through 200 Processing helix chain 'F' and resid 212 through 231 removed outlier: 4.917A pdb=" N ALA F 219 " --> pdb=" O ARG F 215 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU F 220 " --> pdb=" O LEU F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 263 removed outlier: 4.078A pdb=" N ALA F 261 " --> pdb=" O THR F 257 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU F 262 " --> pdb=" O GLU F 258 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU F 263 " --> pdb=" O VAL F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 285 Processing helix chain 'F' and resid 304 through 306 No H-bonds generated for 'chain 'F' and resid 304 through 306' Processing helix chain 'F' and resid 311 through 317 Processing helix chain 'F' and resid 328 through 332 Processing helix chain 'F' and resid 356 through 382 removed outlier: 4.325A pdb=" N ASP F 377 " --> pdb=" O LYS F 373 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE F 378 " --> pdb=" O GLU F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 404 Processing helix chain 'F' and resid 425 through 437 Processing helix chain 'F' and resid 445 through 448 No H-bonds generated for 'chain 'F' and resid 445 through 448' Processing helix chain 'F' and resid 454 through 463 Processing helix chain 'G' and resid 3 through 40 removed outlier: 3.690A pdb=" N ARG G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 57 removed outlier: 3.627A pdb=" N LEU G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 75 Processing helix chain 'H' and resid 2 through 40 removed outlier: 3.840A pdb=" N ARG H 40 " --> pdb=" O GLU H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 59 Proline residue: H 46 - end of helix removed outlier: 3.980A pdb=" N GLY H 57 " --> pdb=" O LEU H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 75 Processing helix chain 'J' and resid 2 through 40 removed outlier: 3.619A pdb=" N GLY J 28 " --> pdb=" O ALA J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 59 Processing helix chain 'J' and resid 61 through 75 Processing helix chain 'K' and resid 3 through 38 Processing helix chain 'K' and resid 42 through 59 Proline residue: K 46 - end of helix Processing helix chain 'K' and resid 61 through 75 Processing helix chain 'L' and resid 3 through 40 Processing helix chain 'L' and resid 45 through 57 Processing helix chain 'L' and resid 61 through 76 Processing helix chain 'O' and resid 2 through 40 removed outlier: 3.677A pdb=" N GLY O 19 " --> pdb=" O LEU O 15 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG O 33 " --> pdb=" O LEU O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 59 Proline residue: O 46 - end of helix removed outlier: 3.804A pdb=" N GLY O 57 " --> pdb=" O LEU O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 74 Processing helix chain 'P' and resid 2 through 40 removed outlier: 3.850A pdb=" N ARG P 33 " --> pdb=" O LEU P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 59 Processing helix chain 'P' and resid 61 through 76 Processing helix chain 'Q' and resid 2 through 40 removed outlier: 3.982A pdb=" N ARG Q 33 " --> pdb=" O LEU Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 76 removed outlier: 3.575A pdb=" N GLY Q 57 " --> pdb=" O PHE Q 53 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU Q 58 " --> pdb=" O LEU Q 54 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP Q 60 " --> pdb=" O ALA Q 56 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA Q 61 " --> pdb=" O GLY Q 57 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N VAL Q 62 " --> pdb=" O LEU Q 58 " (cutoff:3.500A) Proline residue: Q 63 - end of helix Processing helix chain 'R' and resid 2 through 40 Processing helix chain 'R' and resid 42 through 57 Proline residue: R 46 - end of helix Processing helix chain 'R' and resid 61 through 75 Processing helix chain 'S' and resid 3 through 40 Processing helix chain 'S' and resid 43 through 57 Proline residue: S 46 - end of helix removed outlier: 3.506A pdb=" N ALA S 56 " --> pdb=" O PHE S 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 75 Processing helix chain 'a' and resid 16 through 26 removed outlier: 4.211A pdb=" N LYS a 25 " --> pdb=" O MET a 21 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET a 26 " --> pdb=" O THR a 22 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 71 removed outlier: 4.056A pdb=" N VAL a 70 " --> pdb=" O LEU a 66 " (cutoff:3.500A) Processing helix chain 'a' and resid 81 through 100 Processing helix chain 'a' and resid 109 through 127 removed outlier: 4.080A pdb=" N ASP a 126 " --> pdb=" O MET a 122 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU a 127 " --> pdb=" O ASN a 123 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 143 Proline residue: a 134 - end of helix removed outlier: 4.127A pdb=" N PHE a 139 " --> pdb=" O GLN a 135 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL a 140 " --> pdb=" O VAL a 136 " (cutoff:3.500A) Processing helix chain 'a' and resid 148 through 153 removed outlier: 4.351A pdb=" N TYR a 153 " --> pdb=" O PRO a 149 " (cutoff:3.500A) Processing helix chain 'a' and resid 162 through 180 Processing helix chain 'a' and resid 186 through 190 Processing helix chain 'a' and resid 203 through 209 Processing helix chain 'a' and resid 211 through 219 Processing helix chain 'a' and resid 222 through 246 removed outlier: 4.039A pdb=" N ILE a 226 " --> pdb=" O LEU a 222 " (cutoff:3.500A) Processing helix chain 'a' and resid 257 through 288 removed outlier: 4.668A pdb=" N TRP a 261 " --> pdb=" O LEU a 257 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 138 removed outlier: 4.079A pdb=" N PHE b 24 " --> pdb=" O PHE b 20 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N TRP b 26 " --> pdb=" O MET b 22 " (cutoff:3.500A) Proline residue: b 27 - end of helix removed outlier: 3.777A pdb=" N ILE b 33 " --> pdb=" O LEU b 29 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER b 34 " --> pdb=" O ILE b 30 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU b 35 " --> pdb=" O ASN b 31 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA b 52 " --> pdb=" O GLU b 48 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASP b 53 " --> pdb=" O LYS b 49 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU b 54 " --> pdb=" O ALA b 50 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN b 58 " --> pdb=" O LEU b 54 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA b 59 " --> pdb=" O ALA b 55 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN b 60 " --> pdb=" O ASP b 56 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA b 67 " --> pdb=" O GLN b 63 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA b 68 " --> pdb=" O GLU b 64 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS b 69 " --> pdb=" O LEU b 65 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU b 112 " --> pdb=" O ALA b 108 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU b 119 " --> pdb=" O SER b 115 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU b 133 " --> pdb=" O VAL b 129 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LYS b 134 " --> pdb=" O THR b 130 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE b 135 " --> pdb=" O GLY b 131 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU b 136 " --> pdb=" O ALA b 132 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASN b 137 " --> pdb=" O GLU b 133 " (cutoff:3.500A) Processing helix chain 'd' and resid 4 through 22 Proline residue: d 10 - end of helix Processing helix chain 'd' and resid 25 through 40 Processing helix chain 'd' and resid 42 through 48 Processing helix chain 'd' and resid 55 through 66 Processing helix chain 'd' and resid 72 through 83 Processing helix chain 'd' and resid 88 through 104 Proline residue: d 91 - end of helix Processing helix chain 'd' and resid 120 through 132 Processing helix chain 'd' and resid 165 through 175 Processing helix chain 'e' and resid 91 through 125 removed outlier: 3.722A pdb=" N LEU e 95 " --> pdb=" O ALA e 92 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLU e 96 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU e 112 " --> pdb=" O LYS e 109 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP e 113 " --> pdb=" O SER e 110 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA e 115 " --> pdb=" O LEU e 112 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA e 116 " --> pdb=" O ASP e 113 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA e 117 " --> pdb=" O SER e 114 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU e 118 " --> pdb=" O ALA e 115 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA e 119 " --> pdb=" O ALA e 116 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR e 124 " --> pdb=" O LEU e 121 " (cutoff:3.500A) Processing helix chain 'e' and resid 128 through 135 removed outlier: 3.815A pdb=" N ILE e 134 " --> pdb=" O THR e 130 " (cutoff:3.500A) Processing helix chain 'g' and resid 4 through 59 removed outlier: 4.366A pdb=" N ALA g 40 " --> pdb=" O GLN g 36 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN g 41 " --> pdb=" O GLU g 37 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY g 42 " --> pdb=" O ARG g 38 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG g 43 " --> pdb=" O MET g 39 " (cutoff:3.500A) Proline residue: g 44 - end of helix Processing helix chain 'g' and resid 91 through 109 removed outlier: 3.567A pdb=" N GLU g 108 " --> pdb=" O LYS g 104 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLN g 109 " --> pdb=" O ALA g 105 " (cutoff:3.500A) Processing helix chain 'g' and resid 120 through 129 Processing helix chain 'g' and resid 146 through 161 removed outlier: 4.235A pdb=" N GLY g 151 " --> pdb=" O GLU g 147 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N SER g 152 " --> pdb=" O GLN g 148 " (cutoff:3.500A) Processing helix chain 'g' and resid 214 through 286 Processing helix chain 'p' and resid 3 through 138 Proline residue: p 27 - end of helix removed outlier: 4.320A pdb=" N ARG p 121 " --> pdb=" O ARG p 117 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN p 122 " --> pdb=" O GLU p 118 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN p 123 " --> pdb=" O GLU p 119 " (cutoff:3.500A) Processing helix chain 'p' and resid 142 through 155 Processing sheet with id= A, first strand: chain 'A' and resid 29 through 31 removed outlier: 7.198A pdb=" N GLY A 73 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N HIS A 43 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE A 32 " --> pdb=" O HIS A 43 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 97 through 100 removed outlier: 4.301A pdb=" N LEU A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 107 through 110 removed outlier: 4.021A pdb=" N ARG A 107 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 224 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 109 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N CYS A 194 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N VAL A 225 " --> pdb=" O CYS A 194 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR A 196 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ALA A 227 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ALA A 198 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 193 " --> pdb=" O ASP A 256 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 260 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 197 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N SER A 324 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ILE A 259 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N THR A 326 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.310A pdb=" N LEU A 167 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 331 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.525A pdb=" N ALA B 89 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY B 73 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LEU B 67 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N HIS B 43 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ILE B 32 " --> pdb=" O HIS B 43 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 97 through 100 removed outlier: 3.752A pdb=" N LEU B 126 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 107 through 110 removed outlier: 6.695A pdb=" N CYS B 194 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N VAL B 225 " --> pdb=" O CYS B 194 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TYR B 196 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR B 326 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU B 166 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 168 " --> pdb=" O PRO B 329 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLY B 352 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ILE B 169 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE B 354 " --> pdb=" O ILE B 169 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 31 through 36 removed outlier: 6.362A pdb=" N ARG C 41 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY C 73 " --> pdb=" O ASN C 66 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C 64 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLU C 52 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ARG C 94 " --> pdb=" O MET C 53 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLU C 55 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR C 92 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 97 through 100 removed outlier: 4.037A pdb=" N LEU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 107 through 109 removed outlier: 4.144A pdb=" N ARG C 107 " --> pdb=" O THR C 222 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 109 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA C 226 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N CYS C 194 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N VAL C 225 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TYR C 196 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ALA C 227 " --> pdb=" O TYR C 196 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ALA C 198 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER C 324 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE C 259 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N THR C 326 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N TYR C 261 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LEU C 328 " --> pdb=" O TYR C 261 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 353 through 355 removed outlier: 6.200A pdb=" N LEU C 167 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY C 170 " --> pdb=" O ILE C 331 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 3 through 5 removed outlier: 3.918A pdb=" N THR D 38 " --> pdb=" O MET D 55 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE D 53 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARG D 51 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL D 16 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLU D 17 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE D 6 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 75 through 77 Processing sheet with id= N, first strand: chain 'D' and resid 322 through 325 removed outlier: 3.565A pdb=" N ALA D 322 " --> pdb=" O LYS D 143 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N VAL D 144 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N SER D 297 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N LEU D 146 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N GLN D 299 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL D 242 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE D 298 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU D 244 " --> pdb=" O ILE D 298 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ALA D 300 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL D 246 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU D 172 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N PHE D 245 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL D 174 " --> pdb=" O PHE D 245 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 3 through 5 removed outlier: 3.877A pdb=" N THR E 38 " --> pdb=" O MET E 55 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG E 51 " --> pdb=" O GLN E 42 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE E 10 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP E 15 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN E 8 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLU E 17 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE E 6 " --> pdb=" O GLU E 17 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 75 through 77 Processing sheet with id= Q, first strand: chain 'E' and resid 322 through 325 removed outlier: 8.197A pdb=" N VAL E 144 " --> pdb=" O ILE E 295 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER E 297 " --> pdb=" O VAL E 144 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N LEU E 146 " --> pdb=" O SER E 297 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLN E 299 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N GLY E 148 " --> pdb=" O GLN E 299 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL E 301 " --> pdb=" O GLY E 148 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 175 through 178 Processing sheet with id= S, first strand: chain 'F' and resid 3 through 5 removed outlier: 3.529A pdb=" N THR F 38 " --> pdb=" O MET F 55 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE F 53 " --> pdb=" O GLU F 40 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG F 51 " --> pdb=" O GLN F 42 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLU F 17 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE F 6 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 75 through 77 Processing sheet with id= U, first strand: chain 'F' and resid 322 through 324 removed outlier: 9.351A pdb=" N VAL F 144 " --> pdb=" O ILE F 295 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N SER F 297 " --> pdb=" O VAL F 144 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N LEU F 146 " --> pdb=" O SER F 297 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLN F 299 " --> pdb=" O LEU F 146 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'd' and resid 110 through 113 Processing sheet with id= W, first strand: chain 'e' and resid 41 through 45 removed outlier: 4.038A pdb=" N GLY e 67 " --> pdb=" O LEU e 45 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLN e 5 " --> pdb=" O VAL e 76 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VAL e 78 " --> pdb=" O GLN e 5 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP e 7 " --> pdb=" O VAL e 78 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA e 80 " --> pdb=" O ASP e 7 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL e 9 " --> pdb=" O ALA e 80 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N SER e 10 " --> pdb=" O SER e 14 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER e 14 " --> pdb=" O SER e 10 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'e' and resid 31 through 34 removed outlier: 6.037A pdb=" N LYS e 26 " --> pdb=" O PRO e 49 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR e 82 " --> pdb=" O SER e 65 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'g' and resid 181 through 187 removed outlier: 7.736A pdb=" N ARG g 75 " --> pdb=" O ASP g 166 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE g 168 " --> pdb=" O ARG g 75 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLY g 77 " --> pdb=" O ILE g 168 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU g 170 " --> pdb=" O GLY g 77 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ILE g 79 " --> pdb=" O LEU g 170 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N SER g 172 " --> pdb=" O ILE g 79 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL g 81 " --> pdb=" O SER g 172 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N GLY g 174 " --> pdb=" O VAL g 81 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLU g 112 " --> pdb=" O VAL g 76 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N TYR g 78 " --> pdb=" O GLU g 112 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN g 114 " --> pdb=" O TYR g 78 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE g 80 " --> pdb=" O GLN g 114 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ALA g 116 " --> pdb=" O ILE g 80 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N LYS g 132 " --> pdb=" O PHE g 115 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N LEU g 117 " --> pdb=" O LYS g 132 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N LEU g 134 " --> pdb=" O LEU g 117 " (cutoff:3.500A) 2039 hydrogen bonds defined for protein. 5508 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: 14.33 Time building geometry restraints manager: 18.70 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: 11040 1.33 - 1.45: 5110 1.45 - 1.57: 21254 1.57 - 1.69: 19 1.69 - 1.81: 277 Bond restraints: 37700 Sorted by residual: bond pdb=" C1' ADP E 601 " pdb=" N9 ADP E 601 " ideal model delta sigma weight residual 1.485 1.339 0.146 2.00e-02 2.50e+03 5.32e+01 bond pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 1.592 1.663 -0.071 1.10e-02 8.26e+03 4.19e+01 bond pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 1.592 1.663 -0.071 1.10e-02 8.26e+03 4.19e+01 bond pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 1.592 1.663 -0.071 1.10e-02 8.26e+03 4.15e+01 bond pdb=" C5 ATP B 601 " pdb=" N7 ATP B 601 " ideal model delta sigma weight residual 1.387 1.336 0.051 1.00e-02 1.00e+04 2.65e+01 ... (remaining 37695 not shown) Histogram of bond angle deviations from ideal: 93.64 - 102.61: 178 102.61 - 111.58: 17881 111.58 - 120.54: 19015 120.54 - 129.51: 13915 129.51 - 138.47: 122 Bond angle restraints: 51111 Sorted by residual: angle pdb=" N ALA b 57 " pdb=" CA ALA b 57 " pdb=" C ALA b 57 " ideal model delta sigma weight residual 111.07 122.09 -11.02 1.07e+00 8.73e-01 1.06e+02 angle pdb=" N LYS b 51 " pdb=" CA LYS b 51 " pdb=" C LYS b 51 " ideal model delta sigma weight residual 111.07 120.88 -9.81 1.07e+00 8.73e-01 8.41e+01 angle pdb=" C ALA b 57 " pdb=" N GLN b 58 " pdb=" CA GLN b 58 " ideal model delta sigma weight residual 120.38 131.05 -10.67 1.37e+00 5.33e-01 6.06e+01 angle pdb=" C5 ATP B 601 " pdb=" C4 ATP B 601 " pdb=" N3 ATP B 601 " ideal model delta sigma weight residual 126.80 119.29 7.51 1.00e+00 1.00e+00 5.64e+01 angle pdb=" C5 ATP C 601 " pdb=" C4 ATP C 601 " pdb=" N3 ATP C 601 " ideal model delta sigma weight residual 126.80 119.33 7.47 1.00e+00 1.00e+00 5.58e+01 ... (remaining 51106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.20: 21882 25.20 - 50.41: 788 50.41 - 75.61: 110 75.61 - 100.82: 36 100.82 - 126.02: 1 Dihedral angle restraints: 22817 sinusoidal: 8898 harmonic: 13919 Sorted by residual: dihedral pdb=" C THR B 513 " pdb=" N THR B 513 " pdb=" CA THR B 513 " pdb=" CB THR B 513 " ideal model delta harmonic sigma weight residual -122.00 -139.85 17.85 0 2.50e+00 1.60e-01 5.10e+01 dihedral pdb=" O2A ADP E 601 " pdb=" O3A ADP E 601 " pdb=" PA ADP E 601 " pdb=" PB ADP E 601 " ideal model delta sinusoidal sigma weight residual -60.00 66.03 -126.02 1 2.00e+01 2.50e-03 3.81e+01 dihedral pdb=" CA MET B 49 " pdb=" C MET B 49 " pdb=" N TYR B 50 " pdb=" CA TYR B 50 " ideal model delta harmonic sigma weight residual 180.00 150.66 29.34 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 22814 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 5954 0.138 - 0.275: 32 0.275 - 0.413: 1 0.413 - 0.551: 0 0.551 - 0.688: 1 Chirality restraints: 5988 Sorted by residual: chirality pdb=" CA THR B 513 " pdb=" N THR B 513 " pdb=" C THR B 513 " pdb=" CB THR B 513 " both_signs ideal model delta sigma weight residual False 2.53 1.84 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" CA ILE b 40 " pdb=" N ILE b 40 " pdb=" C ILE b 40 " pdb=" CB ILE b 40 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C1' ADP E 601 " pdb=" C2' ADP E 601 " pdb=" N9 ADP E 601 " pdb=" O4' ADP E 601 " both_signs ideal model delta sigma weight residual False 2.48 2.21 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 5985 not shown) Planarity restraints: 6628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE J 18 " 0.036 2.00e-02 2.50e+03 2.63e-02 1.21e+01 pdb=" CG PHE J 18 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE J 18 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE J 18 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE J 18 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE J 18 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE J 18 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 18 " 0.024 2.00e-02 2.50e+03 2.49e-02 1.08e+01 pdb=" CG PHE H 18 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE H 18 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE H 18 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE H 18 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE H 18 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE H 18 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE Q 18 " 0.035 2.00e-02 2.50e+03 2.48e-02 1.08e+01 pdb=" CG PHE Q 18 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE Q 18 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE Q 18 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE Q 18 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE Q 18 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE Q 18 " 0.018 2.00e-02 2.50e+03 ... (remaining 6625 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 308 2.40 - 3.03: 27133 3.03 - 3.65: 63935 3.65 - 4.28: 90820 4.28 - 4.90: 139251 Nonbonded interactions: 321447 Sorted by model distance: nonbonded pdb=" O2B ATP A 601 " pdb="MG MG A 602 " model vdw 1.777 2.170 nonbonded pdb=" O2G ATP C 601 " pdb="MG MG C 602 " model vdw 1.958 2.170 nonbonded pdb=" O PRO E 267 " pdb=" O SER E 268 " model vdw 2.061 3.040 nonbonded pdb=" OD1 ASP E 88 " pdb=" N VAL E 89 " model vdw 2.129 2.520 nonbonded pdb=" OD1 ASP D 88 " pdb=" N VAL D 89 " model vdw 2.172 2.520 ... (remaining 321442 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' and (resid 6 through 511 or resid 601 through 602)) selection = (chain 'B' and (resid 6 through 511 or resid 601 through 602)) selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 2 through 464) selection = (chain 'E' and resid 2 through 464) selection = chain 'F' } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 2 through 80) selection = (chain 'J' and resid 2 through 80) selection = chain 'K' selection = chain 'L' selection = (chain 'O' and resid 2 through 80) selection = (chain 'P' and resid 2 through 80) selection = (chain 'Q' and resid 2 through 80) selection = (chain 'R' and resid 2 through 80) selection = chain 'S' } ncs_group { reference = chain 'b' selection = (chain 'p' and resid 12 through 156) } 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=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 20.250 Check model and map are aligned: 0.640 Set scattering table: 0.310 Process input model: 101.900 Find NCS groups from input model: 2.630 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 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 : 0.005 0.146 37700 Z= 0.342 Angle : 0.851 17.193 51111 Z= 0.499 Chirality : 0.046 0.688 5988 Planarity : 0.005 0.050 6628 Dihedral : 13.803 126.024 13903 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 31.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.44 % Favored : 92.43 % Rotamer: Outliers : 0.21 % Allowed : 0.84 % Favored : 98.96 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.12), residues: 4851 helix: 0.11 (0.10), residues: 2567 sheet: -1.12 (0.21), residues: 551 loop : -1.91 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP a 118 HIS 0.011 0.002 HIS a 151 PHE 0.058 0.002 PHE J 18 TYR 0.024 0.002 TYR a 283 ARG 0.016 0.001 ARG B 279 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 354 time to evaluate : 3.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9125 (mmm) cc_final: 0.8695 (mmm) REVERT: A 171 ASP cc_start: 0.9325 (p0) cc_final: 0.9103 (m-30) REVERT: A 179 MET cc_start: 0.9458 (mtp) cc_final: 0.9210 (mmm) REVERT: A 295 HIS cc_start: 0.9377 (m90) cc_final: 0.9047 (m90) REVERT: A 328 LEU cc_start: 0.9670 (mt) cc_final: 0.9427 (mt) REVERT: B 1 MET cc_start: 0.9209 (ppp) cc_final: 0.8936 (tpp) REVERT: B 53 MET cc_start: 0.8880 (mtm) cc_final: 0.8231 (mtm) REVERT: B 235 MET cc_start: 0.9650 (mmp) cc_final: 0.9383 (mmm) REVERT: B 238 LEU cc_start: 0.9817 (mt) cc_final: 0.9505 (pp) REVERT: B 246 MET cc_start: 0.9646 (mmp) cc_final: 0.9308 (mmm) REVERT: C 49 MET cc_start: 0.6567 (tpt) cc_final: 0.5807 (tpt) REVERT: C 63 MET cc_start: 0.9495 (tmm) cc_final: 0.9197 (tmm) REVERT: C 235 MET cc_start: 0.9438 (mpp) cc_final: 0.8898 (mpp) REVERT: C 237 TYR cc_start: 0.9708 (t80) cc_final: 0.9499 (t80) REVERT: C 484 MET cc_start: 0.9615 (mpp) cc_final: 0.9351 (mpp) REVERT: D 55 MET cc_start: 0.8857 (mmp) cc_final: 0.8345 (mmp) REVERT: D 159 MET cc_start: 0.9803 (mmp) cc_final: 0.9371 (mmm) REVERT: D 192 MET cc_start: 0.9775 (ptp) cc_final: 0.9420 (mtm) REVERT: D 225 MET cc_start: 0.9794 (mmp) cc_final: 0.9535 (mmm) REVERT: D 258 GLU cc_start: 0.9534 (mt-10) cc_final: 0.9319 (mt-10) REVERT: D 280 MET cc_start: 0.9649 (mmp) cc_final: 0.9228 (mmm) REVERT: D 450 MET cc_start: 0.9538 (mmp) cc_final: 0.9209 (mmm) REVERT: E 55 MET cc_start: 0.9569 (mpp) cc_final: 0.9348 (mpp) REVERT: E 192 MET cc_start: 0.9832 (mmm) cc_final: 0.9553 (tpp) REVERT: E 225 MET cc_start: 0.9860 (mmp) cc_final: 0.9537 (mmm) REVERT: E 319 HIS cc_start: 0.8715 (m90) cc_final: 0.8422 (m-70) REVERT: F 159 MET cc_start: 0.9784 (mtm) cc_final: 0.9527 (tpt) REVERT: F 203 MET cc_start: 0.8793 (tpt) cc_final: 0.8576 (tpt) REVERT: F 280 MET cc_start: 0.9693 (tpt) cc_final: 0.9343 (tpp) REVERT: F 285 GLU cc_start: 0.9314 (mm-30) cc_final: 0.7924 (tp30) REVERT: F 450 MET cc_start: 0.9012 (mmp) cc_final: 0.8811 (mmt) REVERT: G 34 PHE cc_start: 0.9531 (t80) cc_final: 0.9250 (t80) REVERT: J 60 ASP cc_start: 0.9163 (p0) cc_final: 0.8374 (t0) REVERT: J 64 MET cc_start: 0.9354 (mmp) cc_final: 0.8957 (mmp) REVERT: K 71 LEU cc_start: 0.9377 (mm) cc_final: 0.9174 (mm) REVERT: L 18 PHE cc_start: 0.8250 (t80) cc_final: 0.8044 (t80) REVERT: L 27 PHE cc_start: 0.9131 (m-10) cc_final: 0.8772 (m-10) REVERT: a 26 MET cc_start: 0.7242 (mpp) cc_final: 0.6003 (mpp) REVERT: a 125 MET cc_start: 0.8723 (ptt) cc_final: 0.8335 (ppp) REVERT: a 277 MET cc_start: 0.9345 (tmm) cc_final: 0.9109 (tmm) REVERT: b 148 MET cc_start: 0.8692 (pmm) cc_final: 0.8438 (pmm) REVERT: e 98 ARG cc_start: 0.8484 (ttm110) cc_final: 0.8177 (ttt180) REVERT: g 32 MET cc_start: 0.9337 (ttt) cc_final: 0.8753 (ttp) REVERT: g 39 MET cc_start: 0.9564 (mmp) cc_final: 0.9325 (mmm) REVERT: g 156 MET cc_start: 0.9619 (tpt) cc_final: 0.9007 (tpp) REVERT: g 229 MET cc_start: 0.8962 (mtm) cc_final: 0.8596 (mtp) REVERT: g 246 MET cc_start: 0.9198 (mtm) cc_final: 0.8831 (mtt) REVERT: p 110 ASP cc_start: 0.9450 (t0) cc_final: 0.9167 (p0) outliers start: 8 outliers final: 2 residues processed: 361 average time/residue: 0.5225 time to fit residues: 301.8284 Evaluate side-chains 256 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 254 time to evaluate : 3.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 7.9990 chunk 363 optimal weight: 0.7980 chunk 201 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 245 optimal weight: 8.9990 chunk 194 optimal weight: 8.9990 chunk 376 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 228 optimal weight: 7.9990 chunk 280 optimal weight: 2.9990 chunk 435 optimal weight: 5.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN B 84 GLN B 426 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN C 362 ASN D 118 GLN D 157 ASN ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 GLN ** E 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 HIS F 8 GLN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 366 GLN J 41 GLN ** a 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 137 ASN ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 138 GLN ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 37700 Z= 0.284 Angle : 0.676 10.706 51111 Z= 0.357 Chirality : 0.042 0.175 5988 Planarity : 0.005 0.053 6628 Dihedral : 7.056 134.596 5364 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 26.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.39 % Favored : 93.59 % Rotamer: Outliers : 0.13 % Allowed : 5.79 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: -0.88 (0.12), residues: 4851 helix: 0.27 (0.10), residues: 2591 sheet: -0.97 (0.21), residues: 537 loop : -1.67 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP a 118 HIS 0.009 0.001 HIS F 358 PHE 0.039 0.002 PHE J 18 TYR 0.026 0.002 TYR E 205 ARG 0.011 0.001 ARG B 279 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 318 time to evaluate : 4.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9204 (mmm) cc_final: 0.8810 (mmm) REVERT: A 171 ASP cc_start: 0.9611 (p0) cc_final: 0.8996 (m-30) REVERT: A 179 MET cc_start: 0.9414 (mtp) cc_final: 0.9157 (mmm) REVERT: A 238 LEU cc_start: 0.9658 (mt) cc_final: 0.9331 (pp) REVERT: A 295 HIS cc_start: 0.9362 (m90) cc_final: 0.8969 (m-70) REVERT: A 328 LEU cc_start: 0.9669 (mt) cc_final: 0.9452 (mt) REVERT: B 53 MET cc_start: 0.8661 (mtm) cc_final: 0.8217 (mtm) REVERT: B 157 MET cc_start: 0.9327 (mmt) cc_final: 0.8815 (mmp) REVERT: B 235 MET cc_start: 0.9617 (mmp) cc_final: 0.9343 (mmm) REVERT: B 238 LEU cc_start: 0.9815 (mt) cc_final: 0.9508 (pp) REVERT: B 246 MET cc_start: 0.9582 (mmp) cc_final: 0.9378 (mmm) REVERT: C 49 MET cc_start: 0.7470 (tpt) cc_final: 0.5717 (tpt) REVERT: C 63 MET cc_start: 0.9509 (tmm) cc_final: 0.9293 (tmm) REVERT: C 182 ASP cc_start: 0.9159 (t0) cc_final: 0.8908 (t0) REVERT: C 235 MET cc_start: 0.9446 (mpp) cc_final: 0.8869 (mpp) REVERT: C 484 MET cc_start: 0.9624 (mpp) cc_final: 0.9394 (mpp) REVERT: D 9 ILE cc_start: 0.9711 (pt) cc_final: 0.9350 (mp) REVERT: D 159 MET cc_start: 0.9793 (mmp) cc_final: 0.9362 (mmm) REVERT: D 192 MET cc_start: 0.9772 (ptp) cc_final: 0.9408 (ptt) REVERT: D 225 MET cc_start: 0.9799 (mmp) cc_final: 0.9502 (mmm) REVERT: D 280 MET cc_start: 0.9688 (mmp) cc_final: 0.9188 (mmm) REVERT: D 450 MET cc_start: 0.9522 (mmp) cc_final: 0.9208 (mmp) REVERT: E 158 MET cc_start: 0.9447 (tpt) cc_final: 0.9162 (tpp) REVERT: E 159 MET cc_start: 0.9642 (mmp) cc_final: 0.9397 (mmm) REVERT: E 192 MET cc_start: 0.9861 (mmm) cc_final: 0.9614 (tpp) REVERT: E 225 MET cc_start: 0.9843 (mmp) cc_final: 0.9550 (mmm) REVERT: E 262 LEU cc_start: 0.9570 (mp) cc_final: 0.9304 (pp) REVERT: E 319 HIS cc_start: 0.8714 (m90) cc_final: 0.8268 (m-70) REVERT: F 280 MET cc_start: 0.9681 (tpt) cc_final: 0.9301 (tpp) REVERT: F 285 GLU cc_start: 0.9342 (mm-30) cc_final: 0.7948 (tp30) REVERT: F 415 PHE cc_start: 0.8843 (t80) cc_final: 0.7976 (m-80) REVERT: G 30 LEU cc_start: 0.9394 (pp) cc_final: 0.9140 (mt) REVERT: G 34 PHE cc_start: 0.9559 (t80) cc_final: 0.9191 (t80) REVERT: J 60 ASP cc_start: 0.9148 (p0) cc_final: 0.8370 (t0) REVERT: J 64 MET cc_start: 0.9404 (mmp) cc_final: 0.9117 (mmp) REVERT: L 27 PHE cc_start: 0.9179 (m-10) cc_final: 0.8768 (m-10) REVERT: a 26 MET cc_start: 0.7184 (mpp) cc_final: 0.6008 (mpp) REVERT: a 125 MET cc_start: 0.8823 (ptt) cc_final: 0.8429 (ppp) REVERT: a 278 MET cc_start: 0.9814 (mmp) cc_final: 0.9466 (mmm) REVERT: b 148 MET cc_start: 0.8606 (pmm) cc_final: 0.8357 (pmm) REVERT: e 24 ILE cc_start: 0.8689 (pt) cc_final: 0.8450 (tp) REVERT: e 98 ARG cc_start: 0.8759 (ttm110) cc_final: 0.8491 (ttt180) REVERT: g 24 MET cc_start: 0.9558 (OUTLIER) cc_final: 0.9252 (mtp) REVERT: g 32 MET cc_start: 0.9322 (ttt) cc_final: 0.8889 (ttp) REVERT: g 39 MET cc_start: 0.9559 (mmp) cc_final: 0.9346 (mmm) REVERT: g 156 MET cc_start: 0.9683 (tpt) cc_final: 0.9008 (tpp) REVERT: g 229 MET cc_start: 0.8927 (mtm) cc_final: 0.8554 (mtp) REVERT: p 110 ASP cc_start: 0.9478 (t0) cc_final: 0.9185 (p0) outliers start: 5 outliers final: 1 residues processed: 320 average time/residue: 0.5243 time to fit residues: 281.1117 Evaluate side-chains 265 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 263 time to evaluate : 4.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 8.9990 chunk 135 optimal weight: 0.1980 chunk 362 optimal weight: 10.0000 chunk 296 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 436 optimal weight: 8.9990 chunk 471 optimal weight: 10.0000 chunk 388 optimal weight: 5.9990 chunk 433 optimal weight: 0.5980 chunk 148 optimal weight: 0.8980 chunk 350 optimal weight: 0.1980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 HIS E 358 HIS ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 196 ASN F 366 GLN J 49 GLN ** Q 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 93 GLN b 137 ASN ** b 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 138 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37700 Z= 0.170 Angle : 0.592 9.879 51111 Z= 0.306 Chirality : 0.041 0.237 5988 Planarity : 0.004 0.063 6628 Dihedral : 6.691 136.619 5364 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.95 % Favored : 95.03 % Rotamer: Outliers : 0.03 % Allowed : 3.76 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: -0.30 (0.12), residues: 4851 helix: 0.75 (0.10), residues: 2595 sheet: -0.82 (0.22), residues: 541 loop : -1.38 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 118 HIS 0.005 0.001 HIS F 358 PHE 0.034 0.001 PHE J 18 TYR 0.012 0.001 TYR g 225 ARG 0.004 0.000 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 344 time to evaluate : 4.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9225 (mmm) cc_final: 0.8932 (tpp) REVERT: A 171 ASP cc_start: 0.9450 (p0) cc_final: 0.8917 (m-30) REVERT: A 295 HIS cc_start: 0.9316 (m90) cc_final: 0.8945 (m-70) REVERT: A 457 MET cc_start: 0.9537 (pmm) cc_final: 0.9038 (pmm) REVERT: B 49 MET cc_start: 0.7565 (mmm) cc_final: 0.7102 (tpt) REVERT: B 53 MET cc_start: 0.8648 (mtm) cc_final: 0.8343 (mtm) REVERT: B 235 MET cc_start: 0.9591 (mmp) cc_final: 0.9252 (mmm) REVERT: B 238 LEU cc_start: 0.9793 (mt) cc_final: 0.9489 (pp) REVERT: C 49 MET cc_start: 0.7344 (tpt) cc_final: 0.5801 (tpt) REVERT: C 53 MET cc_start: 0.9832 (mmt) cc_final: 0.9628 (mmm) REVERT: C 63 MET cc_start: 0.9483 (tmm) cc_final: 0.9262 (tmm) REVERT: C 182 ASP cc_start: 0.9129 (t0) cc_final: 0.8811 (t0) REVERT: C 235 MET cc_start: 0.9369 (mpp) cc_final: 0.8760 (mpp) REVERT: C 330 ILE cc_start: 0.9685 (mm) cc_final: 0.9479 (mm) REVERT: C 484 MET cc_start: 0.9634 (mpp) cc_final: 0.9404 (mpp) REVERT: D 9 ILE cc_start: 0.9692 (pt) cc_final: 0.9333 (mp) REVERT: D 159 MET cc_start: 0.9789 (mmp) cc_final: 0.9480 (mmm) REVERT: D 192 MET cc_start: 0.9693 (ptp) cc_final: 0.9339 (ptt) REVERT: D 225 MET cc_start: 0.9769 (mmp) cc_final: 0.9492 (mmm) REVERT: D 280 MET cc_start: 0.9681 (mmp) cc_final: 0.9210 (mmm) REVERT: D 450 MET cc_start: 0.9558 (mmp) cc_final: 0.9195 (mmp) REVERT: E 158 MET cc_start: 0.9430 (tpt) cc_final: 0.9011 (tpp) REVERT: E 159 MET cc_start: 0.9624 (mmp) cc_final: 0.9303 (mmm) REVERT: E 192 MET cc_start: 0.9814 (mmm) cc_final: 0.9548 (tpp) REVERT: E 225 MET cc_start: 0.9810 (mmp) cc_final: 0.9559 (mmm) REVERT: E 262 LEU cc_start: 0.9544 (mp) cc_final: 0.9325 (pp) REVERT: E 316 THR cc_start: 0.9698 (m) cc_final: 0.9463 (m) REVERT: E 319 HIS cc_start: 0.8621 (m90) cc_final: 0.8274 (m-70) REVERT: F 159 MET cc_start: 0.9791 (mtm) cc_final: 0.9540 (tpt) REVERT: F 280 MET cc_start: 0.9688 (tpt) cc_final: 0.9296 (tpp) REVERT: F 285 GLU cc_start: 0.9369 (mm-30) cc_final: 0.7893 (tp30) REVERT: F 415 PHE cc_start: 0.8855 (t80) cc_final: 0.7959 (m-80) REVERT: G 30 LEU cc_start: 0.9350 (pp) cc_final: 0.9086 (mt) REVERT: G 34 PHE cc_start: 0.9540 (t80) cc_final: 0.9136 (t80) REVERT: G 55 ILE cc_start: 0.9431 (pt) cc_final: 0.9080 (pt) REVERT: H 55 ILE cc_start: 0.9089 (mm) cc_final: 0.8654 (mm) REVERT: J 53 PHE cc_start: 0.9674 (m-80) cc_final: 0.9396 (m-80) REVERT: J 60 ASP cc_start: 0.9160 (p0) cc_final: 0.8339 (t0) REVERT: L 27 PHE cc_start: 0.9090 (m-10) cc_final: 0.8751 (m-10) REVERT: Q 71 LEU cc_start: 0.9608 (mm) cc_final: 0.9381 (pp) REVERT: a 26 MET cc_start: 0.7035 (mpp) cc_final: 0.5807 (mpp) REVERT: a 125 MET cc_start: 0.8765 (ptt) cc_final: 0.8367 (ppp) REVERT: a 278 MET cc_start: 0.9860 (mmp) cc_final: 0.9606 (mmm) REVERT: e 24 ILE cc_start: 0.8558 (pt) cc_final: 0.8350 (tp) REVERT: e 98 ARG cc_start: 0.8698 (ttm110) cc_final: 0.8404 (tmt170) REVERT: e 137 ARG cc_start: 0.7884 (ptp-110) cc_final: 0.7566 (ttm110) REVERT: g 32 MET cc_start: 0.9272 (ttt) cc_final: 0.8712 (ttp) REVERT: g 156 MET cc_start: 0.9561 (tpp) cc_final: 0.8998 (tpp) REVERT: g 229 MET cc_start: 0.8954 (mtm) cc_final: 0.8527 (mtp) outliers start: 1 outliers final: 0 residues processed: 344 average time/residue: 0.4783 time to fit residues: 272.5991 Evaluate side-chains 267 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 4.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 8.9990 chunk 328 optimal weight: 7.9990 chunk 226 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 208 optimal weight: 0.9990 chunk 293 optimal weight: 10.0000 chunk 438 optimal weight: 2.9990 chunk 463 optimal weight: 6.9990 chunk 228 optimal weight: 20.0000 chunk 415 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 HIS F 366 GLN ** G 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 49 GLN ** P 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 137 ASN ** b 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 167 ASN p 138 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 37700 Z= 0.266 Angle : 0.646 15.897 51111 Z= 0.338 Chirality : 0.041 0.196 5988 Planarity : 0.004 0.053 6628 Dihedral : 6.629 145.441 5364 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 25.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.85 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: -0.33 (0.12), residues: 4851 helix: 0.70 (0.10), residues: 2595 sheet: -0.87 (0.21), residues: 564 loop : -1.34 (0.16), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 118 HIS 0.006 0.001 HIS F 358 PHE 0.055 0.002 PHE L 18 TYR 0.033 0.002 TYR a 283 ARG 0.007 0.001 ARG C 284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 4.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ASP cc_start: 0.9515 (p0) cc_final: 0.8945 (m-30) REVERT: A 179 MET cc_start: 0.9536 (tmm) cc_final: 0.9333 (tmm) REVERT: A 235 MET cc_start: 0.8847 (mpp) cc_final: 0.8314 (ptp) REVERT: A 238 LEU cc_start: 0.9641 (mt) cc_final: 0.9339 (pp) REVERT: A 295 HIS cc_start: 0.9309 (m90) cc_final: 0.9021 (m-70) REVERT: B 53 MET cc_start: 0.8521 (mtm) cc_final: 0.8172 (mtm) REVERT: B 157 MET cc_start: 0.9395 (mmt) cc_final: 0.8866 (mmp) REVERT: B 235 MET cc_start: 0.9623 (mmp) cc_final: 0.9349 (mmm) REVERT: B 238 LEU cc_start: 0.9814 (mt) cc_final: 0.9518 (pp) REVERT: B 246 MET cc_start: 0.9574 (mmp) cc_final: 0.9335 (mmm) REVERT: C 49 MET cc_start: 0.7747 (tpt) cc_final: 0.5747 (tpt) REVERT: C 63 MET cc_start: 0.9546 (tmm) cc_final: 0.9333 (tmm) REVERT: C 182 ASP cc_start: 0.9074 (t0) cc_final: 0.8767 (t0) REVERT: C 235 MET cc_start: 0.9393 (mpp) cc_final: 0.8790 (mpp) REVERT: C 484 MET cc_start: 0.9623 (mpp) cc_final: 0.9378 (mpp) REVERT: D 9 ILE cc_start: 0.9729 (pt) cc_final: 0.9406 (mp) REVERT: D 159 MET cc_start: 0.9805 (mmp) cc_final: 0.9473 (mmm) REVERT: D 192 MET cc_start: 0.9716 (ptp) cc_final: 0.9378 (ptt) REVERT: D 225 MET cc_start: 0.9789 (mmp) cc_final: 0.9486 (mmm) REVERT: D 258 GLU cc_start: 0.9405 (mt-10) cc_final: 0.9193 (mt-10) REVERT: D 280 MET cc_start: 0.9715 (mmp) cc_final: 0.9246 (mmm) REVERT: D 450 MET cc_start: 0.9505 (mmp) cc_final: 0.9184 (mmp) REVERT: E 158 MET cc_start: 0.9477 (tpt) cc_final: 0.8988 (tpt) REVERT: E 159 MET cc_start: 0.9625 (mmp) cc_final: 0.9266 (mmm) REVERT: E 192 MET cc_start: 0.9861 (mmm) cc_final: 0.9580 (tpp) REVERT: E 225 MET cc_start: 0.9785 (mmp) cc_final: 0.9544 (mmm) REVERT: E 266 MET cc_start: 0.8466 (mmp) cc_final: 0.8001 (mmp) REVERT: E 319 HIS cc_start: 0.8623 (m90) cc_final: 0.8204 (m-70) REVERT: F 159 MET cc_start: 0.9793 (mtm) cc_final: 0.9527 (tpt) REVERT: F 280 MET cc_start: 0.9690 (tpt) cc_final: 0.9299 (tpp) REVERT: F 285 GLU cc_start: 0.9389 (mm-30) cc_final: 0.7928 (tp30) REVERT: F 415 PHE cc_start: 0.8844 (t80) cc_final: 0.7946 (m-80) REVERT: G 30 LEU cc_start: 0.9356 (pp) cc_final: 0.9055 (mt) REVERT: G 34 PHE cc_start: 0.9569 (t80) cc_final: 0.9183 (t80) REVERT: G 55 ILE cc_start: 0.9438 (pt) cc_final: 0.9199 (pt) REVERT: G 64 MET cc_start: 0.8504 (mmp) cc_final: 0.8292 (mmm) REVERT: H 55 ILE cc_start: 0.9070 (mm) cc_final: 0.8837 (mm) REVERT: J 53 PHE cc_start: 0.9541 (m-80) cc_final: 0.9180 (m-80) REVERT: J 60 ASP cc_start: 0.9171 (p0) cc_final: 0.8275 (t0) REVERT: L 18 PHE cc_start: 0.7957 (t80) cc_final: 0.7426 (t80) REVERT: L 27 PHE cc_start: 0.9068 (m-10) cc_final: 0.8726 (m-80) REVERT: Q 71 LEU cc_start: 0.9575 (mm) cc_final: 0.9335 (pp) REVERT: a 26 MET cc_start: 0.7330 (mpp) cc_final: 0.6005 (mpp) REVERT: a 122 MET cc_start: 0.8908 (tmm) cc_final: 0.8629 (tmm) REVERT: a 125 MET cc_start: 0.8825 (ptt) cc_final: 0.8467 (ppp) REVERT: a 236 MET cc_start: 0.9100 (ttt) cc_final: 0.8599 (ttt) REVERT: a 278 MET cc_start: 0.9850 (mmp) cc_final: 0.9629 (mmm) REVERT: d 172 MET cc_start: 0.9756 (ptp) cc_final: 0.9486 (ptp) REVERT: e 24 ILE cc_start: 0.8559 (pt) cc_final: 0.8329 (tp) REVERT: e 98 ARG cc_start: 0.8733 (ttm110) cc_final: 0.8427 (tmt170) REVERT: g 32 MET cc_start: 0.9226 (ttt) cc_final: 0.8877 (ttp) REVERT: g 156 MET cc_start: 0.9539 (tpp) cc_final: 0.8959 (tpp) REVERT: g 229 MET cc_start: 0.8973 (mtm) cc_final: 0.8533 (mtp) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.4812 time to fit residues: 257.6318 Evaluate side-chains 262 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 3.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 9.9990 chunk 263 optimal weight: 3.9990 chunk 6 optimal weight: 20.0000 chunk 345 optimal weight: 7.9990 chunk 191 optimal weight: 5.9990 chunk 395 optimal weight: 8.9990 chunk 320 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 236 optimal weight: 10.0000 chunk 416 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 366 GLN ** G 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 45 ASN ** p 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 138 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 37700 Z= 0.304 Angle : 0.677 13.480 51111 Z= 0.355 Chirality : 0.042 0.226 5988 Planarity : 0.005 0.070 6628 Dihedral : 6.745 148.443 5364 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 27.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.68 % Favored : 93.30 % Rotamer: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: -0.44 (0.12), residues: 4851 helix: 0.63 (0.10), residues: 2574 sheet: -0.93 (0.21), residues: 553 loop : -1.39 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 118 HIS 0.007 0.001 HIS D 319 PHE 0.046 0.002 PHE J 18 TYR 0.016 0.002 TYR D 336 ARG 0.007 0.001 ARG E 371 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 316 time to evaluate : 4.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ASP cc_start: 0.9505 (p0) cc_final: 0.8968 (m-30) REVERT: A 179 MET cc_start: 0.9585 (tmm) cc_final: 0.9357 (tmm) REVERT: A 238 LEU cc_start: 0.9640 (mt) cc_final: 0.9356 (pp) REVERT: A 295 HIS cc_start: 0.9373 (m90) cc_final: 0.9042 (m-70) REVERT: B 53 MET cc_start: 0.8489 (mtm) cc_final: 0.8149 (mtm) REVERT: B 157 MET cc_start: 0.9368 (mmt) cc_final: 0.8903 (mmp) REVERT: B 235 MET cc_start: 0.9626 (mmp) cc_final: 0.9371 (mmm) REVERT: B 238 LEU cc_start: 0.9829 (mt) cc_final: 0.9544 (pp) REVERT: C 49 MET cc_start: 0.8106 (tpt) cc_final: 0.6267 (tpt) REVERT: C 53 MET cc_start: 0.9800 (mmt) cc_final: 0.9594 (mmm) REVERT: C 182 ASP cc_start: 0.9185 (t0) cc_final: 0.8887 (t0) REVERT: C 235 MET cc_start: 0.9444 (mpp) cc_final: 0.8875 (mpp) REVERT: C 484 MET cc_start: 0.9607 (mpp) cc_final: 0.9369 (mpp) REVERT: D 9 ILE cc_start: 0.9746 (pt) cc_final: 0.9428 (mp) REVERT: D 159 MET cc_start: 0.9808 (mmp) cc_final: 0.9488 (mmm) REVERT: D 192 MET cc_start: 0.9731 (ptp) cc_final: 0.9400 (ptt) REVERT: D 225 MET cc_start: 0.9799 (mmp) cc_final: 0.9502 (mmm) REVERT: D 280 MET cc_start: 0.9724 (mmp) cc_final: 0.9290 (mmm) REVERT: D 450 MET cc_start: 0.9472 (mmp) cc_final: 0.9176 (mmp) REVERT: E 158 MET cc_start: 0.9511 (tpt) cc_final: 0.9003 (tpt) REVERT: E 159 MET cc_start: 0.9649 (mmp) cc_final: 0.9274 (mmm) REVERT: E 192 MET cc_start: 0.9868 (mmm) cc_final: 0.9582 (tpp) REVERT: E 225 MET cc_start: 0.9754 (mmp) cc_final: 0.9515 (mmm) REVERT: E 266 MET cc_start: 0.8538 (mmp) cc_final: 0.8072 (mmp) REVERT: E 319 HIS cc_start: 0.8610 (m90) cc_final: 0.8151 (m-70) REVERT: F 159 MET cc_start: 0.9791 (mtm) cc_final: 0.9531 (tpt) REVERT: F 280 MET cc_start: 0.9686 (tpt) cc_final: 0.9344 (tpp) REVERT: G 30 LEU cc_start: 0.9396 (pp) cc_final: 0.9155 (tp) REVERT: G 34 PHE cc_start: 0.9589 (t80) cc_final: 0.9180 (t80) REVERT: G 55 ILE cc_start: 0.9413 (pt) cc_final: 0.9061 (pt) REVERT: H 55 ILE cc_start: 0.9058 (mm) cc_final: 0.8804 (mm) REVERT: J 53 PHE cc_start: 0.9451 (m-80) cc_final: 0.9127 (m-80) REVERT: J 60 ASP cc_start: 0.9186 (p0) cc_final: 0.8173 (t0) REVERT: L 18 PHE cc_start: 0.7896 (t80) cc_final: 0.7647 (t80) REVERT: L 27 PHE cc_start: 0.9074 (m-10) cc_final: 0.8736 (m-80) REVERT: a 26 MET cc_start: 0.7554 (mpp) cc_final: 0.6415 (mpp) REVERT: a 236 MET cc_start: 0.9122 (ttt) cc_final: 0.8459 (ttt) REVERT: a 277 MET cc_start: 0.9366 (tmm) cc_final: 0.9127 (ppp) REVERT: a 278 MET cc_start: 0.9806 (mmp) cc_final: 0.9568 (mmt) REVERT: d 172 MET cc_start: 0.9726 (ptp) cc_final: 0.9506 (ptp) REVERT: g 32 MET cc_start: 0.9195 (ttt) cc_final: 0.8864 (ttp) REVERT: g 156 MET cc_start: 0.9514 (tpp) cc_final: 0.8940 (tpp) REVERT: g 229 MET cc_start: 0.8981 (mtm) cc_final: 0.8557 (mtp) REVERT: p 110 ASP cc_start: 0.9455 (t0) cc_final: 0.9128 (p0) outliers start: 1 outliers final: 1 residues processed: 317 average time/residue: 0.4649 time to fit residues: 244.7489 Evaluate side-chains 254 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 253 time to evaluate : 4.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 8.9990 chunk 417 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 272 optimal weight: 9.9990 chunk 114 optimal weight: 0.6980 chunk 464 optimal weight: 7.9990 chunk 385 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 153 optimal weight: 10.0000 chunk 243 optimal weight: 6.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 366 GLN F 367 ASN ** P 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 213 ASN ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 137 ASN ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 138 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 37700 Z= 0.267 Angle : 0.651 11.008 51111 Z= 0.341 Chirality : 0.042 0.302 5988 Planarity : 0.004 0.071 6628 Dihedral : 6.741 149.791 5364 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 26.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.18 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: -0.41 (0.12), residues: 4851 helix: 0.65 (0.10), residues: 2575 sheet: -0.95 (0.21), residues: 552 loop : -1.35 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 118 HIS 0.006 0.001 HIS D 319 PHE 0.033 0.002 PHE L 18 TYR 0.016 0.002 TYR F 205 ARG 0.006 0.001 ARG E 371 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 4.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8583 (tpt) cc_final: 0.8222 (tpt) REVERT: A 171 ASP cc_start: 0.9472 (p0) cc_final: 0.8945 (m-30) REVERT: A 179 MET cc_start: 0.9598 (tmm) cc_final: 0.9372 (tmm) REVERT: A 238 LEU cc_start: 0.9629 (mt) cc_final: 0.9339 (pp) REVERT: A 295 HIS cc_start: 0.9395 (m90) cc_final: 0.9043 (m90) REVERT: A 328 LEU cc_start: 0.9637 (mt) cc_final: 0.9416 (mt) REVERT: B 53 MET cc_start: 0.8457 (mtm) cc_final: 0.8141 (mtm) REVERT: B 235 MET cc_start: 0.9622 (mmp) cc_final: 0.9366 (mmm) REVERT: B 238 LEU cc_start: 0.9827 (mt) cc_final: 0.9562 (pp) REVERT: B 246 MET cc_start: 0.9569 (mmp) cc_final: 0.9334 (mmm) REVERT: C 49 MET cc_start: 0.8223 (tpt) cc_final: 0.6466 (tpt) REVERT: C 63 MET cc_start: 0.9412 (tmm) cc_final: 0.9092 (tmm) REVERT: C 182 ASP cc_start: 0.9193 (t0) cc_final: 0.8896 (t0) REVERT: C 235 MET cc_start: 0.9428 (mpp) cc_final: 0.8845 (mpp) REVERT: C 484 MET cc_start: 0.9628 (mpp) cc_final: 0.9376 (mpp) REVERT: D 9 ILE cc_start: 0.9743 (pt) cc_final: 0.9438 (mp) REVERT: D 159 MET cc_start: 0.9795 (mmp) cc_final: 0.9458 (mmm) REVERT: D 192 MET cc_start: 0.9718 (ptp) cc_final: 0.9374 (ptt) REVERT: D 225 MET cc_start: 0.9791 (mmp) cc_final: 0.9502 (mmm) REVERT: D 280 MET cc_start: 0.9721 (mmp) cc_final: 0.9271 (mmm) REVERT: D 450 MET cc_start: 0.9460 (mmp) cc_final: 0.9159 (mmp) REVERT: E 158 MET cc_start: 0.9515 (tpt) cc_final: 0.9017 (tpt) REVERT: E 159 MET cc_start: 0.9644 (mmp) cc_final: 0.9268 (mmm) REVERT: E 192 MET cc_start: 0.9862 (mmm) cc_final: 0.9576 (tpp) REVERT: E 225 MET cc_start: 0.9734 (mmp) cc_final: 0.9530 (mmm) REVERT: E 266 MET cc_start: 0.8464 (mmp) cc_final: 0.8082 (mmm) REVERT: E 319 HIS cc_start: 0.8627 (m90) cc_final: 0.8248 (m90) REVERT: E 366 GLN cc_start: 0.9699 (mp10) cc_final: 0.9221 (tm-30) REVERT: F 159 MET cc_start: 0.9794 (mtm) cc_final: 0.9527 (tpt) REVERT: F 252 TYR cc_start: 0.9750 (t80) cc_final: 0.9218 (t80) REVERT: F 280 MET cc_start: 0.9639 (tpt) cc_final: 0.9362 (tpp) REVERT: F 285 GLU cc_start: 0.9438 (mm-30) cc_final: 0.7948 (tp30) REVERT: F 415 PHE cc_start: 0.8824 (t80) cc_final: 0.7959 (m-80) REVERT: G 30 LEU cc_start: 0.9406 (pp) cc_final: 0.9143 (tp) REVERT: G 34 PHE cc_start: 0.9601 (t80) cc_final: 0.9178 (t80) REVERT: G 55 ILE cc_start: 0.9379 (pt) cc_final: 0.9028 (pt) REVERT: H 55 ILE cc_start: 0.9048 (mm) cc_final: 0.8832 (mm) REVERT: J 53 PHE cc_start: 0.9427 (m-80) cc_final: 0.9170 (m-80) REVERT: J 60 ASP cc_start: 0.9207 (p0) cc_final: 0.8161 (t0) REVERT: L 18 PHE cc_start: 0.7978 (t80) cc_final: 0.7706 (t80) REVERT: L 27 PHE cc_start: 0.9127 (m-10) cc_final: 0.8786 (m-80) REVERT: a 26 MET cc_start: 0.7597 (mpp) cc_final: 0.6550 (mpp) REVERT: a 122 MET cc_start: 0.8984 (tmm) cc_final: 0.8728 (tmm) REVERT: a 277 MET cc_start: 0.9355 (tmm) cc_final: 0.9053 (ppp) REVERT: d 172 MET cc_start: 0.9715 (ptp) cc_final: 0.9430 (ptp) REVERT: e 137 ARG cc_start: 0.8006 (ptp-110) cc_final: 0.7639 (ttm110) REVERT: g 32 MET cc_start: 0.9189 (ttt) cc_final: 0.8785 (ttp) REVERT: g 156 MET cc_start: 0.9506 (tpp) cc_final: 0.8901 (tpp) REVERT: g 229 MET cc_start: 0.8969 (mtm) cc_final: 0.8553 (mtp) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.4772 time to fit residues: 254.1709 Evaluate side-chains 259 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 4.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 264 optimal weight: 6.9990 chunk 339 optimal weight: 5.9990 chunk 262 optimal weight: 4.9990 chunk 390 optimal weight: 5.9990 chunk 259 optimal weight: 9.9990 chunk 462 optimal weight: 0.9990 chunk 289 optimal weight: 6.9990 chunk 282 optimal weight: 20.0000 chunk 213 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 366 GLN Q 77 ASN ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 137 ASN ** b 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 138 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 37700 Z= 0.248 Angle : 0.642 18.699 51111 Z= 0.334 Chirality : 0.042 0.267 5988 Planarity : 0.004 0.050 6628 Dihedral : 6.693 150.532 5364 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 25.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.47 % Favored : 93.51 % Rotamer: Outliers : 0.03 % Allowed : 2.14 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: -0.32 (0.12), residues: 4851 helix: 0.70 (0.10), residues: 2565 sheet: -0.89 (0.22), residues: 543 loop : -1.29 (0.16), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 118 HIS 0.005 0.001 HIS D 319 PHE 0.038 0.002 PHE L 18 TYR 0.014 0.001 TYR C 237 ARG 0.005 0.000 ARG E 371 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 316 time to evaluate : 4.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.9017 (mmp) cc_final: 0.8442 (mmp) REVERT: A 65 LEU cc_start: 0.9457 (mt) cc_final: 0.9200 (mt) REVERT: A 171 ASP cc_start: 0.9407 (p0) cc_final: 0.8918 (m-30) REVERT: A 179 MET cc_start: 0.9600 (tmm) cc_final: 0.9386 (tmm) REVERT: A 238 LEU cc_start: 0.9630 (mt) cc_final: 0.9385 (pp) REVERT: A 295 HIS cc_start: 0.9446 (m90) cc_final: 0.9067 (m90) REVERT: B 53 MET cc_start: 0.8448 (mtm) cc_final: 0.8159 (mtm) REVERT: B 235 MET cc_start: 0.9626 (mmp) cc_final: 0.9368 (mmm) REVERT: B 238 LEU cc_start: 0.9830 (mt) cc_final: 0.9551 (pp) REVERT: B 246 MET cc_start: 0.9538 (mmp) cc_final: 0.9329 (mmm) REVERT: C 49 MET cc_start: 0.8216 (tpt) cc_final: 0.6509 (tpt) REVERT: C 53 MET cc_start: 0.9794 (mmt) cc_final: 0.9584 (mmm) REVERT: C 63 MET cc_start: 0.9434 (tmm) cc_final: 0.9157 (tmm) REVERT: C 182 ASP cc_start: 0.9154 (t0) cc_final: 0.8858 (t0) REVERT: C 235 MET cc_start: 0.9427 (mpp) cc_final: 0.8850 (mpp) REVERT: C 330 ILE cc_start: 0.9705 (mm) cc_final: 0.9457 (mm) REVERT: C 484 MET cc_start: 0.9611 (mpp) cc_final: 0.9365 (mpp) REVERT: D 9 ILE cc_start: 0.9748 (pt) cc_final: 0.9444 (mp) REVERT: D 159 MET cc_start: 0.9790 (mmp) cc_final: 0.9458 (mmm) REVERT: D 192 MET cc_start: 0.9715 (ptp) cc_final: 0.9368 (ptt) REVERT: D 225 MET cc_start: 0.9796 (mmp) cc_final: 0.9490 (mmm) REVERT: D 280 MET cc_start: 0.9714 (mmp) cc_final: 0.9249 (mmm) REVERT: D 450 MET cc_start: 0.9473 (mmp) cc_final: 0.9216 (mmp) REVERT: E 158 MET cc_start: 0.9515 (tpt) cc_final: 0.9037 (tpt) REVERT: E 159 MET cc_start: 0.9637 (mmp) cc_final: 0.9265 (mmm) REVERT: E 192 MET cc_start: 0.9859 (mmm) cc_final: 0.9565 (tpp) REVERT: E 266 MET cc_start: 0.8497 (mmp) cc_final: 0.8113 (mmm) REVERT: E 319 HIS cc_start: 0.8628 (m90) cc_final: 0.8257 (m90) REVERT: E 450 MET cc_start: 0.9274 (tpp) cc_final: 0.9058 (tpp) REVERT: F 159 MET cc_start: 0.9798 (mtm) cc_final: 0.9530 (tpt) REVERT: F 252 TYR cc_start: 0.9748 (t80) cc_final: 0.9261 (t80) REVERT: F 280 MET cc_start: 0.9642 (tpt) cc_final: 0.9346 (tpp) REVERT: F 285 GLU cc_start: 0.9459 (mm-30) cc_final: 0.7986 (tp30) REVERT: F 415 PHE cc_start: 0.8773 (t80) cc_final: 0.7946 (m-80) REVERT: G 30 LEU cc_start: 0.9413 (pp) cc_final: 0.9149 (tp) REVERT: G 34 PHE cc_start: 0.9605 (t80) cc_final: 0.9170 (t80) REVERT: G 55 ILE cc_start: 0.9374 (pt) cc_final: 0.9023 (pt) REVERT: J 53 PHE cc_start: 0.9429 (m-80) cc_final: 0.9176 (m-80) REVERT: J 60 ASP cc_start: 0.9282 (p0) cc_final: 0.8312 (t0) REVERT: L 27 PHE cc_start: 0.9100 (m-10) cc_final: 0.8776 (m-80) REVERT: a 26 MET cc_start: 0.7621 (mpp) cc_final: 0.6454 (mpp) REVERT: a 122 MET cc_start: 0.8852 (tmm) cc_final: 0.8511 (tmm) REVERT: a 236 MET cc_start: 0.8981 (ttt) cc_final: 0.8363 (ttt) REVERT: a 278 MET cc_start: 0.9829 (mmp) cc_final: 0.9558 (mmm) REVERT: d 172 MET cc_start: 0.9709 (ptp) cc_final: 0.9426 (ptp) REVERT: g 32 MET cc_start: 0.9154 (ttt) cc_final: 0.8850 (ttp) REVERT: g 156 MET cc_start: 0.9502 (tpp) cc_final: 0.8892 (tpp) REVERT: g 229 MET cc_start: 0.8983 (mtm) cc_final: 0.8551 (mtp) REVERT: g 246 MET cc_start: 0.9246 (ptp) cc_final: 0.8785 (ptp) REVERT: p 110 ASP cc_start: 0.9504 (t0) cc_final: 0.9126 (p0) outliers start: 1 outliers final: 0 residues processed: 317 average time/residue: 0.4721 time to fit residues: 251.6433 Evaluate side-chains 257 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 4.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 9.9990 chunk 184 optimal weight: 5.9990 chunk 276 optimal weight: 30.0000 chunk 139 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 294 optimal weight: 7.9990 chunk 315 optimal weight: 10.0000 chunk 228 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 363 optimal weight: 5.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 366 GLN ** F 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 77 ASN ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 137 ASN ** b 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 138 GLN ** p 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 37700 Z= 0.385 Angle : 0.772 15.637 51111 Z= 0.405 Chirality : 0.044 0.256 5988 Planarity : 0.005 0.099 6628 Dihedral : 6.946 153.310 5364 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 34.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.79 % Favored : 92.19 % Rotamer: Outliers : 0.03 % Allowed : 1.77 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: -0.76 (0.12), residues: 4851 helix: 0.32 (0.10), residues: 2549 sheet: -0.97 (0.22), residues: 523 loop : -1.45 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP a 55 HIS 0.008 0.002 HIS D 442 PHE 0.040 0.002 PHE H 18 TYR 0.018 0.002 TYR g 210 ARG 0.022 0.001 ARG E 371 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 292 time to evaluate : 4.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8794 (tpt) cc_final: 0.8565 (tpt) REVERT: A 53 MET cc_start: 0.9034 (mmp) cc_final: 0.8688 (mmm) REVERT: A 179 MET cc_start: 0.9625 (tmm) cc_final: 0.9380 (tmm) REVERT: A 238 LEU cc_start: 0.9636 (mt) cc_final: 0.9398 (pp) REVERT: A 295 HIS cc_start: 0.9484 (m90) cc_final: 0.9147 (m90) REVERT: B 53 MET cc_start: 0.8415 (mtm) cc_final: 0.8123 (mtm) REVERT: B 157 MET cc_start: 0.9517 (mmp) cc_final: 0.9017 (mmp) REVERT: B 235 MET cc_start: 0.9642 (mmp) cc_final: 0.9423 (mmm) REVERT: B 238 LEU cc_start: 0.9837 (mt) cc_final: 0.9581 (pp) REVERT: B 325 LEU cc_start: 0.9658 (tp) cc_final: 0.9388 (mt) REVERT: C 49 MET cc_start: 0.8529 (tpt) cc_final: 0.6991 (tpt) REVERT: C 63 MET cc_start: 0.9436 (tmm) cc_final: 0.9224 (tmm) REVERT: C 182 ASP cc_start: 0.9183 (t0) cc_final: 0.8916 (t0) REVERT: C 235 MET cc_start: 0.9441 (mpp) cc_final: 0.8902 (mpp) REVERT: C 484 MET cc_start: 0.9598 (mpp) cc_final: 0.9359 (mpp) REVERT: D 9 ILE cc_start: 0.9771 (pt) cc_final: 0.9494 (mp) REVERT: D 159 MET cc_start: 0.9808 (mmp) cc_final: 0.9528 (mmm) REVERT: D 192 MET cc_start: 0.9761 (ptp) cc_final: 0.9444 (ptt) REVERT: D 225 MET cc_start: 0.9817 (mmp) cc_final: 0.9545 (mmm) REVERT: D 276 LEU cc_start: 0.9682 (pt) cc_final: 0.9433 (pt) REVERT: D 280 MET cc_start: 0.9751 (mmp) cc_final: 0.9234 (mmm) REVERT: D 450 MET cc_start: 0.9351 (mmp) cc_final: 0.9035 (mmp) REVERT: E 158 MET cc_start: 0.9596 (tpt) cc_final: 0.9222 (tpt) REVERT: E 159 MET cc_start: 0.9628 (mmp) cc_final: 0.9400 (mmm) REVERT: E 192 MET cc_start: 0.9883 (mmm) cc_final: 0.9602 (tpp) REVERT: E 225 MET cc_start: 0.9865 (mmp) cc_final: 0.9560 (mmm) REVERT: E 266 MET cc_start: 0.8576 (mmp) cc_final: 0.8232 (mmm) REVERT: E 319 HIS cc_start: 0.8557 (m90) cc_final: 0.8095 (m90) REVERT: F 159 MET cc_start: 0.9796 (mtm) cc_final: 0.9522 (tpt) REVERT: F 252 TYR cc_start: 0.9758 (t80) cc_final: 0.9287 (t80) REVERT: F 280 MET cc_start: 0.9639 (tpt) cc_final: 0.9358 (tpp) REVERT: F 415 PHE cc_start: 0.8699 (t80) cc_final: 0.7862 (m-80) REVERT: G 30 LEU cc_start: 0.9435 (pp) cc_final: 0.9175 (mt) REVERT: J 53 PHE cc_start: 0.9461 (m-80) cc_final: 0.9183 (m-80) REVERT: J 60 ASP cc_start: 0.9286 (p0) cc_final: 0.8323 (t0) REVERT: L 18 PHE cc_start: 0.8023 (t80) cc_final: 0.7816 (t80) REVERT: L 27 PHE cc_start: 0.9128 (m-10) cc_final: 0.8803 (m-80) REVERT: a 26 MET cc_start: 0.7872 (mpp) cc_final: 0.6735 (mpp) REVERT: a 63 PHE cc_start: 0.9396 (t80) cc_final: 0.9180 (t80) REVERT: a 122 MET cc_start: 0.8845 (tmm) cc_final: 0.8540 (tmm) REVERT: a 236 MET cc_start: 0.9074 (ttt) cc_final: 0.8443 (ttt) REVERT: d 172 MET cc_start: 0.9730 (ptp) cc_final: 0.9465 (ptp) REVERT: g 32 MET cc_start: 0.9196 (ttt) cc_final: 0.8852 (ttp) REVERT: g 156 MET cc_start: 0.9474 (tpp) cc_final: 0.8879 (tpp) REVERT: g 229 MET cc_start: 0.8984 (mtm) cc_final: 0.8577 (mtp) REVERT: g 246 MET cc_start: 0.9238 (ptp) cc_final: 0.8829 (ptp) REVERT: p 110 ASP cc_start: 0.9503 (t0) cc_final: 0.9181 (p0) outliers start: 1 outliers final: 0 residues processed: 293 average time/residue: 0.4468 time to fit residues: 221.1326 Evaluate side-chains 240 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 4.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 1.9990 chunk 443 optimal weight: 0.2980 chunk 404 optimal weight: 5.9990 chunk 431 optimal weight: 5.9990 chunk 259 optimal weight: 10.0000 chunk 187 optimal weight: 0.8980 chunk 338 optimal weight: 20.0000 chunk 132 optimal weight: 3.9990 chunk 389 optimal weight: 6.9990 chunk 407 optimal weight: 0.0980 chunk 429 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 284 GLN F 319 HIS F 366 GLN F 367 ASN F 370 GLN Q 77 ASN ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 137 ASN ** b 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 138 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37700 Z= 0.171 Angle : 0.618 14.161 51111 Z= 0.316 Chirality : 0.042 0.241 5988 Planarity : 0.004 0.055 6628 Dihedral : 6.622 150.605 5364 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.97 % Favored : 95.01 % Rotamer: Outliers : 0.03 % Allowed : 0.57 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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 (0.12), residues: 4851 helix: 0.80 (0.10), residues: 2576 sheet: -0.86 (0.22), residues: 540 loop : -1.09 (0.16), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 118 HIS 0.003 0.001 HIS E 190 PHE 0.036 0.001 PHE Q 18 TYR 0.025 0.001 TYR B 514 ARG 0.012 0.000 ARG E 371 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 318 time to evaluate : 4.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8467 (tpt) cc_final: 0.8208 (tpt) REVERT: A 53 MET cc_start: 0.9138 (mmp) cc_final: 0.8833 (mmm) REVERT: A 65 LEU cc_start: 0.9398 (mt) cc_final: 0.9129 (mt) REVERT: A 157 MET cc_start: 0.9335 (mpp) cc_final: 0.9106 (mpp) REVERT: A 179 MET cc_start: 0.9595 (tmm) cc_final: 0.9330 (tmm) REVERT: A 295 HIS cc_start: 0.9466 (m90) cc_final: 0.9069 (m90) REVERT: B 235 MET cc_start: 0.9607 (mmp) cc_final: 0.9343 (mmm) REVERT: B 238 LEU cc_start: 0.9814 (mt) cc_final: 0.9512 (pp) REVERT: B 246 MET cc_start: 0.9564 (mmp) cc_final: 0.9287 (mmm) REVERT: B 258 LEU cc_start: 0.9781 (tp) cc_final: 0.9554 (tp) REVERT: C 49 MET cc_start: 0.7792 (tpt) cc_final: 0.6433 (tpt) REVERT: C 53 MET cc_start: 0.9785 (mmt) cc_final: 0.9521 (mmm) REVERT: C 182 ASP cc_start: 0.9147 (t0) cc_final: 0.8848 (t0) REVERT: C 235 MET cc_start: 0.9409 (mpp) cc_final: 0.8842 (mpp) REVERT: C 330 ILE cc_start: 0.9686 (mm) cc_final: 0.9439 (mm) REVERT: C 484 MET cc_start: 0.9618 (mpp) cc_final: 0.9403 (mpp) REVERT: D 9 ILE cc_start: 0.9760 (pt) cc_final: 0.9454 (mp) REVERT: D 159 MET cc_start: 0.9782 (mmp) cc_final: 0.9444 (mmm) REVERT: D 192 MET cc_start: 0.9695 (ptp) cc_final: 0.9354 (ptt) REVERT: D 225 MET cc_start: 0.9795 (mmp) cc_final: 0.9491 (mmm) REVERT: D 276 LEU cc_start: 0.9639 (pt) cc_final: 0.9411 (pt) REVERT: D 280 MET cc_start: 0.9666 (mmp) cc_final: 0.9162 (mmm) REVERT: E 158 MET cc_start: 0.9546 (tpt) cc_final: 0.9089 (tpt) REVERT: E 159 MET cc_start: 0.9611 (mmp) cc_final: 0.9356 (mmm) REVERT: E 192 MET cc_start: 0.9804 (mmm) cc_final: 0.9515 (tpp) REVERT: E 225 MET cc_start: 0.9843 (mmp) cc_final: 0.9569 (mmm) REVERT: E 266 MET cc_start: 0.8593 (mmp) cc_final: 0.8197 (mmp) REVERT: E 319 HIS cc_start: 0.8618 (m90) cc_final: 0.8161 (m90) REVERT: F 159 MET cc_start: 0.9789 (mtm) cc_final: 0.9508 (tpt) REVERT: F 252 TYR cc_start: 0.9705 (t80) cc_final: 0.9223 (t80) REVERT: F 280 MET cc_start: 0.9639 (tpt) cc_final: 0.9398 (tpp) REVERT: F 285 GLU cc_start: 0.9400 (mm-30) cc_final: 0.7878 (tp30) REVERT: F 415 PHE cc_start: 0.8668 (t80) cc_final: 0.7843 (m-80) REVERT: G 30 LEU cc_start: 0.9420 (pp) cc_final: 0.9109 (mt) REVERT: H 55 ILE cc_start: 0.8995 (mm) cc_final: 0.8704 (mm) REVERT: J 53 PHE cc_start: 0.9406 (m-80) cc_final: 0.9144 (m-80) REVERT: J 60 ASP cc_start: 0.9288 (p0) cc_final: 0.8344 (t0) REVERT: L 18 PHE cc_start: 0.8117 (t80) cc_final: 0.7774 (t80) REVERT: L 27 PHE cc_start: 0.9136 (m-10) cc_final: 0.8834 (m-80) REVERT: a 26 MET cc_start: 0.7526 (mpp) cc_final: 0.6354 (mpp) REVERT: a 63 PHE cc_start: 0.9362 (t80) cc_final: 0.9151 (t80) REVERT: a 122 MET cc_start: 0.8923 (tmm) cc_final: 0.8668 (tmm) REVERT: a 278 MET cc_start: 0.9801 (mmp) cc_final: 0.9591 (mmm) REVERT: b 106 LYS cc_start: 0.8640 (tttt) cc_final: 0.8433 (mmtt) REVERT: d 172 MET cc_start: 0.9685 (ptp) cc_final: 0.9475 (ptp) REVERT: g 32 MET cc_start: 0.9193 (ttt) cc_final: 0.8882 (ttp) REVERT: g 156 MET cc_start: 0.9514 (tpp) cc_final: 0.8933 (tpp) REVERT: g 229 MET cc_start: 0.8957 (mtm) cc_final: 0.8517 (mtp) REVERT: g 246 MET cc_start: 0.9105 (ptp) cc_final: 0.8668 (ptp) outliers start: 1 outliers final: 0 residues processed: 319 average time/residue: 0.4637 time to fit residues: 248.5622 Evaluate side-chains 259 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 4.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 10.0000 chunk 455 optimal weight: 9.9990 chunk 278 optimal weight: 20.0000 chunk 216 optimal weight: 6.9990 chunk 316 optimal weight: 20.0000 chunk 478 optimal weight: 0.8980 chunk 440 optimal weight: 6.9990 chunk 380 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 294 optimal weight: 6.9990 chunk 233 optimal weight: 0.0000 overall best weight: 4.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 366 GLN F 367 ASN Q 77 ASN ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 137 ASN ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 138 GLN ** p 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 37700 Z= 0.248 Angle : 0.650 16.141 51111 Z= 0.338 Chirality : 0.042 0.247 5988 Planarity : 0.004 0.052 6628 Dihedral : 6.601 153.271 5364 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 24.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.50 % Favored : 94.48 % Rotamer: Outliers : 0.03 % Allowed : 0.37 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: -0.24 (0.12), residues: 4851 helix: 0.72 (0.10), residues: 2566 sheet: -0.92 (0.21), residues: 557 loop : -1.14 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 118 HIS 0.005 0.001 HIS D 319 PHE 0.035 0.002 PHE J 18 TYR 0.019 0.001 TYR E 372 ARG 0.007 0.001 ARG E 371 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 299 time to evaluate : 4.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8698 (tpt) cc_final: 0.8430 (tpt) REVERT: A 53 MET cc_start: 0.9139 (mmp) cc_final: 0.8824 (mmm) REVERT: A 65 LEU cc_start: 0.9416 (mt) cc_final: 0.9141 (mt) REVERT: A 179 MET cc_start: 0.9599 (tmm) cc_final: 0.9360 (tmm) REVERT: A 238 LEU cc_start: 0.9616 (mt) cc_final: 0.9377 (pp) REVERT: A 295 HIS cc_start: 0.9476 (m90) cc_final: 0.9098 (m90) REVERT: B 53 MET cc_start: 0.8790 (mtm) cc_final: 0.8505 (mtm) REVERT: B 157 MET cc_start: 0.9504 (mmt) cc_final: 0.8978 (mmp) REVERT: B 235 MET cc_start: 0.9636 (mmp) cc_final: 0.9389 (mmm) REVERT: B 238 LEU cc_start: 0.9834 (mt) cc_final: 0.9549 (pp) REVERT: B 484 MET cc_start: 0.8770 (ptp) cc_final: 0.8561 (ptp) REVERT: C 49 MET cc_start: 0.7876 (tpt) cc_final: 0.6233 (tpt) REVERT: C 53 MET cc_start: 0.9776 (mmt) cc_final: 0.9503 (mmm) REVERT: C 182 ASP cc_start: 0.9184 (t0) cc_final: 0.8903 (t0) REVERT: C 235 MET cc_start: 0.9420 (mpp) cc_final: 0.8853 (mpp) REVERT: C 330 ILE cc_start: 0.9692 (mm) cc_final: 0.9439 (mm) REVERT: C 484 MET cc_start: 0.9611 (mpp) cc_final: 0.9401 (mpp) REVERT: D 55 MET cc_start: 0.8791 (mmp) cc_final: 0.7904 (mmp) REVERT: D 159 MET cc_start: 0.9790 (mmp) cc_final: 0.9468 (mmm) REVERT: D 192 MET cc_start: 0.9707 (ptp) cc_final: 0.9358 (ptt) REVERT: D 225 MET cc_start: 0.9811 (mmp) cc_final: 0.9547 (mmm) REVERT: D 276 LEU cc_start: 0.9665 (pt) cc_final: 0.9424 (pt) REVERT: D 280 MET cc_start: 0.9702 (mmp) cc_final: 0.9178 (mmm) REVERT: E 158 MET cc_start: 0.9561 (tpt) cc_final: 0.9179 (tpt) REVERT: E 159 MET cc_start: 0.9619 (mmp) cc_final: 0.9358 (mmm) REVERT: E 192 MET cc_start: 0.9840 (mmm) cc_final: 0.9562 (tpp) REVERT: E 225 MET cc_start: 0.9846 (mmp) cc_final: 0.9557 (mmm) REVERT: E 266 MET cc_start: 0.8607 (mmp) cc_final: 0.8324 (mmp) REVERT: E 319 HIS cc_start: 0.8626 (m90) cc_final: 0.8206 (m90) REVERT: F 159 MET cc_start: 0.9795 (mtm) cc_final: 0.9512 (tpt) REVERT: F 280 MET cc_start: 0.9659 (tpt) cc_final: 0.9345 (tpp) REVERT: F 285 GLU cc_start: 0.9429 (mm-30) cc_final: 0.8006 (tp30) REVERT: F 415 PHE cc_start: 0.8691 (t80) cc_final: 0.7863 (m-80) REVERT: G 30 LEU cc_start: 0.9431 (pp) cc_final: 0.9136 (mt) REVERT: J 53 PHE cc_start: 0.9443 (m-80) cc_final: 0.9171 (m-80) REVERT: J 60 ASP cc_start: 0.9291 (p0) cc_final: 0.8325 (t0) REVERT: L 27 PHE cc_start: 0.9128 (m-10) cc_final: 0.8817 (m-80) REVERT: a 26 MET cc_start: 0.7615 (mpp) cc_final: 0.6422 (mpp) REVERT: a 63 PHE cc_start: 0.9398 (t80) cc_final: 0.9185 (t80) REVERT: a 122 MET cc_start: 0.8832 (tmm) cc_final: 0.8514 (tmm) REVERT: a 236 MET cc_start: 0.9037 (ttt) cc_final: 0.8613 (ttt) REVERT: a 278 MET cc_start: 0.9795 (mmp) cc_final: 0.9574 (mmm) REVERT: b 106 LYS cc_start: 0.8656 (tttt) cc_final: 0.8368 (mmtt) REVERT: d 172 MET cc_start: 0.9697 (ptp) cc_final: 0.9415 (ptp) REVERT: g 32 MET cc_start: 0.9220 (ttt) cc_final: 0.8899 (ttp) REVERT: g 156 MET cc_start: 0.9503 (tpp) cc_final: 0.8924 (tpp) REVERT: g 229 MET cc_start: 0.8967 (mtm) cc_final: 0.8523 (mtp) REVERT: g 246 MET cc_start: 0.9008 (ptp) cc_final: 0.8418 (ptp) REVERT: p 110 ASP cc_start: 0.9500 (t0) cc_final: 0.9140 (p0) outliers start: 1 outliers final: 0 residues processed: 300 average time/residue: 0.4658 time to fit residues: 236.0988 Evaluate side-chains 249 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 4.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 0.2980 chunk 405 optimal weight: 8.9990 chunk 116 optimal weight: 8.9990 chunk 351 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 381 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 391 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 366 GLN Q 77 ASN a 123 ASN ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 137 ASN ** b 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 138 GLN ** p 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.035379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.025308 restraints weight = 447690.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.026114 restraints weight = 299290.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.026711 restraints weight = 221682.748| |-----------------------------------------------------------------------------| r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2527 r_free = 0.2527 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2527 r_free = 0.2527 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37700 Z= 0.199 Angle : 0.620 15.133 51111 Z= 0.319 Chirality : 0.042 0.225 5988 Planarity : 0.004 0.051 6628 Dihedral : 6.538 155.638 5364 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.36 % Favored : 94.62 % Rotamer: Outliers : 0.05 % Allowed : 0.34 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: -0.13 (0.12), residues: 4851 helix: 0.78 (0.10), residues: 2585 sheet: -0.86 (0.21), residues: 567 loop : -1.03 (0.16), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a 118 HIS 0.003 0.001 HIS D 319 PHE 0.034 0.002 PHE L 18 TYR 0.017 0.001 TYR C 237 ARG 0.008 0.000 ARG E 371 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6823.36 seconds wall clock time: 127 minutes 20.26 seconds (7640.26 seconds total)