Starting phenix.real_space_refine on Tue Dec 12 02:52:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xeo_33157/12_2023/7xeo_33157.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xeo_33157/12_2023/7xeo_33157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xeo_33157/12_2023/7xeo_33157.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xeo_33157/12_2023/7xeo_33157.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xeo_33157/12_2023/7xeo_33157.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xeo_33157/12_2023/7xeo_33157.pdb" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 108 5.16 5 C 13064 2.51 5 N 3372 2.21 5 O 3436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 235": "OE1" <-> "OE2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A GLU 609": "OE1" <-> "OE2" Residue "B GLU 235": "OE1" <-> "OE2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B GLU 556": "OE1" <-> "OE2" Residue "B GLU 609": "OE1" <-> "OE2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C GLU 257": "OE1" <-> "OE2" Residue "C GLU 556": "OE1" <-> "OE2" Residue "C GLU 609": "OE1" <-> "OE2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D GLU 556": "OE1" <-> "OE2" Residue "D GLU 609": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 19980 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4995 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "B" Number of atoms: 4995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4995 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "C" Number of atoms: 4995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4995 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "D" Number of atoms: 4995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4995 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Time building chain proxies: 10.47, per 1000 atoms: 0.52 Number of scatterers: 19980 At special positions: 0 Unit cell: (157.17, 157.17, 117.624, 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 108 16.00 O 3436 8.00 N 3372 7.00 C 13064 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: 7.81 Conformation dependent library (CDL) restraints added in 3.8 seconds 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 63.4% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.554A pdb=" N LEU A 75 " --> pdb=" O ASP A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 86 through 96 removed outlier: 4.070A pdb=" N LEU A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 130 through 142 removed outlier: 3.539A pdb=" N ASP A 140 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER A 141 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 169 removed outlier: 3.609A pdb=" N ILE A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 182 removed outlier: 3.566A pdb=" N VAL A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 Processing helix chain 'A' and resid 217 through 226 removed outlier: 3.551A pdb=" N TYR A 223 " --> pdb=" O ASP A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 251 Processing helix chain 'A' and resid 255 through 277 removed outlier: 3.523A pdb=" N ARG A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 363 through 368 removed outlier: 3.745A pdb=" N ARG A 366 " --> pdb=" O HIS A 363 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 368 " --> pdb=" O HIS A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 408 Proline residue: A 386 - end of helix Processing helix chain 'A' and resid 424 through 454 Processing helix chain 'A' and resid 455 through 458 removed outlier: 3.842A pdb=" N ILE A 458 " --> pdb=" O ARG A 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 455 through 458' Processing helix chain 'A' and resid 467 through 488 removed outlier: 3.975A pdb=" N PHE A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL A 487 " --> pdb=" O VAL A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 506 removed outlier: 3.568A pdb=" N LEU A 495 " --> pdb=" O TRP A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 514 through 531 removed outlier: 4.150A pdb=" N ILE A 519 " --> pdb=" O GLN A 515 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR A 520 " --> pdb=" O HIS A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 553 removed outlier: 3.529A pdb=" N ALA A 549 " --> pdb=" O GLY A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 601 removed outlier: 3.553A pdb=" N SER A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 630 removed outlier: 3.522A pdb=" N LEU A 627 " --> pdb=" O ALA A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 648 removed outlier: 3.523A pdb=" N ASN A 645 " --> pdb=" O SER A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 668 removed outlier: 3.804A pdb=" N ASN A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 removed outlier: 3.699A pdb=" N TRP A 710 " --> pdb=" O ASN A 706 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A 712 " --> pdb=" O ALA A 708 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR A 713 " --> pdb=" O ALA A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 82 removed outlier: 3.554A pdb=" N LEU B 75 " --> pdb=" O ASP B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 85 No H-bonds generated for 'chain 'B' and resid 83 through 85' Processing helix chain 'B' and resid 86 through 96 removed outlier: 4.070A pdb=" N LEU B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B 92 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 130 through 142 removed outlier: 3.539A pdb=" N ASP B 140 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER B 141 " --> pdb=" O ILE B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 169 removed outlier: 3.609A pdb=" N ILE B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 182 removed outlier: 3.567A pdb=" N VAL B 175 " --> pdb=" O SER B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 215 Processing helix chain 'B' and resid 217 through 226 removed outlier: 3.500A pdb=" N VAL B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR B 223 " --> pdb=" O ASP B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 251 Processing helix chain 'B' and resid 255 through 277 removed outlier: 3.523A pdb=" N ARG B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 301 Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 363 through 368 removed outlier: 3.746A pdb=" N ARG B 366 " --> pdb=" O HIS B 363 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 368 " --> pdb=" O HIS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 408 Proline residue: B 386 - end of helix Processing helix chain 'B' and resid 424 through 454 Processing helix chain 'B' and resid 455 through 458 removed outlier: 3.842A pdb=" N ILE B 458 " --> pdb=" O ARG B 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 455 through 458' Processing helix chain 'B' and resid 467 through 488 removed outlier: 3.975A pdb=" N PHE B 486 " --> pdb=" O GLN B 482 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 487 " --> pdb=" O VAL B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 506 removed outlier: 3.567A pdb=" N LEU B 495 " --> pdb=" O TRP B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 510 Processing helix chain 'B' and resid 514 through 531 removed outlier: 4.150A pdb=" N ILE B 519 " --> pdb=" O GLN B 515 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR B 520 " --> pdb=" O HIS B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 553 removed outlier: 3.529A pdb=" N ALA B 549 " --> pdb=" O GLY B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 601 removed outlier: 3.552A pdb=" N SER B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 630 removed outlier: 3.522A pdb=" N LEU B 627 " --> pdb=" O ALA B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 648 removed outlier: 3.523A pdb=" N ASN B 645 " --> pdb=" O SER B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 668 removed outlier: 3.803A pdb=" N ASN B 668 " --> pdb=" O LEU B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 removed outlier: 3.699A pdb=" N TRP B 710 " --> pdb=" O ASN B 706 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS B 712 " --> pdb=" O ALA B 708 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR B 713 " --> pdb=" O ALA B 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 82 removed outlier: 3.554A pdb=" N LEU C 75 " --> pdb=" O ASP C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 86 through 96 removed outlier: 4.069A pdb=" N LEU C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU C 92 " --> pdb=" O THR C 88 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 114 through 121 Processing helix chain 'C' and resid 130 through 142 removed outlier: 3.539A pdb=" N ASP C 140 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER C 141 " --> pdb=" O ILE C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 169 removed outlier: 3.609A pdb=" N ILE C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 182 removed outlier: 3.566A pdb=" N VAL C 175 " --> pdb=" O SER C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 215 Processing helix chain 'C' and resid 217 through 226 removed outlier: 3.551A pdb=" N TYR C 223 " --> pdb=" O ASP C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 251 Processing helix chain 'C' and resid 255 through 277 removed outlier: 3.522A pdb=" N ARG C 275 " --> pdb=" O GLN C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 301 Processing helix chain 'C' and resid 302 through 311 Processing helix chain 'C' and resid 350 through 358 Processing helix chain 'C' and resid 363 through 368 removed outlier: 3.744A pdb=" N ARG C 366 " --> pdb=" O HIS C 363 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 368 " --> pdb=" O HIS C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 408 Proline residue: C 386 - end of helix Processing helix chain 'C' and resid 424 through 454 Processing helix chain 'C' and resid 455 through 458 removed outlier: 3.842A pdb=" N ILE C 458 " --> pdb=" O ARG C 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 455 through 458' Processing helix chain 'C' and resid 467 through 488 removed outlier: 3.976A pdb=" N PHE C 486 " --> pdb=" O GLN C 482 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL C 487 " --> pdb=" O VAL C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 506 removed outlier: 3.568A pdb=" N LEU C 495 " --> pdb=" O TRP C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 510 Processing helix chain 'C' and resid 514 through 531 removed outlier: 4.151A pdb=" N ILE C 519 " --> pdb=" O GLN C 515 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR C 520 " --> pdb=" O HIS C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 553 removed outlier: 3.529A pdb=" N ALA C 549 " --> pdb=" O GLY C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 601 removed outlier: 3.552A pdb=" N SER C 592 " --> pdb=" O ILE C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 630 removed outlier: 3.521A pdb=" N LEU C 627 " --> pdb=" O ALA C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 648 removed outlier: 3.523A pdb=" N ASN C 645 " --> pdb=" O SER C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 668 removed outlier: 3.804A pdb=" N ASN C 668 " --> pdb=" O LEU C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 removed outlier: 3.700A pdb=" N TRP C 710 " --> pdb=" O ASN C 706 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS C 712 " --> pdb=" O ALA C 708 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR C 713 " --> pdb=" O ALA C 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 82 removed outlier: 3.554A pdb=" N LEU D 75 " --> pdb=" O ASP D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 86 through 96 removed outlier: 4.070A pdb=" N LEU D 90 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU D 92 " --> pdb=" O THR D 88 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 99 No H-bonds generated for 'chain 'D' and resid 97 through 99' Processing helix chain 'D' and resid 114 through 121 Processing helix chain 'D' and resid 130 through 142 removed outlier: 3.538A pdb=" N ASP D 140 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER D 141 " --> pdb=" O ILE D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 169 removed outlier: 3.609A pdb=" N ILE D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 182 removed outlier: 3.567A pdb=" N VAL D 175 " --> pdb=" O SER D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 215 Processing helix chain 'D' and resid 217 through 226 removed outlier: 3.552A pdb=" N TYR D 223 " --> pdb=" O ASP D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 251 Processing helix chain 'D' and resid 255 through 277 removed outlier: 3.523A pdb=" N ARG D 275 " --> pdb=" O GLN D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 301 Processing helix chain 'D' and resid 302 through 311 Processing helix chain 'D' and resid 350 through 358 Processing helix chain 'D' and resid 363 through 368 removed outlier: 3.745A pdb=" N ARG D 366 " --> pdb=" O HIS D 363 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL D 368 " --> pdb=" O HIS D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 408 Proline residue: D 386 - end of helix Processing helix chain 'D' and resid 424 through 454 Processing helix chain 'D' and resid 455 through 458 removed outlier: 3.843A pdb=" N ILE D 458 " --> pdb=" O ARG D 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 455 through 458' Processing helix chain 'D' and resid 467 through 488 removed outlier: 3.976A pdb=" N PHE D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL D 487 " --> pdb=" O VAL D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 506 removed outlier: 3.568A pdb=" N LEU D 495 " --> pdb=" O TRP D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 510 Processing helix chain 'D' and resid 514 through 531 removed outlier: 4.150A pdb=" N ILE D 519 " --> pdb=" O GLN D 515 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR D 520 " --> pdb=" O HIS D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 553 removed outlier: 3.529A pdb=" N ALA D 549 " --> pdb=" O GLY D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 601 removed outlier: 3.552A pdb=" N SER D 592 " --> pdb=" O ILE D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 630 removed outlier: 3.522A pdb=" N LEU D 627 " --> pdb=" O ALA D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 648 removed outlier: 3.523A pdb=" N ASN D 645 " --> pdb=" O SER D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 668 removed outlier: 3.804A pdb=" N ASN D 668 " --> pdb=" O LEU D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 713 removed outlier: 3.699A pdb=" N TRP D 710 " --> pdb=" O ASN D 706 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS D 712 " --> pdb=" O ALA D 708 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR D 713 " --> pdb=" O ALA D 709 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 333 through 339 removed outlier: 4.094A pdb=" N ARG A 697 " --> pdb=" O LEU A 684 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 684 " --> pdb=" O ARG A 697 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 333 through 339 removed outlier: 4.094A pdb=" N ARG B 697 " --> pdb=" O LEU B 684 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 684 " --> pdb=" O ARG B 697 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 333 through 339 removed outlier: 4.094A pdb=" N ARG C 697 " --> pdb=" O LEU C 684 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 684 " --> pdb=" O ARG C 697 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 333 through 339 removed outlier: 4.094A pdb=" N ARG D 697 " --> pdb=" O LEU D 684 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 684 " --> pdb=" O ARG D 697 " (cutoff:3.500A) 1027 hydrogen bonds defined for protein. 3045 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: 5.78 Time building geometry restraints manager: 8.52 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: 6019 1.34 - 1.46: 3242 1.46 - 1.57: 11063 1.57 - 1.69: 0 1.69 - 1.81: 160 Bond restraints: 20484 Sorted by residual: bond pdb=" CA GLU A 371 " pdb=" CB GLU A 371 " ideal model delta sigma weight residual 1.530 1.490 0.040 1.58e-02 4.01e+03 6.34e+00 bond pdb=" CA GLU D 371 " pdb=" CB GLU D 371 " ideal model delta sigma weight residual 1.530 1.490 0.040 1.58e-02 4.01e+03 6.25e+00 bond pdb=" CA GLU C 371 " pdb=" CB GLU C 371 " ideal model delta sigma weight residual 1.530 1.491 0.039 1.58e-02 4.01e+03 6.10e+00 bond pdb=" CA GLU B 371 " pdb=" CB GLU B 371 " ideal model delta sigma weight residual 1.530 1.491 0.039 1.58e-02 4.01e+03 5.94e+00 bond pdb=" CA GLU C 371 " pdb=" C GLU C 371 " ideal model delta sigma weight residual 1.524 1.496 0.028 1.26e-02 6.30e+03 5.02e+00 ... (remaining 20479 not shown) Histogram of bond angle deviations from ideal: 99.20 - 106.17: 412 106.17 - 113.14: 11130 113.14 - 120.11: 7128 120.11 - 127.08: 8864 127.08 - 134.05: 262 Bond angle restraints: 27796 Sorted by residual: angle pdb=" N VAL A 148 " pdb=" CA VAL A 148 " pdb=" C VAL A 148 " ideal model delta sigma weight residual 113.53 108.75 4.78 9.80e-01 1.04e+00 2.38e+01 angle pdb=" N VAL B 148 " pdb=" CA VAL B 148 " pdb=" C VAL B 148 " ideal model delta sigma weight residual 113.53 108.75 4.78 9.80e-01 1.04e+00 2.38e+01 angle pdb=" N VAL C 148 " pdb=" CA VAL C 148 " pdb=" C VAL C 148 " ideal model delta sigma weight residual 113.53 108.75 4.78 9.80e-01 1.04e+00 2.38e+01 angle pdb=" N VAL D 148 " pdb=" CA VAL D 148 " pdb=" C VAL D 148 " ideal model delta sigma weight residual 113.53 108.79 4.74 9.80e-01 1.04e+00 2.34e+01 angle pdb=" N LEU B 532 " pdb=" CA LEU B 532 " pdb=" C LEU B 532 " ideal model delta sigma weight residual 114.75 108.88 5.87 1.26e+00 6.30e-01 2.17e+01 ... (remaining 27791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 10948 17.21 - 34.43: 887 34.43 - 51.64: 153 51.64 - 68.85: 16 68.85 - 86.07: 20 Dihedral angle restraints: 12024 sinusoidal: 4856 harmonic: 7168 Sorted by residual: dihedral pdb=" N GLU A 371 " pdb=" C GLU A 371 " pdb=" CA GLU A 371 " pdb=" CB GLU A 371 " ideal model delta harmonic sigma weight residual 122.80 138.19 -15.39 0 2.50e+00 1.60e-01 3.79e+01 dihedral pdb=" N GLU B 371 " pdb=" C GLU B 371 " pdb=" CA GLU B 371 " pdb=" CB GLU B 371 " ideal model delta harmonic sigma weight residual 122.80 138.17 -15.37 0 2.50e+00 1.60e-01 3.78e+01 dihedral pdb=" N GLU C 371 " pdb=" C GLU C 371 " pdb=" CA GLU C 371 " pdb=" CB GLU C 371 " ideal model delta harmonic sigma weight residual 122.80 138.15 -15.35 0 2.50e+00 1.60e-01 3.77e+01 ... (remaining 12021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 3123 0.140 - 0.280: 13 0.280 - 0.420: 0 0.420 - 0.560: 0 0.560 - 0.700: 4 Chirality restraints: 3140 Sorted by residual: chirality pdb=" CA GLU A 371 " pdb=" N GLU A 371 " pdb=" C GLU A 371 " pdb=" CB GLU A 371 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" CA GLU C 371 " pdb=" N GLU C 371 " pdb=" C GLU C 371 " pdb=" CB GLU C 371 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" CA GLU B 371 " pdb=" N GLU B 371 " pdb=" C GLU B 371 " pdb=" CB GLU B 371 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.22e+01 ... (remaining 3137 not shown) Planarity restraints: 3432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 70 " 0.019 2.00e-02 2.50e+03 1.82e-02 5.78e+00 pdb=" CG PHE C 70 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE C 70 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 70 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 70 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 70 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 70 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 70 " -0.019 2.00e-02 2.50e+03 1.82e-02 5.78e+00 pdb=" CG PHE B 70 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE B 70 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 70 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 70 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 70 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE B 70 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 70 " 0.019 2.00e-02 2.50e+03 1.81e-02 5.76e+00 pdb=" CG PHE D 70 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE D 70 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE D 70 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE D 70 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 70 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE D 70 " 0.000 2.00e-02 2.50e+03 ... (remaining 3429 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2311 2.75 - 3.29: 20093 3.29 - 3.83: 33115 3.83 - 4.36: 37144 4.36 - 4.90: 65414 Nonbonded interactions: 158077 Sorted by model distance: nonbonded pdb=" OD1 ASN A 143 " pdb=" CD PRO A 144 " model vdw 2.214 3.440 nonbonded pdb=" OD1 ASN C 143 " pdb=" CD PRO C 144 " model vdw 2.214 3.440 nonbonded pdb=" OD1 ASN B 143 " pdb=" CD PRO B 144 " model vdw 2.214 3.440 nonbonded pdb=" OD1 ASN D 143 " pdb=" CD PRO D 144 " model vdw 2.215 3.440 nonbonded pdb=" N GLN C 145 " pdb=" OE1 GLN C 145 " model vdw 2.252 2.520 ... (remaining 158072 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 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: 0.010 Extract box with map and model: 4.160 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 51.580 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 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 : 0.003 0.040 20484 Z= 0.174 Angle : 0.698 10.281 27796 Z= 0.412 Chirality : 0.046 0.700 3140 Planarity : 0.003 0.031 3432 Dihedral : 12.941 86.069 7400 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.99 % Allowed : 4.28 % Favored : 94.74 % Rotamer: Outliers : 0.74 % Allowed : 0.37 % Favored : 98.90 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.18), residues: 2432 helix: 1.74 (0.14), residues: 1444 sheet: -4.18 (0.42), residues: 84 loop : -2.56 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 652 HIS 0.005 0.001 HIS B 516 PHE 0.042 0.001 PHE B 70 TYR 0.010 0.001 TYR C 93 ARG 0.003 0.000 ARG D 485 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 285 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 300 average time/residue: 1.2236 time to fit residues: 418.0584 Evaluate side-chains 196 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 188 time to evaluate : 2.271 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 3.0318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 191 optimal weight: 0.3980 chunk 74 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 221 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 20484 Z= 0.258 Angle : 0.630 9.398 27796 Z= 0.316 Chirality : 0.041 0.237 3140 Planarity : 0.004 0.041 3432 Dihedral : 4.028 25.591 2696 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.73 % Favored : 94.94 % Rotamer: Outliers : 2.99 % Allowed : 11.86 % Favored : 85.16 % 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: 0.41 (0.18), residues: 2432 helix: 1.94 (0.14), residues: 1484 sheet: -3.91 (0.42), residues: 84 loop : -2.40 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 698 HIS 0.007 0.001 HIS C 516 PHE 0.030 0.001 PHE A 70 TYR 0.015 0.001 TYR B 223 ARG 0.005 0.000 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 184 time to evaluate : 2.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 35 residues processed: 224 average time/residue: 1.0196 time to fit residues: 268.7491 Evaluate side-chains 197 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 162 time to evaluate : 2.495 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 20 residues processed: 15 average time/residue: 0.2152 time to fit residues: 9.0442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 7.9990 chunk 68 optimal weight: 0.3980 chunk 184 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 221 optimal weight: 10.0000 chunk 239 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 chunk 220 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 GLN B 525 GLN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 525 GLN D 525 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20484 Z= 0.296 Angle : 0.607 9.512 27796 Z= 0.304 Chirality : 0.040 0.188 3140 Planarity : 0.004 0.061 3432 Dihedral : 3.988 26.947 2696 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.35 % Favored : 94.33 % Rotamer: Outliers : 4.27 % Allowed : 12.96 % Favored : 82.77 % 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 (0.18), residues: 2432 helix: 2.28 (0.14), residues: 1428 sheet: -3.87 (0.40), residues: 84 loop : -2.26 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 698 HIS 0.005 0.001 HIS D 516 PHE 0.026 0.001 PHE B 70 TYR 0.012 0.001 TYR D 492 ARG 0.004 0.000 ARG C 485 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 158 time to evaluate : 2.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 43 residues processed: 215 average time/residue: 0.9816 time to fit residues: 248.5397 Evaluate side-chains 190 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 147 time to evaluate : 2.041 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 23 residues processed: 20 average time/residue: 0.2310 time to fit residues: 10.6261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 0.7980 chunk 166 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 222 optimal weight: 0.7980 chunk 235 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 211 optimal weight: 0.8980 chunk 63 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20484 Z= 0.151 Angle : 0.562 13.969 27796 Z= 0.273 Chirality : 0.038 0.334 3140 Planarity : 0.004 0.068 3432 Dihedral : 3.775 27.418 2696 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.35 % Favored : 94.33 % Rotamer: Outliers : 3.12 % Allowed : 14.20 % Favored : 82.67 % 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: 1.01 (0.18), residues: 2432 helix: 2.54 (0.14), residues: 1432 sheet: -3.41 (0.46), residues: 84 loop : -2.15 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 173 HIS 0.005 0.001 HIS D 516 PHE 0.020 0.001 PHE A 70 TYR 0.011 0.001 TYR B 466 ARG 0.002 0.000 ARG C 485 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 160 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 37 residues processed: 213 average time/residue: 1.0054 time to fit residues: 251.4962 Evaluate side-chains 191 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 154 time to evaluate : 2.243 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 27 residues processed: 10 average time/residue: 0.2799 time to fit residues: 7.2983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.1162 > 50: distance: 9 - 30: 7.107 distance: 14 - 38: 8.914 distance: 18 - 42: 4.561 distance: 22 - 23: 3.195 distance: 23 - 24: 3.535 distance: 24 - 25: 5.272 distance: 24 - 30: 3.725 distance: 25 - 46: 7.695 distance: 26 - 27: 3.770 distance: 27 - 28: 6.158 distance: 27 - 29: 5.092 distance: 30 - 31: 3.477 distance: 32 - 38: 5.753 distance: 33 - 54: 12.781 distance: 34 - 35: 4.598 distance: 35 - 36: 7.720 distance: 35 - 37: 7.806 distance: 39 - 40: 6.450 distance: 40 - 41: 3.629 distance: 41 - 66: 20.773 distance: 42 - 43: 4.957 distance: 43 - 44: 4.657 distance: 44 - 45: 3.268 distance: 44 - 46: 6.255 distance: 45 - 74: 9.896 distance: 46 - 47: 4.651 distance: 48 - 49: 5.228 distance: 49 - 82: 10.114 distance: 50 - 51: 3.051 distance: 51 - 53: 4.863 distance: 55 - 56: 3.577 distance: 56 - 57: 6.992 distance: 56 - 66: 13.483 distance: 57 - 90: 4.305 distance: 58 - 59: 3.859 distance: 59 - 60: 5.674 distance: 59 - 61: 3.510 distance: 60 - 62: 4.374 distance: 61 - 63: 4.755 distance: 63 - 64: 6.213 distance: 64 - 65: 4.923 distance: 66 - 67: 25.711 distance: 67 - 68: 9.453 distance: 67 - 70: 13.789 distance: 69 - 94: 3.568 distance: 70 - 71: 11.337 distance: 71 - 72: 6.334 distance: 71 - 73: 8.561 distance: 75 - 78: 5.601 distance: 76 - 82: 3.508 distance: 77 - 102: 4.186 distance: 78 - 79: 12.931 distance: 79 - 80: 24.357 distance: 79 - 81: 27.695 distance: 83 - 84: 3.571 distance: 83 - 86: 5.741 distance: 85 - 110: 4.797 distance: 86 - 87: 7.678 distance: 87 - 88: 14.012 distance: 87 - 89: 12.394 distance: 93 - 118: 3.350