Starting phenix.real_space_refine on Sun Jan 26 00:11:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7feb_31551/01_2025/7feb_31551.cif Found real_map, /net/cci-nas-00/data/ceres_data/7feb_31551/01_2025/7feb_31551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7feb_31551/01_2025/7feb_31551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7feb_31551/01_2025/7feb_31551.map" model { file = "/net/cci-nas-00/data/ceres_data/7feb_31551/01_2025/7feb_31551.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7feb_31551/01_2025/7feb_31551.cif" } resolution = 2.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.061 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 15354 2.51 5 N 4140 2.21 5 O 4473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 24075 Number of models: 1 Model: "" Number of chains: 9 Chain: "E" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "A" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "B" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "C" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "D" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "F" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "G" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "H" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "I" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Time building chain proxies: 14.78, per 1000 atoms: 0.61 Number of scatterers: 24075 At special positions: 0 Unit cell: (180.466, 178.78, 79.2702, 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 4473 8.00 N 4140 7.00 C 15354 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 - 3.00 Amino acid : True - 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: 6.23 Conformation dependent library (CDL) restraints added in 3.0 seconds 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5742 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 36 sheets defined 50.0% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'E' and resid 365 through 382 Processing helix chain 'E' and resid 447 through 458 Processing helix chain 'E' and resid 464 through 479 removed outlier: 4.009A pdb=" N ILE E 468 " --> pdb=" O GLY E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 484 removed outlier: 3.807A pdb=" N ILE E 484 " --> pdb=" O GLY E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 485 through 497 Processing helix chain 'E' and resid 500 through 511 Processing helix chain 'E' and resid 512 through 526 removed outlier: 3.609A pdb=" N GLU E 526 " --> pdb=" O ARG E 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 544 Processing helix chain 'E' and resid 549 through 561 Processing helix chain 'E' and resid 561 through 570 Processing helix chain 'E' and resid 582 through 591 Processing helix chain 'E' and resid 605 through 619 Processing helix chain 'E' and resid 631 through 633 No H-bonds generated for 'chain 'E' and resid 631 through 633' Processing helix chain 'E' and resid 634 through 643 Processing helix chain 'E' and resid 655 through 657 No H-bonds generated for 'chain 'E' and resid 655 through 657' Processing helix chain 'A' and resid 365 through 382 Processing helix chain 'A' and resid 447 through 458 Processing helix chain 'A' and resid 464 through 479 removed outlier: 4.009A pdb=" N ILE A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 484 removed outlier: 3.807A pdb=" N ILE A 484 " --> pdb=" O GLY A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 497 Processing helix chain 'A' and resid 500 through 511 Processing helix chain 'A' and resid 512 through 526 removed outlier: 3.609A pdb=" N GLU A 526 " --> pdb=" O ARG A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 544 Processing helix chain 'A' and resid 549 through 561 Processing helix chain 'A' and resid 561 through 570 Processing helix chain 'A' and resid 582 through 591 Processing helix chain 'A' and resid 605 through 619 Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 634 through 643 Processing helix chain 'A' and resid 655 through 657 No H-bonds generated for 'chain 'A' and resid 655 through 657' Processing helix chain 'B' and resid 365 through 382 Processing helix chain 'B' and resid 447 through 458 Processing helix chain 'B' and resid 464 through 479 removed outlier: 4.008A pdb=" N ILE B 468 " --> pdb=" O GLY B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 484 removed outlier: 3.807A pdb=" N ILE B 484 " --> pdb=" O GLY B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 497 Processing helix chain 'B' and resid 500 through 511 Processing helix chain 'B' and resid 512 through 526 removed outlier: 3.609A pdb=" N GLU B 526 " --> pdb=" O ARG B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 544 Processing helix chain 'B' and resid 549 through 561 Processing helix chain 'B' and resid 561 through 570 Processing helix chain 'B' and resid 582 through 591 Processing helix chain 'B' and resid 605 through 619 Processing helix chain 'B' and resid 631 through 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 634 through 643 Processing helix chain 'B' and resid 655 through 657 No H-bonds generated for 'chain 'B' and resid 655 through 657' Processing helix chain 'C' and resid 365 through 382 Processing helix chain 'C' and resid 447 through 458 Processing helix chain 'C' and resid 464 through 479 removed outlier: 4.009A pdb=" N ILE C 468 " --> pdb=" O GLY C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 484 removed outlier: 3.808A pdb=" N ILE C 484 " --> pdb=" O GLY C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 497 Processing helix chain 'C' and resid 500 through 511 Processing helix chain 'C' and resid 512 through 526 removed outlier: 3.608A pdb=" N GLU C 526 " --> pdb=" O ARG C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 544 Processing helix chain 'C' and resid 549 through 561 Processing helix chain 'C' and resid 561 through 570 Processing helix chain 'C' and resid 582 through 591 Processing helix chain 'C' and resid 605 through 619 Processing helix chain 'C' and resid 631 through 633 No H-bonds generated for 'chain 'C' and resid 631 through 633' Processing helix chain 'C' and resid 634 through 643 Processing helix chain 'C' and resid 655 through 657 No H-bonds generated for 'chain 'C' and resid 655 through 657' Processing helix chain 'D' and resid 365 through 382 Processing helix chain 'D' and resid 447 through 458 Processing helix chain 'D' and resid 464 through 479 removed outlier: 4.009A pdb=" N ILE D 468 " --> pdb=" O GLY D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 484 removed outlier: 3.807A pdb=" N ILE D 484 " --> pdb=" O GLY D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 497 Processing helix chain 'D' and resid 500 through 511 Processing helix chain 'D' and resid 512 through 526 removed outlier: 3.608A pdb=" N GLU D 526 " --> pdb=" O ARG D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 544 Processing helix chain 'D' and resid 549 through 561 Processing helix chain 'D' and resid 561 through 570 Processing helix chain 'D' and resid 582 through 591 Processing helix chain 'D' and resid 605 through 619 Processing helix chain 'D' and resid 631 through 633 No H-bonds generated for 'chain 'D' and resid 631 through 633' Processing helix chain 'D' and resid 634 through 643 Processing helix chain 'D' and resid 655 through 657 No H-bonds generated for 'chain 'D' and resid 655 through 657' Processing helix chain 'F' and resid 365 through 382 Processing helix chain 'F' and resid 447 through 458 Processing helix chain 'F' and resid 464 through 479 removed outlier: 4.009A pdb=" N ILE F 468 " --> pdb=" O GLY F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 484 removed outlier: 3.807A pdb=" N ILE F 484 " --> pdb=" O GLY F 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 485 through 497 Processing helix chain 'F' and resid 500 through 511 Processing helix chain 'F' and resid 512 through 526 removed outlier: 3.609A pdb=" N GLU F 526 " --> pdb=" O ARG F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 544 Processing helix chain 'F' and resid 549 through 561 Processing helix chain 'F' and resid 561 through 570 Processing helix chain 'F' and resid 582 through 591 Processing helix chain 'F' and resid 605 through 619 Processing helix chain 'F' and resid 631 through 633 No H-bonds generated for 'chain 'F' and resid 631 through 633' Processing helix chain 'F' and resid 634 through 643 Processing helix chain 'F' and resid 655 through 657 No H-bonds generated for 'chain 'F' and resid 655 through 657' Processing helix chain 'G' and resid 365 through 382 Processing helix chain 'G' and resid 447 through 458 Processing helix chain 'G' and resid 464 through 479 removed outlier: 4.009A pdb=" N ILE G 468 " --> pdb=" O GLY G 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 480 through 484 removed outlier: 3.807A pdb=" N ILE G 484 " --> pdb=" O GLY G 481 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 497 Processing helix chain 'G' and resid 500 through 511 Processing helix chain 'G' and resid 512 through 526 removed outlier: 3.609A pdb=" N GLU G 526 " --> pdb=" O ARG G 522 " (cutoff:3.500A) Processing helix chain 'G' and resid 532 through 544 Processing helix chain 'G' and resid 549 through 561 Processing helix chain 'G' and resid 561 through 570 Processing helix chain 'G' and resid 582 through 591 Processing helix chain 'G' and resid 605 through 619 Processing helix chain 'G' and resid 631 through 633 No H-bonds generated for 'chain 'G' and resid 631 through 633' Processing helix chain 'G' and resid 634 through 643 Processing helix chain 'G' and resid 655 through 657 No H-bonds generated for 'chain 'G' and resid 655 through 657' Processing helix chain 'H' and resid 365 through 382 Processing helix chain 'H' and resid 447 through 458 Processing helix chain 'H' and resid 464 through 479 removed outlier: 4.009A pdb=" N ILE H 468 " --> pdb=" O GLY H 464 " (cutoff:3.500A) Processing helix chain 'H' and resid 480 through 484 removed outlier: 3.807A pdb=" N ILE H 484 " --> pdb=" O GLY H 481 " (cutoff:3.500A) Processing helix chain 'H' and resid 485 through 497 Processing helix chain 'H' and resid 500 through 511 Processing helix chain 'H' and resid 512 through 526 removed outlier: 3.608A pdb=" N GLU H 526 " --> pdb=" O ARG H 522 " (cutoff:3.500A) Processing helix chain 'H' and resid 532 through 544 Processing helix chain 'H' and resid 549 through 561 Processing helix chain 'H' and resid 561 through 570 Processing helix chain 'H' and resid 582 through 591 Processing helix chain 'H' and resid 605 through 619 Processing helix chain 'H' and resid 631 through 633 No H-bonds generated for 'chain 'H' and resid 631 through 633' Processing helix chain 'H' and resid 634 through 643 Processing helix chain 'H' and resid 655 through 657 No H-bonds generated for 'chain 'H' and resid 655 through 657' Processing helix chain 'I' and resid 365 through 382 Processing helix chain 'I' and resid 447 through 458 Processing helix chain 'I' and resid 464 through 479 removed outlier: 4.009A pdb=" N ILE I 468 " --> pdb=" O GLY I 464 " (cutoff:3.500A) Processing helix chain 'I' and resid 480 through 484 removed outlier: 3.808A pdb=" N ILE I 484 " --> pdb=" O GLY I 481 " (cutoff:3.500A) Processing helix chain 'I' and resid 485 through 497 Processing helix chain 'I' and resid 500 through 511 Processing helix chain 'I' and resid 512 through 526 removed outlier: 3.609A pdb=" N GLU I 526 " --> pdb=" O ARG I 522 " (cutoff:3.500A) Processing helix chain 'I' and resid 532 through 544 Processing helix chain 'I' and resid 549 through 561 Processing helix chain 'I' and resid 561 through 570 Processing helix chain 'I' and resid 582 through 591 Processing helix chain 'I' and resid 605 through 619 Processing helix chain 'I' and resid 631 through 633 No H-bonds generated for 'chain 'I' and resid 631 through 633' Processing helix chain 'I' and resid 634 through 643 Processing helix chain 'I' and resid 655 through 657 No H-bonds generated for 'chain 'I' and resid 655 through 657' Processing sheet with id=AA1, first strand: chain 'E' and resid 389 through 392 removed outlier: 6.457A pdb=" N LEU E 404 " --> pdb=" O PRO E 408 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 420 through 423 removed outlier: 3.642A pdb=" N TYR E 420 " --> pdb=" O LEU E 446 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 651 through 653 removed outlier: 6.331A pdb=" N ILE E 628 " --> pdb=" O LEU E 652 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE E 578 " --> pdb=" O VAL E 666 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER E 668 " --> pdb=" O ILE E 578 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG E 580 " --> pdb=" O SER E 668 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 593 through 596 Processing sheet with id=AA5, first strand: chain 'A' and resid 389 through 392 removed outlier: 6.458A pdb=" N LEU A 404 " --> pdb=" O PRO A 408 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 420 through 423 removed outlier: 3.642A pdb=" N TYR A 420 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 651 through 653 removed outlier: 6.331A pdb=" N ILE A 628 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE A 578 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER A 668 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG A 580 " --> pdb=" O SER A 668 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 593 through 596 Processing sheet with id=AA9, first strand: chain 'B' and resid 389 through 392 removed outlier: 6.457A pdb=" N LEU B 404 " --> pdb=" O PRO B 408 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 420 through 423 removed outlier: 3.642A pdb=" N TYR B 420 " --> pdb=" O LEU B 446 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 651 through 653 removed outlier: 6.331A pdb=" N ILE B 628 " --> pdb=" O LEU B 652 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE B 578 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER B 668 " --> pdb=" O ILE B 578 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG B 580 " --> pdb=" O SER B 668 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 593 through 596 Processing sheet with id=AB4, first strand: chain 'C' and resid 389 through 392 removed outlier: 6.457A pdb=" N LEU C 404 " --> pdb=" O PRO C 408 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 420 through 423 removed outlier: 3.642A pdb=" N TYR C 420 " --> pdb=" O LEU C 446 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 651 through 653 removed outlier: 6.331A pdb=" N ILE C 628 " --> pdb=" O LEU C 652 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE C 578 " --> pdb=" O VAL C 666 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER C 668 " --> pdb=" O ILE C 578 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG C 580 " --> pdb=" O SER C 668 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 593 through 596 Processing sheet with id=AB8, first strand: chain 'D' and resid 389 through 392 removed outlier: 6.457A pdb=" N LEU D 404 " --> pdb=" O PRO D 408 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 420 through 423 removed outlier: 3.642A pdb=" N TYR D 420 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 651 through 653 removed outlier: 6.332A pdb=" N ILE D 628 " --> pdb=" O LEU D 652 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE D 578 " --> pdb=" O VAL D 666 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER D 668 " --> pdb=" O ILE D 578 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG D 580 " --> pdb=" O SER D 668 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 593 through 596 Processing sheet with id=AC3, first strand: chain 'F' and resid 389 through 392 removed outlier: 6.457A pdb=" N LEU F 404 " --> pdb=" O PRO F 408 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 420 through 423 removed outlier: 3.641A pdb=" N TYR F 420 " --> pdb=" O LEU F 446 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 651 through 653 removed outlier: 6.332A pdb=" N ILE F 628 " --> pdb=" O LEU F 652 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE F 578 " --> pdb=" O VAL F 666 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER F 668 " --> pdb=" O ILE F 578 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG F 580 " --> pdb=" O SER F 668 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 593 through 596 Processing sheet with id=AC7, first strand: chain 'G' and resid 389 through 392 removed outlier: 6.458A pdb=" N LEU G 404 " --> pdb=" O PRO G 408 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 420 through 423 removed outlier: 3.642A pdb=" N TYR G 420 " --> pdb=" O LEU G 446 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 651 through 653 removed outlier: 6.332A pdb=" N ILE G 628 " --> pdb=" O LEU G 652 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE G 578 " --> pdb=" O VAL G 666 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER G 668 " --> pdb=" O ILE G 578 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG G 580 " --> pdb=" O SER G 668 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 593 through 596 Processing sheet with id=AD2, first strand: chain 'H' and resid 389 through 392 removed outlier: 6.458A pdb=" N LEU H 404 " --> pdb=" O PRO H 408 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 420 through 423 removed outlier: 3.641A pdb=" N TYR H 420 " --> pdb=" O LEU H 446 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 651 through 653 removed outlier: 6.331A pdb=" N ILE H 628 " --> pdb=" O LEU H 652 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE H 578 " --> pdb=" O VAL H 666 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER H 668 " --> pdb=" O ILE H 578 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG H 580 " --> pdb=" O SER H 668 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 593 through 596 Processing sheet with id=AD6, first strand: chain 'I' and resid 389 through 392 removed outlier: 6.458A pdb=" N LEU I 404 " --> pdb=" O PRO I 408 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 420 through 423 removed outlier: 3.642A pdb=" N TYR I 420 " --> pdb=" O LEU I 446 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 651 through 653 removed outlier: 6.331A pdb=" N ILE I 628 " --> pdb=" O LEU I 652 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE I 578 " --> pdb=" O VAL I 666 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER I 668 " --> pdb=" O ILE I 578 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG I 580 " --> pdb=" O SER I 668 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 593 through 596 1188 hydrogen bonds defined for protein. 3483 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: 8.75 Time building geometry restraints manager: 7.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4086 1.31 - 1.43: 5715 1.43 - 1.56: 14472 1.56 - 1.68: 9 1.68 - 1.81: 189 Bond restraints: 24471 Sorted by residual: bond pdb=" C TRP D 375 " pdb=" O TRP D 375 " ideal model delta sigma weight residual 1.237 1.193 0.043 1.19e-02 7.06e+03 1.31e+01 bond pdb=" C TRP G 375 " pdb=" O TRP G 375 " ideal model delta sigma weight residual 1.237 1.194 0.042 1.19e-02 7.06e+03 1.27e+01 bond pdb=" C TRP E 375 " pdb=" O TRP E 375 " ideal model delta sigma weight residual 1.237 1.196 0.041 1.17e-02 7.31e+03 1.24e+01 bond pdb=" C PRO C 437 " pdb=" O PRO C 437 " ideal model delta sigma weight residual 1.232 1.186 0.046 1.31e-02 5.83e+03 1.22e+01 bond pdb=" C TRP C 375 " pdb=" O TRP C 375 " ideal model delta sigma weight residual 1.237 1.195 0.041 1.19e-02 7.06e+03 1.21e+01 ... (remaining 24466 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 31920 1.52 - 3.05: 1004 3.05 - 4.57: 133 4.57 - 6.10: 75 6.10 - 7.62: 24 Bond angle restraints: 33156 Sorted by residual: angle pdb=" C ASN D 438 " pdb=" CA ASN D 438 " pdb=" CB ASN D 438 " ideal model delta sigma weight residual 111.51 117.67 -6.16 1.58e+00 4.01e-01 1.52e+01 angle pdb=" C ASN C 438 " pdb=" CA ASN C 438 " pdb=" CB ASN C 438 " ideal model delta sigma weight residual 111.51 117.67 -6.16 1.58e+00 4.01e-01 1.52e+01 angle pdb=" C ASN I 438 " pdb=" CA ASN I 438 " pdb=" CB ASN I 438 " ideal model delta sigma weight residual 111.51 117.66 -6.15 1.58e+00 4.01e-01 1.52e+01 angle pdb=" C ASN E 438 " pdb=" CA ASN E 438 " pdb=" CB ASN E 438 " ideal model delta sigma weight residual 111.51 117.64 -6.13 1.58e+00 4.01e-01 1.50e+01 angle pdb=" C ASN F 438 " pdb=" CA ASN F 438 " pdb=" CB ASN F 438 " ideal model delta sigma weight residual 111.51 117.63 -6.12 1.58e+00 4.01e-01 1.50e+01 ... (remaining 33151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 12989 15.99 - 31.97: 1555 31.97 - 47.96: 477 47.96 - 63.95: 72 63.95 - 79.94: 45 Dihedral angle restraints: 15138 sinusoidal: 6327 harmonic: 8811 Sorted by residual: dihedral pdb=" CA LEU H 662 " pdb=" C LEU H 662 " pdb=" N ILE H 663 " pdb=" CA ILE H 663 " ideal model delta harmonic sigma weight residual -180.00 -156.03 -23.97 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA LEU B 662 " pdb=" C LEU B 662 " pdb=" N ILE B 663 " pdb=" CA ILE B 663 " ideal model delta harmonic sigma weight residual 180.00 -156.05 -23.95 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA LEU C 662 " pdb=" C LEU C 662 " pdb=" N ILE C 663 " pdb=" CA ILE C 663 " ideal model delta harmonic sigma weight residual 180.00 -156.05 -23.95 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 15135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2956 0.046 - 0.092: 699 0.092 - 0.138: 235 0.138 - 0.184: 16 0.184 - 0.230: 18 Chirality restraints: 3924 Sorted by residual: chirality pdb=" CA ASN D 438 " pdb=" N ASN D 438 " pdb=" C ASN D 438 " pdb=" CB ASN D 438 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA ASN C 438 " pdb=" N ASN C 438 " pdb=" C ASN C 438 " pdb=" CB ASN C 438 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ASN H 438 " pdb=" N ASN H 438 " pdb=" C ASN H 438 " pdb=" CB ASN H 438 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 3921 not shown) Planarity restraints: 4239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 590 " -0.189 9.50e-02 1.11e+02 8.52e-02 5.75e+00 pdb=" NE ARG C 590 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG C 590 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG C 590 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C 590 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 590 " 0.188 9.50e-02 1.11e+02 8.50e-02 5.74e+00 pdb=" NE ARG D 590 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG D 590 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG D 590 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG D 590 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 590 " -0.189 9.50e-02 1.11e+02 8.52e-02 5.74e+00 pdb=" NE ARG E 590 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG E 590 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG E 590 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG E 590 " -0.000 2.00e-02 2.50e+03 ... (remaining 4236 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2486 2.75 - 3.29: 23619 3.29 - 3.82: 40810 3.82 - 4.36: 47015 4.36 - 4.90: 78742 Nonbonded interactions: 192672 Sorted by model distance: nonbonded pdb=" O LEU F 576 " pdb=" NE2 GLN F 664 " model vdw 2.211 3.120 nonbonded pdb=" O LEU B 576 " pdb=" NE2 GLN B 664 " model vdw 2.211 3.120 nonbonded pdb=" O LEU I 576 " pdb=" NE2 GLN I 664 " model vdw 2.211 3.120 nonbonded pdb=" O LEU G 576 " pdb=" NE2 GLN G 664 " model vdw 2.212 3.120 nonbonded pdb=" O LEU D 576 " pdb=" NE2 GLN D 664 " model vdw 2.212 3.120 ... (remaining 192667 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.21 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' } 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: 11.430 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 53.330 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.120 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:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 : 0.004 0.046 24471 Z= 0.234 Angle : 0.652 7.624 33156 Z= 0.386 Chirality : 0.046 0.230 3924 Planarity : 0.006 0.085 4239 Dihedral : 15.912 79.936 9396 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.30 % Allowed : 16.63 % Favored : 83.07 % 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: 0.07 (0.15), residues: 3006 helix: 1.22 (0.14), residues: 1395 sheet: -0.73 (0.21), residues: 549 loop : -1.01 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 375 HIS 0.003 0.001 HIS F 564 PHE 0.005 0.001 PHE C 378 TYR 0.011 0.001 TYR D 405 ARG 0.020 0.001 ARG D 590 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 365 time to evaluate : 2.913 Fit side-chains REVERT: A 438 ASN cc_start: 0.8407 (t0) cc_final: 0.8147 (t0) REVERT: A 562 ARG cc_start: 0.8209 (ptt90) cc_final: 0.7987 (ptt90) REVERT: B 438 ASN cc_start: 0.8444 (t0) cc_final: 0.8194 (t0) REVERT: C 632 VAL cc_start: 0.8509 (t) cc_final: 0.8303 (p) REVERT: F 632 VAL cc_start: 0.8369 (t) cc_final: 0.8150 (p) REVERT: G 563 ARG cc_start: 0.7436 (ttp-170) cc_final: 0.7229 (pmt-80) REVERT: H 438 ASN cc_start: 0.8446 (t0) cc_final: 0.8199 (t0) REVERT: H 562 ARG cc_start: 0.8232 (ptt90) cc_final: 0.7849 (ptt90) outliers start: 8 outliers final: 13 residues processed: 365 average time/residue: 1.7456 time to fit residues: 712.4409 Evaluate side-chains 312 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 299 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 610 THR Chi-restraints excluded: chain E residue 633 ASP Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 633 ASP Chi-restraints excluded: chain G residue 610 THR Chi-restraints excluded: chain G residue 633 ASP Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 633 ASP Chi-restraints excluded: chain I residue 610 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 0.7980 chunk 225 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 151 optimal weight: 0.5980 chunk 120 optimal weight: 0.8980 chunk 232 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 173 optimal weight: 0.9980 chunk 269 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 434 GLN E 438 ASN A 434 GLN A 438 ASN B 434 GLN B 438 ASN C 434 GLN C 438 ASN D 434 GLN D 438 ASN D 614 GLN F 434 GLN F 438 ASN F 508 GLN G 434 GLN H 434 GLN H 438 ASN I 434 GLN I 438 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.199491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.120724 restraints weight = 24357.832| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.07 r_work: 0.3243 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24471 Z= 0.158 Angle : 0.511 6.035 33156 Z= 0.256 Chirality : 0.042 0.218 3924 Planarity : 0.004 0.038 4239 Dihedral : 4.128 82.120 3303 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.57 % Allowed : 15.32 % Favored : 82.10 % 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: 0.61 (0.15), residues: 3006 helix: 1.84 (0.14), residues: 1413 sheet: -0.75 (0.21), residues: 549 loop : -0.90 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 375 HIS 0.003 0.001 HIS A 564 PHE 0.009 0.001 PHE F 378 TYR 0.014 0.001 TYR C 405 ARG 0.009 0.001 ARG F 590 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 314 time to evaluate : 2.924 Fit side-chains REVERT: E 453 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6905 (ptmm) REVERT: A 400 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7411 (pt) REVERT: A 434 GLN cc_start: 0.6513 (OUTLIER) cc_final: 0.5995 (pt0) REVERT: A 442 GLN cc_start: 0.8442 (mm-40) cc_final: 0.7910 (mm-40) REVERT: A 453 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.7072 (ptmm) REVERT: A 562 ARG cc_start: 0.8586 (ptt90) cc_final: 0.8322 (ptt90) REVERT: A 662 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6810 (pp) REVERT: B 662 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6893 (pp) REVERT: C 632 VAL cc_start: 0.8433 (t) cc_final: 0.8168 (p) REVERT: D 662 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6863 (pp) REVERT: F 400 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7425 (pt) REVERT: F 453 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6947 (ptmm) REVERT: F 632 VAL cc_start: 0.8363 (t) cc_final: 0.8061 (p) REVERT: F 662 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6842 (pp) REVERT: G 598 MET cc_start: 0.6623 (mmt) cc_final: 0.6158 (mmt) REVERT: H 434 GLN cc_start: 0.6824 (OUTLIER) cc_final: 0.6352 (pt0) REVERT: H 442 GLN cc_start: 0.8409 (mm-40) cc_final: 0.7787 (mm-40) REVERT: H 562 ARG cc_start: 0.8572 (ptt90) cc_final: 0.8319 (ptt90) REVERT: H 574 LYS cc_start: 0.8174 (pttm) cc_final: 0.7812 (pmtt) REVERT: H 580 ARG cc_start: 0.7656 (ttp-110) cc_final: 0.7429 (ttp-110) REVERT: H 662 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6872 (pp) REVERT: I 434 GLN cc_start: 0.6739 (OUTLIER) cc_final: 0.6301 (pt0) REVERT: I 442 GLN cc_start: 0.8422 (mm-40) cc_final: 0.7749 (mm-40) REVERT: I 527 ARG cc_start: 0.8740 (mpt180) cc_final: 0.8074 (mtp180) REVERT: I 567 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7640 (tmt170) REVERT: I 632 VAL cc_start: 0.8400 (t) cc_final: 0.8197 (p) REVERT: I 662 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6877 (pp) outliers start: 69 outliers final: 17 residues processed: 369 average time/residue: 1.6424 time to fit residues: 683.5164 Evaluate side-chains 326 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 294 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 669 ILE Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 453 LYS Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 633 ASP Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain H residue 434 GLN Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain H residue 662 LEU Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 434 GLN Chi-restraints excluded: chain I residue 567 ARG Chi-restraints excluded: chain I residue 581 ILE Chi-restraints excluded: chain I residue 662 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 236 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 253 optimal weight: 3.9990 chunk 288 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 202 optimal weight: 0.1980 chunk 169 optimal weight: 0.0010 overall best weight: 1.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 434 GLN A 438 ASN C 434 GLN D 434 GLN F 434 GLN G 434 GLN H 438 ASN H 570 ASN I 438 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.197825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.118644 restraints weight = 24131.815| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.06 r_work: 0.3219 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 24471 Z= 0.234 Angle : 0.555 7.531 33156 Z= 0.278 Chirality : 0.044 0.220 3924 Planarity : 0.005 0.040 4239 Dihedral : 4.202 82.497 3287 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.50 % Allowed : 15.96 % Favored : 81.54 % 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: 0.61 (0.15), residues: 3006 helix: 1.82 (0.14), residues: 1413 sheet: -0.79 (0.21), residues: 549 loop : -0.84 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 375 HIS 0.004 0.001 HIS A 564 PHE 0.011 0.002 PHE G 483 TYR 0.016 0.002 TYR C 405 ARG 0.011 0.001 ARG C 590 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 316 time to evaluate : 2.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7364 (pt) REVERT: A 562 ARG cc_start: 0.8617 (ptt90) cc_final: 0.8411 (ptt90) REVERT: C 632 VAL cc_start: 0.8414 (t) cc_final: 0.8165 (p) REVERT: F 632 VAL cc_start: 0.8393 (t) cc_final: 0.8117 (p) REVERT: G 598 MET cc_start: 0.6615 (mmt) cc_final: 0.6359 (mmt) REVERT: H 562 ARG cc_start: 0.8624 (ptt90) cc_final: 0.8379 (ptt90) REVERT: I 527 ARG cc_start: 0.8743 (mpt180) cc_final: 0.8078 (mtp180) REVERT: I 567 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7686 (tmt170) REVERT: I 662 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6957 (pp) outliers start: 67 outliers final: 21 residues processed: 370 average time/residue: 1.7238 time to fit residues: 719.5412 Evaluate side-chains 316 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 292 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 669 ILE Chi-restraints excluded: chain F residue 453 LYS Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain H residue 484 ILE Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 567 ARG Chi-restraints excluded: chain I residue 581 ILE Chi-restraints excluded: chain I residue 662 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.1394 > 50: distance: 8 - 15: 13.127 distance: 15 - 16: 25.501 distance: 15 - 21: 23.430 distance: 16 - 17: 30.296 distance: 16 - 19: 32.389 distance: 17 - 18: 39.806 distance: 17 - 22: 23.541 distance: 19 - 20: 13.004 distance: 20 - 21: 65.143 distance: 22 - 23: 34.740 distance: 23 - 24: 14.844 distance: 23 - 26: 14.469 distance: 24 - 25: 21.288 distance: 24 - 30: 15.598 distance: 26 - 27: 17.245 distance: 27 - 28: 24.227 distance: 27 - 29: 21.114 distance: 30 - 31: 35.127 distance: 30 - 36: 21.191 distance: 31 - 32: 20.186 distance: 31 - 34: 24.421 distance: 32 - 33: 5.667 distance: 32 - 37: 52.848 distance: 34 - 35: 50.364 distance: 35 - 36: 21.932 distance: 38 - 39: 28.382 distance: 39 - 40: 25.605 distance: 39 - 45: 32.015 distance: 41 - 42: 11.224 distance: 41 - 43: 19.421 distance: 42 - 44: 31.564 distance: 45 - 46: 6.073 distance: 45 - 139: 25.945 distance: 46 - 47: 12.108 distance: 46 - 49: 13.197 distance: 47 - 48: 5.831 distance: 47 - 53: 29.201 distance: 48 - 154: 22.935 distance: 49 - 50: 21.448 distance: 50 - 51: 10.269 distance: 50 - 52: 10.310 distance: 54 - 55: 19.579 distance: 54 - 57: 16.299 distance: 55 - 56: 15.612 distance: 55 - 64: 44.166 distance: 57 - 58: 58.559 distance: 58 - 59: 10.560 distance: 59 - 60: 35.527 distance: 60 - 61: 10.849 distance: 61 - 62: 6.314 distance: 61 - 63: 21.953 distance: 64 - 65: 14.142 distance: 64 - 157: 28.274 distance: 65 - 66: 13.843 distance: 65 - 68: 56.183 distance: 66 - 67: 11.366 distance: 66 - 72: 26.021 distance: 68 - 69: 32.860 distance: 68 - 70: 27.914 distance: 69 - 71: 27.762 distance: 72 - 73: 27.459 distance: 73 - 74: 44.239 distance: 74 - 76: 4.000 distance: 75 - 97: 37.387 distance: 76 - 77: 3.320 distance: 77 - 78: 9.924 distance: 77 - 80: 28.100 distance: 78 - 79: 5.846 distance: 78 - 85: 9.480 distance: 79 - 106: 27.201 distance: 80 - 81: 19.333 distance: 81 - 82: 9.819 distance: 82 - 83: 10.993 distance: 82 - 84: 22.043 distance: 85 - 86: 17.388 distance: 86 - 87: 20.430 distance: 87 - 88: 21.073 distance: 87 - 89: 9.036 distance: 88 - 114: 30.414