Starting phenix.real_space_refine (version: dev) on Fri Apr 8 20:35:51 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld0_23278/04_2022/7ld0_23278.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld0_23278/04_2022/7ld0_23278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld0_23278/04_2022/7ld0_23278.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld0_23278/04_2022/7ld0_23278.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld0_23278/04_2022/7ld0_23278.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld0_23278/04_2022/7ld0_23278.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.026 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 36976 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "B" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "C" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "D" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "E" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "F" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "G" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "H" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Time building chain proxies: 20.72, per 1000 atoms: 0.56 Number of scatterers: 36976 At special positions: 0 Unit cell: (206.01, 206.01, 82.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 152 16.00 O 6744 8.00 N 6664 7.00 C 23416 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: 15.95 Conformation dependent library (CDL) restraints added in 5.7 seconds 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8800 Finding SS restraints... Secondary structure from input PDB file: 336 helices and 8 sheets defined 72.6% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 61 through 68 removed outlier: 3.527A pdb=" N LEU A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 79 removed outlier: 3.872A pdb=" N ALA A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 104 removed outlier: 3.521A pdb=" N ALA A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 101 " --> pdb=" O GLN A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 124 removed outlier: 3.665A pdb=" N GLN A 114 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 141 through 151 removed outlier: 4.170A pdb=" N GLN A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 164 removed outlier: 3.965A pdb=" N ARG A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 163 " --> pdb=" O ARG A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 172 removed outlier: 3.680A pdb=" N LEU A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 193 removed outlier: 4.139A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.812A pdb=" N ALA A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 214 removed outlier: 3.561A pdb=" N TRP A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 219 through 237 Processing helix chain 'A' and resid 238 through 248 Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 283 through 289 Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.634A pdb=" N LEU A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 309 removed outlier: 3.632A pdb=" N PHE A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA A 309 " --> pdb=" O PRO A 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 309' Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.504A pdb=" N GLN A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 removed outlier: 3.766A pdb=" N LEU A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 359 Processing helix chain 'A' and resid 363 through 369 removed outlier: 3.834A pdb=" N ASP A 367 " --> pdb=" O LYS A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.799A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 397 Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 430 through 437 Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 461 through 477 Processing helix chain 'A' and resid 486 through 495 removed outlier: 3.731A pdb=" N TRP A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 494 " --> pdb=" O TRP A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 500 No H-bonds generated for 'chain 'A' and resid 498 through 500' Processing helix chain 'A' and resid 501 through 508 removed outlier: 3.657A pdb=" N CYS A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 521 through 526 Processing helix chain 'A' and resid 531 through 543 removed outlier: 3.610A pdb=" N ARG A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 587 removed outlier: 3.528A pdb=" N SER A 578 " --> pdb=" O SER A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 614 Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.506A pdb=" N LYS A 628 " --> pdb=" O ALA A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 650 removed outlier: 3.683A pdb=" N CYS A 649 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 699 removed outlier: 3.656A pdb=" N ARG A 697 " --> pdb=" O GLU A 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 68 removed outlier: 3.782A pdb=" N GLU B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 79 removed outlier: 3.872A pdb=" N ALA B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 104 removed outlier: 3.521A pdb=" N ALA B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU B 101 " --> pdb=" O GLN B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 124 removed outlier: 3.665A pdb=" N GLN B 114 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 133 Processing helix chain 'B' and resid 141 through 151 removed outlier: 4.170A pdb=" N GLN B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 164 removed outlier: 3.964A pdb=" N ARG B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 163 " --> pdb=" O ARG B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 172 removed outlier: 3.679A pdb=" N LEU B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 193 removed outlier: 4.139A pdb=" N SER B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLY B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.812A pdb=" N ALA B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 214 removed outlier: 3.561A pdb=" N TRP B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 219 through 237 Processing helix chain 'B' and resid 238 through 248 Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 283 through 289 Processing helix chain 'B' and resid 295 through 303 removed outlier: 3.635A pdb=" N LEU B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 removed outlier: 3.633A pdb=" N PHE B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA B 309 " --> pdb=" O PRO B 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 304 through 309' Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.504A pdb=" N GLN B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.765A pdb=" N LEU B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 359 Processing helix chain 'B' and resid 363 through 369 removed outlier: 3.835A pdb=" N ASP B 367 " --> pdb=" O LYS B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 removed outlier: 3.800A pdb=" N SER B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 397 Processing helix chain 'B' and resid 413 through 423 Processing helix chain 'B' and resid 430 through 437 Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 447 through 454 Processing helix chain 'B' and resid 461 through 477 Processing helix chain 'B' and resid 486 through 495 removed outlier: 3.731A pdb=" N TRP B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 494 " --> pdb=" O TRP B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 500 No H-bonds generated for 'chain 'B' and resid 498 through 500' Processing helix chain 'B' and resid 501 through 508 removed outlier: 3.657A pdb=" N CYS B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 518 Processing helix chain 'B' and resid 521 through 526 Processing helix chain 'B' and resid 531 through 543 removed outlier: 3.610A pdb=" N ARG B 535 " --> pdb=" O LEU B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 587 removed outlier: 3.527A pdb=" N SER B 578 " --> pdb=" O SER B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 614 Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.506A pdb=" N LYS B 628 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 650 removed outlier: 3.681A pdb=" N CYS B 649 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 699 removed outlier: 3.657A pdb=" N ARG B 697 " --> pdb=" O GLU B 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 removed outlier: 3.782A pdb=" N GLU C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 79 removed outlier: 3.872A pdb=" N ALA C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 104 removed outlier: 3.520A pdb=" N ALA C 93 " --> pdb=" O GLY C 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU C 94 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU C 101 " --> pdb=" O GLN C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 124 removed outlier: 3.665A pdb=" N GLN C 114 " --> pdb=" O ARG C 110 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 133 Processing helix chain 'C' and resid 141 through 151 removed outlier: 4.171A pdb=" N GLN C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE C 151 " --> pdb=" O LEU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 164 removed outlier: 3.964A pdb=" N ARG C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE C 163 " --> pdb=" O ARG C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 172 removed outlier: 3.679A pdb=" N LEU C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 193 removed outlier: 4.139A pdb=" N SER C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY C 186 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.811A pdb=" N ALA C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 214 removed outlier: 3.561A pdb=" N TRP C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 217 No H-bonds generated for 'chain 'C' and resid 215 through 217' Processing helix chain 'C' and resid 219 through 237 Processing helix chain 'C' and resid 238 through 248 removed outlier: 3.534A pdb=" N GLN C 242 " --> pdb=" O GLY C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 295 through 303 removed outlier: 3.635A pdb=" N LEU C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 309 removed outlier: 3.633A pdb=" N PHE C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA C 309 " --> pdb=" O PRO C 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 304 through 309' Processing helix chain 'C' and resid 323 through 329 removed outlier: 3.504A pdb=" N GLN C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG C 329 " --> pdb=" O ASP C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 335 removed outlier: 3.765A pdb=" N LEU C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 359 Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.836A pdb=" N ASP C 367 " --> pdb=" O LYS C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 removed outlier: 3.800A pdb=" N SER C 373 " --> pdb=" O GLY C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 397 Processing helix chain 'C' and resid 413 through 423 Processing helix chain 'C' and resid 430 through 437 Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 447 through 454 Processing helix chain 'C' and resid 461 through 477 Processing helix chain 'C' and resid 486 through 495 removed outlier: 3.731A pdb=" N TRP C 490 " --> pdb=" O ASN C 486 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 494 " --> pdb=" O TRP C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 500 No H-bonds generated for 'chain 'C' and resid 498 through 500' Processing helix chain 'C' and resid 501 through 508 removed outlier: 3.658A pdb=" N CYS C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 518 Processing helix chain 'C' and resid 521 through 526 Processing helix chain 'C' and resid 531 through 543 removed outlier: 3.610A pdb=" N ARG C 535 " --> pdb=" O LEU C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 587 removed outlier: 3.528A pdb=" N SER C 578 " --> pdb=" O SER C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 614 Processing helix chain 'C' and resid 625 through 629 removed outlier: 3.505A pdb=" N LYS C 628 " --> pdb=" O ALA C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 650 removed outlier: 3.681A pdb=" N CYS C 649 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 699 removed outlier: 3.656A pdb=" N ARG C 697 " --> pdb=" O GLU C 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 68 removed outlier: 3.782A pdb=" N GLU D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 79 removed outlier: 3.872A pdb=" N ALA D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 104 removed outlier: 3.521A pdb=" N ALA D 93 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D 95 " --> pdb=" O GLY D 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU D 101 " --> pdb=" O GLN D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 124 removed outlier: 3.665A pdb=" N GLN D 114 " --> pdb=" O ARG D 110 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 133 Processing helix chain 'D' and resid 141 through 151 removed outlier: 4.171A pdb=" N GLN D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE D 151 " --> pdb=" O LEU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 164 removed outlier: 3.964A pdb=" N ARG D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE D 163 " --> pdb=" O ARG D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 172 removed outlier: 3.680A pdb=" N LEU D 169 " --> pdb=" O LEU D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 193 removed outlier: 4.138A pdb=" N SER D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY D 186 " --> pdb=" O ARG D 182 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.812A pdb=" N ALA D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 214 removed outlier: 3.561A pdb=" N TRP D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 217 No H-bonds generated for 'chain 'D' and resid 215 through 217' Processing helix chain 'D' and resid 219 through 237 Processing helix chain 'D' and resid 238 through 248 Processing helix chain 'D' and resid 251 through 253 No H-bonds generated for 'chain 'D' and resid 251 through 253' Processing helix chain 'D' and resid 254 through 259 Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 283 through 289 Processing helix chain 'D' and resid 295 through 303 removed outlier: 3.635A pdb=" N LEU D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 309 removed outlier: 3.631A pdb=" N PHE D 308 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA D 309 " --> pdb=" O PRO D 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 304 through 309' Processing helix chain 'D' and resid 323 through 329 removed outlier: 3.504A pdb=" N GLN D 328 " --> pdb=" O PRO D 324 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG D 329 " --> pdb=" O ASP D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 335 removed outlier: 3.767A pdb=" N LEU D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 359 Processing helix chain 'D' and resid 363 through 369 removed outlier: 3.835A pdb=" N ASP D 367 " --> pdb=" O LYS D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 removed outlier: 3.800A pdb=" N SER D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 413 through 423 Processing helix chain 'D' and resid 430 through 437 Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 447 through 454 Processing helix chain 'D' and resid 461 through 477 Processing helix chain 'D' and resid 486 through 495 removed outlier: 3.731A pdb=" N TRP D 490 " --> pdb=" O ASN D 486 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 494 " --> pdb=" O TRP D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 500 No H-bonds generated for 'chain 'D' and resid 498 through 500' Processing helix chain 'D' and resid 501 through 508 removed outlier: 3.657A pdb=" N CYS D 508 " --> pdb=" O GLY D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 518 Processing helix chain 'D' and resid 521 through 526 Processing helix chain 'D' and resid 531 through 543 removed outlier: 3.610A pdb=" N ARG D 535 " --> pdb=" O LEU D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 587 removed outlier: 3.528A pdb=" N SER D 578 " --> pdb=" O SER D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 614 removed outlier: 3.856A pdb=" N MET D 612 " --> pdb=" O ILE D 608 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY D 613 " --> pdb=" O GLN D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 629 removed outlier: 3.506A pdb=" N LYS D 628 " --> pdb=" O ALA D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 650 removed outlier: 3.682A pdb=" N CYS D 649 " --> pdb=" O THR D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 699 removed outlier: 3.656A pdb=" N ARG D 697 " --> pdb=" O GLU D 693 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 68 removed outlier: 3.782A pdb=" N GLU E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 79 removed outlier: 3.871A pdb=" N ALA E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 104 removed outlier: 3.521A pdb=" N ALA E 93 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU E 94 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL E 95 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU E 101 " --> pdb=" O GLN E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 124 removed outlier: 3.665A pdb=" N GLN E 114 " --> pdb=" O ARG E 110 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY E 115 " --> pdb=" O GLU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 133 Processing helix chain 'E' and resid 141 through 151 removed outlier: 4.171A pdb=" N GLN E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE E 151 " --> pdb=" O LEU E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 164 removed outlier: 3.964A pdb=" N ARG E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE E 163 " --> pdb=" O ARG E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 172 removed outlier: 3.681A pdb=" N LEU E 169 " --> pdb=" O LEU E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 193 removed outlier: 4.138A pdb=" N SER E 183 " --> pdb=" O GLU E 179 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS E 193 " --> pdb=" O GLU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.813A pdb=" N ALA E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 214 removed outlier: 3.562A pdb=" N TRP E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 217 No H-bonds generated for 'chain 'E' and resid 215 through 217' Processing helix chain 'E' and resid 219 through 237 Processing helix chain 'E' and resid 238 through 248 Processing helix chain 'E' and resid 251 through 253 No H-bonds generated for 'chain 'E' and resid 251 through 253' Processing helix chain 'E' and resid 254 through 259 Processing helix chain 'E' and resid 264 through 278 Processing helix chain 'E' and resid 283 through 289 Processing helix chain 'E' and resid 295 through 303 removed outlier: 3.635A pdb=" N LEU E 299 " --> pdb=" O LEU E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 309 removed outlier: 3.632A pdb=" N PHE E 308 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA E 309 " --> pdb=" O PRO E 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 304 through 309' Processing helix chain 'E' and resid 323 through 329 removed outlier: 3.504A pdb=" N GLN E 328 " --> pdb=" O PRO E 324 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG E 329 " --> pdb=" O ASP E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 335 removed outlier: 3.765A pdb=" N LEU E 334 " --> pdb=" O LEU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 359 Processing helix chain 'E' and resid 363 through 369 removed outlier: 3.835A pdb=" N ASP E 367 " --> pdb=" O LYS E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 removed outlier: 3.799A pdb=" N SER E 373 " --> pdb=" O GLY E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 397 Processing helix chain 'E' and resid 413 through 423 Processing helix chain 'E' and resid 430 through 437 Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 447 through 454 Processing helix chain 'E' and resid 461 through 477 Processing helix chain 'E' and resid 486 through 495 removed outlier: 3.730A pdb=" N TRP E 490 " --> pdb=" O ASN E 486 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU E 494 " --> pdb=" O TRP E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 500 No H-bonds generated for 'chain 'E' and resid 498 through 500' Processing helix chain 'E' and resid 501 through 508 removed outlier: 3.656A pdb=" N CYS E 508 " --> pdb=" O GLY E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 518 Processing helix chain 'E' and resid 521 through 526 Processing helix chain 'E' and resid 531 through 543 removed outlier: 3.611A pdb=" N ARG E 535 " --> pdb=" O LEU E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 587 removed outlier: 3.528A pdb=" N SER E 578 " --> pdb=" O SER E 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 614 removed outlier: 3.636A pdb=" N MET E 612 " --> pdb=" O ILE E 608 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY E 613 " --> pdb=" O GLN E 609 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA E 614 " --> pdb=" O SER E 610 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 629 removed outlier: 3.505A pdb=" N LYS E 628 " --> pdb=" O ALA E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 650 removed outlier: 3.682A pdb=" N CYS E 649 " --> pdb=" O THR E 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 690 through 699 removed outlier: 3.656A pdb=" N ARG E 697 " --> pdb=" O GLU E 693 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 68 removed outlier: 3.781A pdb=" N GLU F 66 " --> pdb=" O GLN F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 79 removed outlier: 3.872A pdb=" N ALA F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 104 removed outlier: 3.521A pdb=" N ALA F 93 " --> pdb=" O GLY F 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL F 95 " --> pdb=" O GLY F 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU F 101 " --> pdb=" O GLN F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 124 removed outlier: 3.665A pdb=" N GLN F 114 " --> pdb=" O ARG F 110 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 133 Processing helix chain 'F' and resid 141 through 151 removed outlier: 4.170A pdb=" N GLN F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE F 151 " --> pdb=" O LEU F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 164 removed outlier: 3.964A pdb=" N ARG F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE F 163 " --> pdb=" O ARG F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 172 removed outlier: 3.680A pdb=" N LEU F 169 " --> pdb=" O LEU F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 193 removed outlier: 4.138A pdb=" N SER F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY F 186 " --> pdb=" O ARG F 182 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 206 removed outlier: 3.812A pdb=" N ALA F 204 " --> pdb=" O GLN F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 214 removed outlier: 3.561A pdb=" N TRP F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 217 No H-bonds generated for 'chain 'F' and resid 215 through 217' Processing helix chain 'F' and resid 219 through 237 Processing helix chain 'F' and resid 238 through 248 Processing helix chain 'F' and resid 251 through 253 No H-bonds generated for 'chain 'F' and resid 251 through 253' Processing helix chain 'F' and resid 254 through 259 Processing helix chain 'F' and resid 264 through 278 Processing helix chain 'F' and resid 283 through 289 Processing helix chain 'F' and resid 295 through 303 removed outlier: 3.635A pdb=" N LEU F 299 " --> pdb=" O LEU F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 309 removed outlier: 3.631A pdb=" N PHE F 308 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA F 309 " --> pdb=" O PRO F 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 304 through 309' Processing helix chain 'F' and resid 323 through 329 removed outlier: 3.503A pdb=" N GLN F 328 " --> pdb=" O PRO F 324 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG F 329 " --> pdb=" O ASP F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 335 removed outlier: 3.766A pdb=" N LEU F 334 " --> pdb=" O LEU F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 359 Processing helix chain 'F' and resid 363 through 369 removed outlier: 3.835A pdb=" N ASP F 367 " --> pdb=" O LYS F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 removed outlier: 3.799A pdb=" N SER F 373 " --> pdb=" O GLY F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 413 through 423 Processing helix chain 'F' and resid 430 through 437 Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 447 through 454 Processing helix chain 'F' and resid 461 through 477 Processing helix chain 'F' and resid 486 through 495 removed outlier: 3.731A pdb=" N TRP F 490 " --> pdb=" O ASN F 486 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU F 494 " --> pdb=" O TRP F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 500 No H-bonds generated for 'chain 'F' and resid 498 through 500' Processing helix chain 'F' and resid 501 through 508 removed outlier: 3.657A pdb=" N CYS F 508 " --> pdb=" O GLY F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 518 Processing helix chain 'F' and resid 521 through 526 Processing helix chain 'F' and resid 531 through 543 removed outlier: 3.610A pdb=" N ARG F 535 " --> pdb=" O LEU F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 587 removed outlier: 3.528A pdb=" N SER F 578 " --> pdb=" O SER F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 606 through 614 Processing helix chain 'F' and resid 625 through 629 removed outlier: 3.506A pdb=" N LYS F 628 " --> pdb=" O ALA F 625 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 650 removed outlier: 3.682A pdb=" N CYS F 649 " --> pdb=" O THR F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 690 through 699 removed outlier: 3.656A pdb=" N ARG F 697 " --> pdb=" O GLU F 693 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 68 removed outlier: 3.781A pdb=" N GLU G 66 " --> pdb=" O GLN G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 79 removed outlier: 3.873A pdb=" N ALA G 75 " --> pdb=" O GLU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 104 removed outlier: 3.521A pdb=" N ALA G 93 " --> pdb=" O GLY G 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU G 94 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL G 95 " --> pdb=" O GLY G 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU G 101 " --> pdb=" O GLN G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 124 removed outlier: 3.666A pdb=" N GLN G 114 " --> pdb=" O ARG G 110 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY G 115 " --> pdb=" O GLU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 133 Processing helix chain 'G' and resid 141 through 151 removed outlier: 4.169A pdb=" N GLN G 150 " --> pdb=" O ARG G 146 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 164 removed outlier: 3.964A pdb=" N ARG G 159 " --> pdb=" O GLU G 155 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE G 163 " --> pdb=" O ARG G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 172 removed outlier: 3.680A pdb=" N LEU G 169 " --> pdb=" O LEU G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 193 removed outlier: 4.138A pdb=" N SER G 183 " --> pdb=" O GLU G 179 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY G 186 " --> pdb=" O ARG G 182 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS G 193 " --> pdb=" O GLU G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 removed outlier: 3.813A pdb=" N ALA G 204 " --> pdb=" O GLN G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 214 removed outlier: 3.562A pdb=" N TRP G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 217 No H-bonds generated for 'chain 'G' and resid 215 through 217' Processing helix chain 'G' and resid 219 through 237 Processing helix chain 'G' and resid 238 through 248 Processing helix chain 'G' and resid 251 through 253 No H-bonds generated for 'chain 'G' and resid 251 through 253' Processing helix chain 'G' and resid 254 through 259 Processing helix chain 'G' and resid 264 through 278 Processing helix chain 'G' and resid 283 through 289 Processing helix chain 'G' and resid 295 through 303 removed outlier: 3.634A pdb=" N LEU G 299 " --> pdb=" O LEU G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 309 removed outlier: 3.633A pdb=" N PHE G 308 " --> pdb=" O ASP G 304 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA G 309 " --> pdb=" O PRO G 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 304 through 309' Processing helix chain 'G' and resid 323 through 329 removed outlier: 3.504A pdb=" N GLN G 328 " --> pdb=" O PRO G 324 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG G 329 " --> pdb=" O ASP G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 335 removed outlier: 3.765A pdb=" N LEU G 334 " --> pdb=" O LEU G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 359 Processing helix chain 'G' and resid 363 through 369 removed outlier: 3.835A pdb=" N ASP G 367 " --> pdb=" O LYS G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 379 removed outlier: 3.799A pdb=" N SER G 373 " --> pdb=" O GLY G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 397 Processing helix chain 'G' and resid 413 through 423 Processing helix chain 'G' and resid 430 through 437 Processing helix chain 'G' and resid 439 through 444 Processing helix chain 'G' and resid 447 through 454 Processing helix chain 'G' and resid 461 through 477 Processing helix chain 'G' and resid 486 through 495 removed outlier: 3.731A pdb=" N TRP G 490 " --> pdb=" O ASN G 486 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU G 494 " --> pdb=" O TRP G 490 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 500 No H-bonds generated for 'chain 'G' and resid 498 through 500' Processing helix chain 'G' and resid 501 through 508 removed outlier: 3.657A pdb=" N CYS G 508 " --> pdb=" O GLY G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 514 through 518 Processing helix chain 'G' and resid 521 through 526 Processing helix chain 'G' and resid 531 through 543 removed outlier: 3.610A pdb=" N ARG G 535 " --> pdb=" O LEU G 531 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 587 removed outlier: 3.528A pdb=" N SER G 578 " --> pdb=" O SER G 574 " (cutoff:3.500A) Processing helix chain 'G' and resid 606 through 614 Processing helix chain 'G' and resid 625 through 629 removed outlier: 3.505A pdb=" N LYS G 628 " --> pdb=" O ALA G 625 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 650 removed outlier: 3.682A pdb=" N CYS G 649 " --> pdb=" O THR G 645 " (cutoff:3.500A) Processing helix chain 'G' and resid 690 through 699 removed outlier: 3.656A pdb=" N ARG G 697 " --> pdb=" O GLU G 693 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 68 removed outlier: 3.781A pdb=" N GLU H 66 " --> pdb=" O GLN H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 79 removed outlier: 3.872A pdb=" N ALA H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 104 removed outlier: 3.521A pdb=" N ALA H 93 " --> pdb=" O GLY H 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL H 95 " --> pdb=" O GLY H 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU H 101 " --> pdb=" O GLN H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 124 removed outlier: 3.666A pdb=" N GLN H 114 " --> pdb=" O ARG H 110 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 133 Processing helix chain 'H' and resid 141 through 151 removed outlier: 4.170A pdb=" N GLN H 150 " --> pdb=" O ARG H 146 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE H 151 " --> pdb=" O LEU H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 164 removed outlier: 3.964A pdb=" N ARG H 159 " --> pdb=" O GLU H 155 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE H 163 " --> pdb=" O ARG H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 172 removed outlier: 3.680A pdb=" N LEU H 169 " --> pdb=" O LEU H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 193 removed outlier: 4.138A pdb=" N SER H 183 " --> pdb=" O GLU H 179 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY H 186 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS H 193 " --> pdb=" O GLU H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 206 removed outlier: 3.812A pdb=" N ALA H 204 " --> pdb=" O GLN H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 214 removed outlier: 3.561A pdb=" N TRP H 214 " --> pdb=" O ALA H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 217 No H-bonds generated for 'chain 'H' and resid 215 through 217' Processing helix chain 'H' and resid 219 through 237 Processing helix chain 'H' and resid 238 through 248 Processing helix chain 'H' and resid 251 through 253 No H-bonds generated for 'chain 'H' and resid 251 through 253' Processing helix chain 'H' and resid 254 through 259 Processing helix chain 'H' and resid 264 through 278 Processing helix chain 'H' and resid 283 through 289 Processing helix chain 'H' and resid 295 through 303 removed outlier: 3.635A pdb=" N LEU H 299 " --> pdb=" O LEU H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 309 removed outlier: 3.632A pdb=" N PHE H 308 " --> pdb=" O ASP H 304 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA H 309 " --> pdb=" O PRO H 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 304 through 309' Processing helix chain 'H' and resid 323 through 329 removed outlier: 3.505A pdb=" N GLN H 328 " --> pdb=" O PRO H 324 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG H 329 " --> pdb=" O ASP H 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 330 through 335 removed outlier: 3.767A pdb=" N LEU H 334 " --> pdb=" O LEU H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 359 Processing helix chain 'H' and resid 363 through 369 removed outlier: 3.835A pdb=" N ASP H 367 " --> pdb=" O LYS H 363 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 removed outlier: 3.800A pdb=" N SER H 373 " --> pdb=" O GLY H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 397 Processing helix chain 'H' and resid 413 through 423 Processing helix chain 'H' and resid 430 through 437 Processing helix chain 'H' and resid 439 through 444 Processing helix chain 'H' and resid 447 through 454 Processing helix chain 'H' and resid 461 through 477 Processing helix chain 'H' and resid 486 through 495 removed outlier: 3.731A pdb=" N TRP H 490 " --> pdb=" O ASN H 486 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU H 494 " --> pdb=" O TRP H 490 " (cutoff:3.500A) Processing helix chain 'H' and resid 498 through 500 No H-bonds generated for 'chain 'H' and resid 498 through 500' Processing helix chain 'H' and resid 501 through 508 removed outlier: 3.657A pdb=" N CYS H 508 " --> pdb=" O GLY H 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 514 through 518 Processing helix chain 'H' and resid 521 through 526 Processing helix chain 'H' and resid 531 through 543 removed outlier: 3.610A pdb=" N ARG H 535 " --> pdb=" O LEU H 531 " (cutoff:3.500A) Processing helix chain 'H' and resid 573 through 587 removed outlier: 3.528A pdb=" N SER H 578 " --> pdb=" O SER H 574 " (cutoff:3.500A) Processing helix chain 'H' and resid 606 through 614 Processing helix chain 'H' and resid 625 through 629 removed outlier: 3.506A pdb=" N LYS H 628 " --> pdb=" O ALA H 625 " (cutoff:3.500A) Processing helix chain 'H' and resid 638 through 650 removed outlier: 3.682A pdb=" N CYS H 649 " --> pdb=" O THR H 645 " (cutoff:3.500A) Processing helix chain 'H' and resid 690 through 699 removed outlier: 3.657A pdb=" N ARG H 697 " --> pdb=" O GLU H 693 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 566 through 567 removed outlier: 6.840A pdb=" N SER A 567 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 681 " --> pdb=" O PRO A 655 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 566 through 567 removed outlier: 6.840A pdb=" N SER B 567 " --> pdb=" O VAL B 620 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 681 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 566 through 567 removed outlier: 6.841A pdb=" N SER C 567 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 681 " --> pdb=" O PRO C 655 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 566 through 567 removed outlier: 6.841A pdb=" N SER D 567 " --> pdb=" O VAL D 620 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE D 681 " --> pdb=" O PRO D 655 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 566 through 567 removed outlier: 6.840A pdb=" N SER E 567 " --> pdb=" O VAL E 620 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE E 681 " --> pdb=" O PRO E 655 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 566 through 567 removed outlier: 6.841A pdb=" N SER F 567 " --> pdb=" O VAL F 620 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE F 681 " --> pdb=" O PRO F 655 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 566 through 567 removed outlier: 6.840A pdb=" N SER G 567 " --> pdb=" O VAL G 620 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE G 681 " --> pdb=" O PRO G 655 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 566 through 567 removed outlier: 6.840A pdb=" N SER H 567 " --> pdb=" O VAL H 620 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE H 681 " --> pdb=" O PRO H 655 " (cutoff:3.500A) 1882 hydrogen bonds defined for protein. 5574 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: 13.31 Time building geometry restraints manager: 16.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12508 1.34 - 1.46: 5545 1.46 - 1.58: 19307 1.58 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 37552 Sorted by residual: bond pdb=" N ILE D 608 " pdb=" CA ILE D 608 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.51e+00 bond pdb=" N VAL B 611 " pdb=" CA VAL B 611 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.46e+00 bond pdb=" N ILE E 608 " pdb=" CA ILE E 608 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.42e+00 bond pdb=" CA SER D 381 " pdb=" CB SER D 381 " ideal model delta sigma weight residual 1.530 1.489 0.040 1.48e-02 4.57e+03 7.41e+00 bond pdb=" N VAL C 611 " pdb=" CA VAL C 611 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.37e+00 ... (remaining 37547 not shown) Histogram of bond angle deviations from ideal: 99.37 - 106.32: 683 106.32 - 113.28: 20906 113.28 - 120.24: 13822 120.24 - 127.20: 14946 127.20 - 134.16: 371 Bond angle restraints: 50728 Sorted by residual: angle pdb=" CA SER F 77 " pdb=" C SER F 77 " pdb=" O SER F 77 " ideal model delta sigma weight residual 122.14 117.34 4.80 1.24e+00 6.50e-01 1.50e+01 angle pdb=" N ALA F 78 " pdb=" CA ALA F 78 " pdb=" C ALA F 78 " ideal model delta sigma weight residual 112.86 108.21 4.65 1.22e+00 6.72e-01 1.45e+01 angle pdb=" N VAL H 611 " pdb=" CA VAL H 611 " pdb=" C VAL H 611 " ideal model delta sigma weight residual 110.62 106.80 3.82 1.02e+00 9.61e-01 1.40e+01 angle pdb=" N LEU A 607 " pdb=" CA LEU A 607 " pdb=" C LEU A 607 " ideal model delta sigma weight residual 111.28 107.33 3.95 1.09e+00 8.42e-01 1.31e+01 angle pdb=" CA ALA B 78 " pdb=" C ALA B 78 " pdb=" O ALA B 78 " ideal model delta sigma weight residual 120.32 116.09 4.23 1.18e+00 7.18e-01 1.29e+01 ... (remaining 50723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 20467 17.03 - 34.06: 2026 34.06 - 51.09: 273 51.09 - 68.13: 42 68.13 - 85.16: 32 Dihedral angle restraints: 22840 sinusoidal: 9296 harmonic: 13544 Sorted by residual: dihedral pdb=" CA THR B 140 " pdb=" C THR B 140 " pdb=" N ARG B 141 " pdb=" CA ARG B 141 " ideal model delta harmonic sigma weight residual 180.00 156.36 23.64 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA THR C 140 " pdb=" C THR C 140 " pdb=" N ARG C 141 " pdb=" CA ARG C 141 " ideal model delta harmonic sigma weight residual 180.00 156.37 23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA THR E 140 " pdb=" C THR E 140 " pdb=" N ARG E 141 " pdb=" CA ARG E 141 " ideal model delta harmonic sigma weight residual 180.00 156.38 23.62 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 22837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 4832 0.051 - 0.102: 866 0.102 - 0.153: 122 0.153 - 0.203: 23 0.203 - 0.254: 5 Chirality restraints: 5848 Sorted by residual: chirality pdb=" CA LEU A 607 " pdb=" N LEU A 607 " pdb=" C LEU A 607 " pdb=" CB LEU A 607 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA LEU D 607 " pdb=" N LEU D 607 " pdb=" C LEU D 607 " pdb=" CB LEU D 607 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA LEU B 607 " pdb=" N LEU B 607 " pdb=" C LEU B 607 " pdb=" CB LEU B 607 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 5845 not shown) Planarity restraints: 6536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 79 " 0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C LEU D 79 " -0.063 2.00e-02 2.50e+03 pdb=" O LEU D 79 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS D 80 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 79 " 0.017 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C LEU C 79 " -0.062 2.00e-02 2.50e+03 pdb=" O LEU C 79 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS C 80 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 79 " -0.017 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C LEU E 79 " 0.062 2.00e-02 2.50e+03 pdb=" O LEU E 79 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS E 80 " -0.022 2.00e-02 2.50e+03 ... (remaining 6533 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 7152 2.76 - 3.30: 38646 3.30 - 3.83: 57420 3.83 - 4.37: 70395 4.37 - 4.90: 115408 Nonbonded interactions: 289021 Sorted by model distance: nonbonded pdb=" N VAL C 61 " pdb=" OD1 ASP C 63 " model vdw 2.229 2.520 nonbonded pdb=" N VAL H 61 " pdb=" OD1 ASP H 63 " model vdw 2.229 2.520 nonbonded pdb=" N VAL F 61 " pdb=" OD1 ASP F 63 " model vdw 2.229 2.520 nonbonded pdb=" N VAL A 61 " pdb=" OD1 ASP A 63 " model vdw 2.230 2.520 nonbonded pdb=" N VAL E 61 " pdb=" OD1 ASP E 63 " model vdw 2.230 2.520 ... (remaining 289016 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 152 5.16 5 C 23416 2.51 5 N 6664 2.21 5 O 6744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 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: 0.040 Extract box with map and model: 12.220 Check model and map are aligned: 0.570 Convert atoms to be neutral: 0.340 Process input model: 92.960 Find NCS groups from input model: 2.370 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.040 37552 Z= 0.377 Angle : 0.651 6.745 50728 Z= 0.405 Chirality : 0.040 0.254 5848 Planarity : 0.006 0.049 6536 Dihedral : 13.277 85.157 14040 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.12), residues: 4624 helix: -0.77 (0.09), residues: 3040 sheet: -3.47 (0.29), residues: 144 loop : -2.19 (0.16), residues: 1440 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1119 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1119 time to evaluate : 4.148 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 outliers start: 0 outliers final: 0 residues processed: 1119 average time/residue: 0.5248 time to fit residues: 908.7621 Evaluate side-chains 1015 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1015 time to evaluate : 4.613 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.6819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 398 optimal weight: 0.0270 chunk 357 optimal weight: 0.0770 chunk 198 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 241 optimal weight: 0.7980 chunk 191 optimal weight: 0.5980 chunk 369 optimal weight: 0.2980 chunk 143 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 275 optimal weight: 0.5980 chunk 428 optimal weight: 4.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 522 GLN A 534 HIS B 156 ASN B 232 ASN B 522 GLN C 156 ASN C 437 GLN C 534 HIS C 571 ASN D 156 ASN D 232 ASN D 571 ASN E 156 ASN ** F 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 685 HIS G 156 ASN G 522 GLN H 232 ASN H 383 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 37552 Z= 0.212 Angle : 0.697 12.373 50728 Z= 0.346 Chirality : 0.043 0.175 5848 Planarity : 0.005 0.045 6536 Dihedral : 4.591 22.536 5128 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.12), residues: 4624 helix: 0.16 (0.09), residues: 3152 sheet: -3.28 (0.31), residues: 160 loop : -2.07 (0.17), residues: 1312 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1132 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1062 time to evaluate : 4.261 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 outliers start: 70 outliers final: 34 residues processed: 1088 average time/residue: 0.5521 time to fit residues: 924.1192 Evaluate side-chains 991 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 957 time to evaluate : 4.361 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.3247 time to fit residues: 27.1262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 238 optimal weight: 4.9990 chunk 133 optimal weight: 0.6980 chunk 356 optimal weight: 3.9990 chunk 291 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 429 optimal weight: 3.9990 chunk 463 optimal weight: 3.9990 chunk 382 optimal weight: 0.9990 chunk 425 optimal weight: 2.9990 chunk 146 optimal weight: 0.3980 chunk 344 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 232 ASN B 685 HIS ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN C 587 HIS ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN D 232 ASN ** D 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 685 HIS ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN E 437 GLN E 534 HIS F 73 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 ASN F 587 HIS ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 ASN G 437 GLN G 534 HIS G 585 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 ASN H 232 ASN H 383 ASN H 522 GLN H 685 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.093 37552 Z= 0.398 Angle : 0.713 11.242 50728 Z= 0.360 Chirality : 0.047 0.317 5848 Planarity : 0.005 0.089 6536 Dihedral : 4.854 25.390 5128 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.12), residues: 4624 helix: -0.04 (0.09), residues: 3160 sheet: -3.06 (0.34), residues: 160 loop : -1.98 (0.17), residues: 1304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1133 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1040 time to evaluate : 4.476 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 outliers start: 93 outliers final: 49 residues processed: 1093 average time/residue: 0.5601 time to fit residues: 951.0284 Evaluate side-chains 1031 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 982 time to evaluate : 4.523 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.3532 time to fit residues: 38.0129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 424 optimal weight: 2.9990 chunk 322 optimal weight: 0.5980 chunk 222 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 288 optimal weight: 3.9990 chunk 430 optimal weight: 0.5980 chunk 456 optimal weight: 0.0770 chunk 225 optimal weight: 6.9990 chunk 408 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 522 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN D 422 GLN D 522 GLN D 585 GLN D 685 HIS ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 383 ASN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 232 ASN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 ASN H 571 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.098 37552 Z= 0.213 Angle : 0.648 14.879 50728 Z= 0.317 Chirality : 0.041 0.163 5848 Planarity : 0.005 0.078 6536 Dihedral : 4.534 23.139 5128 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 2.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.13), residues: 4624 helix: 0.38 (0.10), residues: 3152 sheet: -2.83 (0.36), residues: 160 loop : -2.04 (0.16), residues: 1312 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1085 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1005 time to evaluate : 4.156 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 outliers start: 80 outliers final: 37 residues processed: 1038 average time/residue: 0.5798 time to fit residues: 925.7396 Evaluate side-chains 1000 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 963 time to evaluate : 4.267 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.3590 time to fit residues: 31.0477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 379 optimal weight: 4.9990 chunk 258 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 339 optimal weight: 1.9990 chunk 188 optimal weight: 0.0040 chunk 389 optimal weight: 1.9990 chunk 315 optimal weight: 0.4980 chunk 0 optimal weight: 8.9990 chunk 232 optimal weight: 0.7980 chunk 409 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN A 200 GLN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 ASN D 73 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN D 522 GLN D 585 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 418 GLN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 232 ASN H 522 GLN H 652 ASN H 685 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.106 37552 Z= 0.239 Angle : 0.641 11.394 50728 Z= 0.317 Chirality : 0.042 0.175 5848 Planarity : 0.005 0.085 6536 Dihedral : 4.488 24.742 5128 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 4624 helix: 0.41 (0.10), residues: 3184 sheet: -2.71 (0.37), residues: 160 loop : -2.08 (0.17), residues: 1280 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1082 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 996 time to evaluate : 4.383 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 outliers start: 86 outliers final: 31 residues processed: 1041 average time/residue: 0.5596 time to fit residues: 891.1615 Evaluate side-chains 1004 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 973 time to evaluate : 4.330 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.3725 time to fit residues: 27.5534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 153 optimal weight: 2.9990 chunk 410 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 267 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 456 optimal weight: 0.9990 chunk 379 optimal weight: 0.0010 chunk 211 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 239 optimal weight: 10.0000 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 522 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN D 422 GLN D 522 GLN D 585 GLN D 685 HIS ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 418 GLN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.146 37552 Z= 0.261 Angle : 0.657 13.104 50728 Z= 0.325 Chirality : 0.042 0.169 5848 Planarity : 0.005 0.086 6536 Dihedral : 4.509 24.302 5128 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.13), residues: 4624 helix: 0.45 (0.10), residues: 3152 sheet: -2.65 (0.37), residues: 160 loop : -2.05 (0.16), residues: 1312 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1075 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 998 time to evaluate : 4.668 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 outliers start: 77 outliers final: 33 residues processed: 1028 average time/residue: 0.5906 time to fit residues: 932.6638 Evaluate side-chains 994 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 961 time to evaluate : 3.895 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.3112 time to fit residues: 24.7816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 440 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 260 optimal weight: 0.9990 chunk 333 optimal weight: 2.9990 chunk 258 optimal weight: 0.7980 chunk 384 optimal weight: 2.9990 chunk 255 optimal weight: 1.9990 chunk 454 optimal weight: 0.9980 chunk 284 optimal weight: 4.9990 chunk 277 optimal weight: 0.6980 chunk 210 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN D 422 GLN D 522 GLN D 585 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN E 585 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 418 GLN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN G 585 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 587 HIS H 685 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.149 37552 Z= 0.281 Angle : 0.679 13.018 50728 Z= 0.335 Chirality : 0.043 0.170 5848 Planarity : 0.005 0.090 6536 Dihedral : 4.553 24.105 5128 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.13), residues: 4624 helix: 0.38 (0.10), residues: 3160 sheet: -2.54 (0.38), residues: 160 loop : -2.06 (0.16), residues: 1304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1054 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 996 time to evaluate : 4.385 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 outliers start: 58 outliers final: 34 residues processed: 1019 average time/residue: 0.5679 time to fit residues: 888.5143 Evaluate side-chains 1006 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 972 time to evaluate : 4.208 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.3521 time to fit residues: 27.8848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 281 optimal weight: 0.6980 chunk 181 optimal weight: 6.9990 chunk 271 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 289 optimal weight: 4.9990 chunk 309 optimal weight: 0.9980 chunk 224 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 357 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 522 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN D 422 GLN D 522 GLN D 585 GLN D 685 HIS ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN E 585 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 418 GLN F 422 GLN F 522 GLN F 585 GLN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 587 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.134 37552 Z= 0.248 Angle : 0.687 12.377 50728 Z= 0.336 Chirality : 0.042 0.192 5848 Planarity : 0.005 0.071 6536 Dihedral : 4.494 23.756 5128 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.13), residues: 4624 helix: 0.47 (0.10), residues: 3152 sheet: -2.45 (0.38), residues: 160 loop : -1.99 (0.16), residues: 1312 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1004 time to evaluate : 4.324 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 outliers start: 44 outliers final: 24 residues processed: 1022 average time/residue: 0.5755 time to fit residues: 898.8665 Evaluate side-chains 981 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 957 time to evaluate : 4.561 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.3711 time to fit residues: 22.5054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 413 optimal weight: 10.0000 chunk 435 optimal weight: 3.9990 chunk 397 optimal weight: 0.9990 chunk 423 optimal weight: 0.0770 chunk 255 optimal weight: 0.0870 chunk 184 optimal weight: 3.9990 chunk 332 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 383 optimal weight: 1.9990 chunk 400 optimal weight: 0.6980 chunk 422 optimal weight: 0.8980 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN B 232 ASN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN D 422 GLN D 522 GLN D 585 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN E 585 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 418 GLN F 422 GLN F 522 GLN F 585 GLN F 587 HIS G 81 GLN G 422 GLN G 522 GLN G 585 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 522 GLN H 587 HIS H 685 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.281 37552 Z= 0.219 Angle : 0.699 14.957 50728 Z= 0.344 Chirality : 0.042 0.440 5848 Planarity : 0.005 0.105 6536 Dihedral : 4.398 23.308 5128 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.13), residues: 4624 helix: 0.56 (0.10), residues: 3160 sheet: -2.35 (0.39), residues: 160 loop : -1.87 (0.17), residues: 1304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1013 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 982 time to evaluate : 4.258 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 outliers start: 31 outliers final: 10 residues processed: 995 average time/residue: 0.5703 time to fit residues: 870.3903 Evaluate side-chains 950 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 940 time to evaluate : 4.301 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4184 time to fit residues: 13.7939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 278 optimal weight: 0.7980 chunk 448 optimal weight: 0.9990 chunk 273 optimal weight: 0.8980 chunk 212 optimal weight: 0.8980 chunk 311 optimal weight: 0.5980 chunk 470 optimal weight: 3.9990 chunk 432 optimal weight: 1.9990 chunk 374 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 289 optimal weight: 0.3980 chunk 229 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN B 232 ASN B 522 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN D 422 GLN D 522 GLN D 585 GLN D 685 HIS ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 418 GLN F 422 GLN F 522 GLN F 585 GLN F 587 HIS G 422 GLN G 522 GLN G 585 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.346 37552 Z= 0.276 Angle : 0.716 17.603 50728 Z= 0.354 Chirality : 0.042 0.416 5848 Planarity : 0.005 0.107 6536 Dihedral : 4.409 23.544 5128 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.13), residues: 4624 helix: 0.54 (0.10), residues: 3192 sheet: -2.35 (0.37), residues: 168 loop : -1.89 (0.17), residues: 1264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 988 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 978 time to evaluate : 4.193 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 outliers start: 10 outliers final: 5 residues processed: 982 average time/residue: 0.5662 time to fit residues: 848.7752 Evaluate side-chains 964 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 959 time to evaluate : 4.158 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3191 time to fit residues: 8.8695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 297 optimal weight: 1.9990 chunk 398 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 chunk 345 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 375 optimal weight: 0.8980 chunk 156 optimal weight: 0.0010 chunk 385 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 0.0170 overall best weight: 0.5226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 587 HIS ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN D 522 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 418 GLN F 522 GLN F 585 GLN F 587 HIS G 422 GLN ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 585 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 587 HIS H 685 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.157844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.131365 restraints weight = 56420.951| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.46 r_work: 0.3632 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work: 0.3604 rms_B_bonded: 2.28 restraints_weight: 0.1250 r_work: 0.3588 rms_B_bonded: 2.39 restraints_weight: 0.0625 r_work: 0.3570 rms_B_bonded: 2.55 restraints_weight: 0.0312 r_work: 0.3551 rms_B_bonded: 2.76 restraints_weight: 0.0156 r_work: 0.3530 rms_B_bonded: 3.02 restraints_weight: 0.0078 r_work: 0.3507 rms_B_bonded: 3.33 restraints_weight: 0.0039 r_work: 0.3481 rms_B_bonded: 3.69 restraints_weight: 0.0020 r_work: 0.3452 rms_B_bonded: 4.13 restraints_weight: 0.0010 r_work: 0.3420 rms_B_bonded: 4.64 restraints_weight: 0.0005 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.510 37552 Z= 0.231 Angle : 0.725 24.615 50728 Z= 0.358 Chirality : 0.041 0.219 5848 Planarity : 0.005 0.094 6536 Dihedral : 4.371 23.073 5128 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.13), residues: 4624 helix: 0.60 (0.10), residues: 3192 sheet: -2.29 (0.38), residues: 168 loop : -1.82 (0.17), residues: 1264 =============================================================================== Job complete usr+sys time: 12397.51 seconds wall clock time: 221 minutes 30.34 seconds (13290.34 seconds total)