Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 11:26:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rvx_10016/04_2023/6rvx_10016.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rvx_10016/04_2023/6rvx_10016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rvx_10016/04_2023/6rvx_10016.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rvx_10016/04_2023/6rvx_10016.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rvx_10016/04_2023/6rvx_10016.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rvx_10016/04_2023/6rvx_10016.pdb" } resolution = 3.61 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= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 6300 2.51 5 N 1602 2.21 5 O 1680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 50": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "B ARG 50": "NH1" <-> "NH2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 217": "NH1" <-> "NH2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C ARG 189": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 365": "OE1" <-> "OE2" Residue "C ARG 465": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 9627 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3209 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 16, 'TRANS': 413} Chain breaks: 1 Chain: "B" Number of atoms: 3209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3209 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 16, 'TRANS': 413} Chain breaks: 1 Chain: "C" Number of atoms: 3209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3209 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 16, 'TRANS': 413} Chain breaks: 1 Time building chain proxies: 5.46, per 1000 atoms: 0.57 Number of scatterers: 9627 At special positions: 0 Unit cell: (117.392, 120.428, 81.972, 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 45 16.00 O 1680 8.00 N 1602 7.00 C 6300 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: 3.54 Conformation dependent library (CDL) restraints added in 1.6 seconds 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2334 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 3 sheets defined 69.8% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 52 through 74 removed outlier: 3.611A pdb=" N ALA A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 90 removed outlier: 4.321A pdb=" N SER A 87 " --> pdb=" O PRO A 83 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ALA A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 117 removed outlier: 4.185A pdb=" N LEU A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Proline residue: A 106 - end of helix removed outlier: 3.809A pdb=" N VAL A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 127 No H-bonds generated for 'chain 'A' and resid 125 through 127' Processing helix chain 'A' and resid 128 through 153 Processing helix chain 'A' and resid 184 through 192 removed outlier: 4.047A pdb=" N ASN A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 248 removed outlier: 3.812A pdb=" N VAL A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.800A pdb=" N ILE A 256 " --> pdb=" O GLY A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 292 removed outlier: 3.986A pdb=" N VAL A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Proline residue: A 278 - end of helix removed outlier: 3.781A pdb=" N MET A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 320 Processing helix chain 'A' and resid 320 through 329 removed outlier: 3.840A pdb=" N PHE A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 340 removed outlier: 3.949A pdb=" N PHE A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 356 through 367 removed outlier: 4.288A pdb=" N GLU A 365 " --> pdb=" O MET A 361 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU A 366 " --> pdb=" O LYS A 362 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN A 367 " --> pdb=" O CYS A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 397 Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'A' and resid 410 through 423 removed outlier: 3.980A pdb=" N ILE A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N THR A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 445 removed outlier: 3.675A pdb=" N LEU A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 removed outlier: 3.877A pdb=" N HIS A 452 " --> pdb=" O PRO A 449 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER A 454 " --> pdb=" O ASP A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 483 removed outlier: 3.803A pdb=" N VAL A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N VAL A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 472 " --> pdb=" O THR A 468 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASP A 475 " --> pdb=" O ASN A 471 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 74 removed outlier: 3.611A pdb=" N ALA B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 90 removed outlier: 4.321A pdb=" N SER B 87 " --> pdb=" O PRO B 83 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ALA B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 117 removed outlier: 4.184A pdb=" N LEU B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Proline residue: B 106 - end of helix removed outlier: 3.810A pdb=" N VAL B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE B 113 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B 114 " --> pdb=" O CYS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 127 No H-bonds generated for 'chain 'B' and resid 125 through 127' Processing helix chain 'B' and resid 128 through 153 Processing helix chain 'B' and resid 184 through 192 removed outlier: 4.047A pdb=" N ASN B 190 " --> pdb=" O ASP B 186 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 248 removed outlier: 3.814A pdb=" N VAL B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 251 No H-bonds generated for 'chain 'B' and resid 249 through 251' Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.800A pdb=" N ILE B 256 " --> pdb=" O GLY B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 292 removed outlier: 3.987A pdb=" N VAL B 268 " --> pdb=" O GLU B 264 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LEU B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) Proline residue: B 278 - end of helix removed outlier: 3.780A pdb=" N MET B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 320 Processing helix chain 'B' and resid 320 through 329 removed outlier: 3.839A pdb=" N PHE B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.950A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 356 through 367 removed outlier: 4.288A pdb=" N GLU B 365 " --> pdb=" O MET B 361 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU B 366 " --> pdb=" O LYS B 362 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN B 367 " --> pdb=" O CYS B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 397 Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 410 through 423 removed outlier: 3.981A pdb=" N ILE B 415 " --> pdb=" O PHE B 411 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N THR B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 445 removed outlier: 3.675A pdb=" N LEU B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE B 442 " --> pdb=" O THR B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 454 removed outlier: 3.877A pdb=" N HIS B 452 " --> pdb=" O PRO B 449 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER B 454 " --> pdb=" O ASP B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 483 removed outlier: 3.803A pdb=" N VAL B 463 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N VAL B 469 " --> pdb=" O ARG B 465 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU B 470 " --> pdb=" O SER B 466 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B 472 " --> pdb=" O THR B 468 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 74 removed outlier: 3.610A pdb=" N ALA C 67 " --> pdb=" O VAL C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 90 removed outlier: 4.321A pdb=" N SER C 87 " --> pdb=" O PRO C 83 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ALA C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 117 removed outlier: 4.186A pdb=" N LEU C 97 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU C 105 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Proline residue: C 106 - end of helix removed outlier: 3.810A pdb=" N VAL C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY C 114 " --> pdb=" O CYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 127 No H-bonds generated for 'chain 'C' and resid 125 through 127' Processing helix chain 'C' and resid 128 through 153 Processing helix chain 'C' and resid 184 through 192 removed outlier: 4.047A pdb=" N ASN C 190 " --> pdb=" O ASP C 186 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE C 192 " --> pdb=" O ALA C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 248 removed outlier: 3.813A pdb=" N VAL C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 262 removed outlier: 3.800A pdb=" N ILE C 256 " --> pdb=" O GLY C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 292 removed outlier: 3.987A pdb=" N VAL C 268 " --> pdb=" O GLU C 264 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU C 269 " --> pdb=" O ALA C 265 " (cutoff:3.500A) Proline residue: C 278 - end of helix removed outlier: 3.780A pdb=" N MET C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 320 Processing helix chain 'C' and resid 320 through 329 removed outlier: 3.839A pdb=" N PHE C 328 " --> pdb=" O ILE C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 340 removed outlier: 3.950A pdb=" N PHE C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 351 Processing helix chain 'C' and resid 356 through 367 removed outlier: 4.288A pdb=" N GLU C 365 " --> pdb=" O MET C 361 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU C 366 " --> pdb=" O LYS C 362 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN C 367 " --> pdb=" O CYS C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 397 Processing helix chain 'C' and resid 400 through 404 Processing helix chain 'C' and resid 410 through 423 removed outlier: 3.980A pdb=" N ILE C 415 " --> pdb=" O PHE C 411 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N THR C 420 " --> pdb=" O THR C 416 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA C 421 " --> pdb=" O ILE C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 445 removed outlier: 3.674A pdb=" N LEU C 439 " --> pdb=" O GLY C 435 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE C 442 " --> pdb=" O THR C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 454 removed outlier: 3.876A pdb=" N HIS C 452 " --> pdb=" O PRO C 449 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER C 454 " --> pdb=" O ASP C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 483 removed outlier: 3.803A pdb=" N VAL C 463 " --> pdb=" O VAL C 459 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N VAL C 469 " --> pdb=" O ARG C 465 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU C 470 " --> pdb=" O SER C 466 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL C 472 " --> pdb=" O THR C 468 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 210 removed outlier: 3.659A pdb=" N VAL A 220 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 202 through 210 removed outlier: 3.659A pdb=" N VAL B 220 " --> pdb=" O GLU B 209 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 202 through 210 removed outlier: 3.658A pdb=" N VAL C 220 " --> pdb=" O GLU C 209 " (cutoff:3.500A) 546 hydrogen bonds defined for protein. 1611 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: 2.55 Time building geometry restraints manager: 3.84 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: 2892 1.34 - 1.46: 1438 1.46 - 1.57: 5396 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 9798 Sorted by residual: bond pdb=" CG1 ILE B 273 " pdb=" CD1 ILE B 273 " ideal model delta sigma weight residual 1.513 1.451 0.062 3.90e-02 6.57e+02 2.50e+00 bond pdb=" CG1 ILE C 273 " pdb=" CD1 ILE C 273 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.48e+00 bond pdb=" CG1 ILE A 273 " pdb=" CD1 ILE A 273 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.44e+00 bond pdb=" CG LEU A 112 " pdb=" CD1 LEU A 112 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.15e+00 bond pdb=" CG LEU C 112 " pdb=" CD1 LEU C 112 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.07e+00 ... (remaining 9793 not shown) Histogram of bond angle deviations from ideal: 100.09 - 106.91: 243 106.91 - 113.72: 5671 113.72 - 120.54: 4155 120.54 - 127.35: 3189 127.35 - 134.17: 86 Bond angle restraints: 13344 Sorted by residual: angle pdb=" N VAL A 197 " pdb=" CA VAL A 197 " pdb=" C VAL A 197 " ideal model delta sigma weight residual 112.96 107.26 5.70 1.00e+00 1.00e+00 3.25e+01 angle pdb=" N VAL C 197 " pdb=" CA VAL C 197 " pdb=" C VAL C 197 " ideal model delta sigma weight residual 112.96 107.26 5.70 1.00e+00 1.00e+00 3.24e+01 angle pdb=" N VAL B 197 " pdb=" CA VAL B 197 " pdb=" C VAL B 197 " ideal model delta sigma weight residual 112.96 107.30 5.66 1.00e+00 1.00e+00 3.20e+01 angle pdb=" N ILE B 456 " pdb=" CA ILE B 456 " pdb=" C ILE B 456 " ideal model delta sigma weight residual 111.90 107.84 4.06 8.10e-01 1.52e+00 2.51e+01 angle pdb=" N ILE A 456 " pdb=" CA ILE A 456 " pdb=" C ILE A 456 " ideal model delta sigma weight residual 111.90 107.86 4.04 8.10e-01 1.52e+00 2.49e+01 ... (remaining 13339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.69: 4846 13.69 - 27.38: 689 27.38 - 41.07: 195 41.07 - 54.76: 27 54.76 - 68.45: 9 Dihedral angle restraints: 5766 sinusoidal: 2127 harmonic: 3639 Sorted by residual: dihedral pdb=" CA THR B 416 " pdb=" C THR B 416 " pdb=" N ILE B 417 " pdb=" CA ILE B 417 " ideal model delta harmonic sigma weight residual 180.00 156.57 23.43 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA THR C 416 " pdb=" C THR C 416 " pdb=" N ILE C 417 " pdb=" CA ILE C 417 " ideal model delta harmonic sigma weight residual 180.00 156.59 23.41 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA THR A 416 " pdb=" C THR A 416 " pdb=" N ILE A 417 " pdb=" CA ILE A 417 " ideal model delta harmonic sigma weight residual 180.00 156.63 23.37 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 5763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1411 0.070 - 0.140: 218 0.140 - 0.210: 30 0.210 - 0.280: 6 0.280 - 0.350: 3 Chirality restraints: 1668 Sorted by residual: chirality pdb=" CB VAL B 90 " pdb=" CA VAL B 90 " pdb=" CG1 VAL B 90 " pdb=" CG2 VAL B 90 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CB VAL C 90 " pdb=" CA VAL C 90 " pdb=" CG1 VAL C 90 " pdb=" CG2 VAL C 90 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CB VAL A 90 " pdb=" CA VAL A 90 " pdb=" CG1 VAL A 90 " pdb=" CG2 VAL A 90 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 1665 not shown) Planarity restraints: 1656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 277 " -0.055 5.00e-02 4.00e+02 8.27e-02 1.10e+01 pdb=" N PRO C 278 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO C 278 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 278 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 277 " -0.055 5.00e-02 4.00e+02 8.27e-02 1.09e+01 pdb=" N PRO B 278 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 278 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 278 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 277 " 0.055 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO A 278 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 278 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 278 " 0.046 5.00e-02 4.00e+02 ... (remaining 1653 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2391 2.79 - 3.32: 8551 3.32 - 3.84: 15658 3.84 - 4.37: 17932 4.37 - 4.90: 31395 Nonbonded interactions: 75927 Sorted by model distance: nonbonded pdb=" O GLY A 434 " pdb=" OG1 THR A 438 " model vdw 2.261 2.440 nonbonded pdb=" O GLY C 434 " pdb=" OG1 THR C 438 " model vdw 2.261 2.440 nonbonded pdb=" O GLY B 434 " pdb=" OG1 THR B 438 " model vdw 2.262 2.440 nonbonded pdb=" O SER B 198 " pdb=" OG SER B 198 " model vdw 2.323 2.440 nonbonded pdb=" O SER A 198 " pdb=" OG SER A 198 " model vdw 2.323 2.440 ... (remaining 75922 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.510 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 26.930 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 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 0.062 9798 Z= 0.398 Angle : 0.986 9.992 13344 Z= 0.541 Chirality : 0.055 0.350 1668 Planarity : 0.008 0.083 1656 Dihedral : 14.073 68.451 3432 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer Outliers : 0.29 % 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: -5.46 (0.16), residues: 1278 helix: -3.44 (0.11), residues: 942 sheet: -3.34 (0.67), residues: 30 loop : -3.32 (0.30), residues: 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 153 time to evaluate : 1.118 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 153 average time/residue: 0.2318 time to fit residues: 49.0658 Evaluate side-chains 117 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.053 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS A 316 HIS A 386 ASN ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS B 386 ASN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 HIS C 386 ASN ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 9798 Z= 0.181 Angle : 0.613 7.908 13344 Z= 0.317 Chirality : 0.039 0.155 1668 Planarity : 0.006 0.066 1656 Dihedral : 5.515 20.438 1365 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer Outliers : 1.37 % 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: -3.48 (0.21), residues: 1278 helix: -1.83 (0.15), residues: 951 sheet: -3.32 (0.63), residues: 36 loop : -3.14 (0.32), residues: 291 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 145 time to evaluate : 1.079 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 154 average time/residue: 0.2126 time to fit residues: 46.7988 Evaluate side-chains 135 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 128 time to evaluate : 0.992 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1809 time to fit residues: 3.2453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 HIS B 394 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 HIS C 394 GLN ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 9798 Z= 0.385 Angle : 0.722 9.368 13344 Z= 0.360 Chirality : 0.045 0.177 1668 Planarity : 0.006 0.064 1656 Dihedral : 5.679 22.397 1365 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer Outliers : 2.84 % 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: -2.89 (0.22), residues: 1278 helix: -1.37 (0.16), residues: 936 sheet: -3.30 (0.67), residues: 36 loop : -2.93 (0.34), residues: 306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 1.044 Fit side-chains outliers start: 29 outliers final: 9 residues processed: 158 average time/residue: 0.1989 time to fit residues: 45.6872 Evaluate side-chains 127 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 1.131 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0902 time to fit residues: 2.9806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.0050 chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 117 optimal weight: 20.0000 chunk 124 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 9798 Z= 0.165 Angle : 0.609 9.498 13344 Z= 0.305 Chirality : 0.040 0.175 1668 Planarity : 0.005 0.061 1656 Dihedral : 5.028 19.444 1365 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 1.37 % 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: -1.97 (0.24), residues: 1278 helix: -0.64 (0.18), residues: 915 sheet: -2.20 (0.75), residues: 42 loop : -2.80 (0.33), residues: 321 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 1.077 Fit side-chains outliers start: 14 outliers final: 1 residues processed: 153 average time/residue: 0.2032 time to fit residues: 44.6615 Evaluate side-chains 125 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 1.081 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0890 time to fit residues: 1.6334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 0.0470 chunk 51 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 overall best weight: 1.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 9798 Z= 0.217 Angle : 0.636 8.803 13344 Z= 0.314 Chirality : 0.041 0.180 1668 Planarity : 0.005 0.060 1656 Dihedral : 4.946 19.715 1365 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % 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: -1.76 (0.24), residues: 1278 helix: -0.47 (0.18), residues: 912 sheet: -2.05 (0.75), residues: 42 loop : -2.76 (0.34), residues: 324 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 1.124 Fit side-chains outliers start: 20 outliers final: 6 residues processed: 139 average time/residue: 0.2016 time to fit residues: 40.7673 Evaluate side-chains 124 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 118 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0903 time to fit residues: 2.5701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 9798 Z= 0.233 Angle : 0.640 8.090 13344 Z= 0.316 Chirality : 0.042 0.175 1668 Planarity : 0.005 0.060 1656 Dihedral : 4.919 17.935 1365 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.24), residues: 1278 helix: -0.36 (0.18), residues: 912 sheet: -2.01 (0.74), residues: 42 loop : -2.68 (0.34), residues: 324 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 1.054 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 136 average time/residue: 0.2270 time to fit residues: 44.4711 Evaluate side-chains 126 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 0.982 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0852 time to fit residues: 3.1181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 9798 Z= 0.212 Angle : 0.635 9.390 13344 Z= 0.312 Chirality : 0.041 0.185 1668 Planarity : 0.004 0.060 1656 Dihedral : 4.813 18.789 1365 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 0.78 % 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: -1.37 (0.25), residues: 1278 helix: -0.21 (0.18), residues: 915 sheet: -1.87 (0.74), residues: 42 loop : -2.55 (0.35), residues: 321 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 123 time to evaluate : 0.999 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 130 average time/residue: 0.2217 time to fit residues: 41.7897 Evaluate side-chains 118 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 1.078 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0886 time to fit residues: 1.9557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 9798 Z= 0.188 Angle : 0.630 9.167 13344 Z= 0.308 Chirality : 0.041 0.183 1668 Planarity : 0.004 0.059 1656 Dihedral : 4.650 17.548 1365 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 0.78 % 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: -1.24 (0.25), residues: 1278 helix: -0.10 (0.18), residues: 930 sheet: -1.73 (0.74), residues: 42 loop : -2.71 (0.34), residues: 306 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 1.120 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 137 average time/residue: 0.2061 time to fit residues: 41.2403 Evaluate side-chains 121 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0951 time to fit residues: 1.8946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.5980 chunk 115 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 9798 Z= 0.207 Angle : 0.637 8.942 13344 Z= 0.312 Chirality : 0.041 0.195 1668 Planarity : 0.004 0.059 1656 Dihedral : 4.632 18.300 1365 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer Outliers : 0.29 % 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: -1.08 (0.25), residues: 1278 helix: -0.00 (0.18), residues: 918 sheet: -1.65 (0.73), residues: 42 loop : -2.46 (0.35), residues: 318 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 121 time to evaluate : 1.030 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 124 average time/residue: 0.2125 time to fit residues: 37.9279 Evaluate side-chains 117 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0887 time to fit residues: 1.8289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.0170 chunk 58 optimal weight: 0.5980 chunk 85 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 81 optimal weight: 0.6980 chunk 109 optimal weight: 0.0770 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 9798 Z= 0.157 Angle : 0.621 8.969 13344 Z= 0.303 Chirality : 0.040 0.190 1668 Planarity : 0.004 0.054 1656 Dihedral : 4.385 16.657 1365 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 0.20 % 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: -0.74 (0.25), residues: 1278 helix: 0.25 (0.19), residues: 924 sheet: -1.35 (0.74), residues: 42 loop : -2.41 (0.36), residues: 312 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 1.082 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 139 average time/residue: 0.2088 time to fit residues: 41.9669 Evaluate side-chains 127 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 1.154 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0947 time to fit residues: 1.7395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.5980 chunk 94 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 102 optimal weight: 0.0770 chunk 42 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 89 optimal weight: 0.0980 chunk 5 optimal weight: 0.7980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.164037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.127363 restraints weight = 10434.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.125525 restraints weight = 15252.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.127073 restraints weight = 14915.599| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 9798 Z= 0.162 Angle : 0.623 8.895 13344 Z= 0.304 Chirality : 0.040 0.241 1668 Planarity : 0.004 0.053 1656 Dihedral : 4.302 17.129 1365 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.25), residues: 1278 helix: 0.39 (0.19), residues: 912 sheet: -1.25 (0.73), residues: 42 loop : -2.51 (0.34), residues: 324 =============================================================================== Job complete usr+sys time: 1692.37 seconds wall clock time: 31 minutes 31.95 seconds (1891.95 seconds total)