Starting phenix.real_space_refine on Thu Mar 5 17:10:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7feb_31551/03_2026/7feb_31551.cif Found real_map, /net/cci-nas-00/data/ceres_data/7feb_31551/03_2026/7feb_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 { model { file = "/net/cci-nas-00/data/ceres_data/7feb_31551/03_2026/7feb_31551.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7feb_31551/03_2026/7feb_31551.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7feb_31551/03_2026/7feb_31551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7feb_31551/03_2026/7feb_31551.map" } resolution = 2.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 5.07, per 1000 atoms: 0.21 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: 2.24 Conformation dependent library (CDL) restraints added in 1.5 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: 0.89 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: 6.18 Time building geometry restraints manager: 3.01 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: 0.07 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 8.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.730 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.970 ------------------------------------------------------------------------------- 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= 0.227 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.020 0.001 ARG D 590 TYR 0.011 0.001 TYR D 405 PHE 0.005 0.001 PHE C 378 TRP 0.013 0.002 TRP G 375 HIS 0.003 0.001 HIS F 564 Details of bonding type rmsd covalent geometry : bond 0.00356 (24471) covalent geometry : angle 0.65170 (33156) hydrogen bonds : bond 0.13879 ( 1188) hydrogen bonds : angle 5.58595 ( 3483) *********************** 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 : 0.895 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: 0.8095 time to fit residues: 328.6891 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 : 0.899 ------------------------------------------------------------------------------- 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 197 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 E 508 GLN A 434 GLN A 438 ASN A 508 GLN B 434 GLN B 438 ASN B 508 GLN C 434 GLN C 438 ASN D 434 GLN D 438 ASN D 508 GLN D 614 GLN F 434 GLN F 438 ASN F 508 GLN G 434 GLN H 434 GLN H 438 ASN H 508 GLN I 434 GLN I 438 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.196170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.116926 restraints weight = 24350.572| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.05 r_work: 0.3198 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 24471 Z= 0.270 Angle : 0.659 6.987 33156 Z= 0.335 Chirality : 0.050 0.292 3924 Planarity : 0.006 0.048 4239 Dihedral : 4.778 81.078 3303 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.43 % Allowed : 14.39 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 3006 helix: 1.40 (0.13), residues: 1404 sheet: -0.95 (0.21), residues: 549 loop : -0.94 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 590 TYR 0.019 0.003 TYR C 405 PHE 0.018 0.002 PHE G 483 TRP 0.012 0.002 TRP E 375 HIS 0.005 0.001 HIS A 564 Details of bonding type rmsd covalent geometry : bond 0.00633 (24471) covalent geometry : angle 0.65872 (33156) hydrogen bonds : bond 0.05848 ( 1188) hydrogen bonds : angle 4.47043 ( 3483) *********************** 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 410 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 318 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: E 369 ASP cc_start: 0.7364 (t0) cc_final: 0.7137 (t0) REVERT: E 563 ARG cc_start: 0.8006 (ttm170) cc_final: 0.7113 (pmt-80) REVERT: E 640 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7904 (ptpt) REVERT: E 662 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6920 (pp) REVERT: A 434 GLN cc_start: 0.6551 (OUTLIER) cc_final: 0.6087 (pt0) REVERT: A 442 GLN cc_start: 0.8469 (mm-40) cc_final: 0.7939 (mm-40) REVERT: A 563 ARG cc_start: 0.7775 (ttm170) cc_final: 0.6920 (pmt-80) REVERT: A 662 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.7074 (pp) REVERT: B 423 ILE cc_start: 0.7532 (OUTLIER) cc_final: 0.7030 (mm) REVERT: B 563 ARG cc_start: 0.7912 (ttm170) cc_final: 0.7003 (pmt-80) REVERT: B 662 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6944 (pp) REVERT: C 662 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6933 (pp) REVERT: D 563 ARG cc_start: 0.8010 (ttm170) cc_final: 0.7113 (pmt-80) REVERT: D 662 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.7056 (pp) REVERT: F 563 ARG cc_start: 0.7983 (ttp-170) cc_final: 0.7174 (pmt-80) REVERT: F 632 VAL cc_start: 0.8403 (t) cc_final: 0.8187 (p) REVERT: F 662 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6894 (pp) REVERT: G 563 ARG cc_start: 0.7984 (ttp-170) cc_final: 0.7159 (pmt-80) REVERT: G 662 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6983 (pp) REVERT: H 423 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7052 (mm) REVERT: H 562 ARG cc_start: 0.8698 (ptt90) cc_final: 0.8433 (ptt90) REVERT: H 563 ARG cc_start: 0.7791 (ttm170) cc_final: 0.6985 (pmt-80) REVERT: H 662 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7086 (pp) REVERT: I 496 MET cc_start: 0.9226 (mmm) cc_final: 0.8986 (mmm) REVERT: I 527 ARG cc_start: 0.8749 (mpt180) cc_final: 0.8084 (mtp180) REVERT: I 567 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7760 (tmt170) REVERT: I 614 GLN cc_start: 0.8804 (mt0) cc_final: 0.8547 (pt0) REVERT: I 662 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.7019 (pp) outliers start: 92 outliers final: 30 residues processed: 389 average time/residue: 0.7594 time to fit residues: 330.9271 Evaluate side-chains 342 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 298 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 640 LYS Chi-restraints excluded: chain E residue 662 LEU Chi-restraints excluded: chain E residue 666 VAL 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 423 ILE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 640 LYS Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 640 LYS Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 669 ILE Chi-restraints excluded: chain F residue 453 LYS Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain G residue 640 LYS Chi-restraints excluded: chain G residue 662 LEU Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain H residue 423 ILE Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain H residue 662 LEU Chi-restraints excluded: chain H residue 666 VAL 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 190 optimal weight: 0.7980 chunk 141 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 274 optimal weight: 10.0000 chunk 260 optimal weight: 0.9980 chunk 221 optimal weight: 5.9990 chunk 182 optimal weight: 0.6980 chunk 124 optimal weight: 0.0670 chunk 102 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 434 GLN E 508 GLN A 508 GLN B 434 GLN B 438 ASN B 508 GLN C 434 GLN D 434 GLN D 508 GLN F 434 GLN F 508 GLN G 434 GLN H 434 GLN H 438 ASN H 508 GLN I 434 GLN I 438 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.198687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.121501 restraints weight = 24344.771| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.00 r_work: 0.3250 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24471 Z= 0.105 Angle : 0.509 6.603 33156 Z= 0.254 Chirality : 0.042 0.189 3924 Planarity : 0.004 0.042 4239 Dihedral : 3.836 22.264 3285 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.54 % Allowed : 16.74 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.15), residues: 3006 helix: 1.91 (0.14), residues: 1413 sheet: -0.83 (0.21), residues: 549 loop : -0.84 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 590 TYR 0.012 0.001 TYR F 405 PHE 0.008 0.001 PHE H 378 TRP 0.009 0.001 TRP B 375 HIS 0.003 0.001 HIS A 564 Details of bonding type rmsd covalent geometry : bond 0.00229 (24471) covalent geometry : angle 0.50854 (33156) hydrogen bonds : bond 0.03754 ( 1188) hydrogen bonds : angle 4.02594 ( 3483) *********************** 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 389 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 321 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 453 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6866 (ptmm) REVERT: A 400 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7409 (pt) REVERT: A 453 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.6913 (ptmm) REVERT: A 563 ARG cc_start: 0.7829 (ttm170) cc_final: 0.7052 (pmt-80) REVERT: B 586 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7536 (mt-10) REVERT: B 662 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6916 (pp) REVERT: C 567 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7001 (tmm160) REVERT: D 662 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6943 (pp) REVERT: F 632 VAL cc_start: 0.8395 (t) cc_final: 0.8162 (p) REVERT: G 563 ARG cc_start: 0.7913 (ttp-170) cc_final: 0.7158 (pmt-80) REVERT: G 662 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6942 (pp) REVERT: H 434 GLN cc_start: 0.6857 (OUTLIER) cc_final: 0.6399 (pt0) REVERT: H 442 GLN cc_start: 0.8463 (mm-40) cc_final: 0.7820 (mm-40) REVERT: H 562 ARG cc_start: 0.8523 (ptt90) cc_final: 0.8294 (ptt90) REVERT: H 563 ARG cc_start: 0.7772 (ttm170) cc_final: 0.6979 (pmt-80) REVERT: H 574 LYS cc_start: 0.8210 (pttm) cc_final: 0.7815 (pmtt) REVERT: I 527 ARG cc_start: 0.8729 (mpt180) cc_final: 0.8097 (mtp180) REVERT: I 567 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7641 (tmt170) REVERT: I 614 GLN cc_start: 0.8784 (mt0) cc_final: 0.8539 (pt0) outliers start: 68 outliers final: 15 residues processed: 381 average time/residue: 0.7172 time to fit residues: 306.8329 Evaluate side-chains 320 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 296 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 453 LYS Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 666 VAL 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 566 LEU Chi-restraints excluded: chain C residue 567 ARG 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 F residue 581 ILE Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain G residue 585 ILE Chi-restraints excluded: chain G residue 662 LEU Chi-restraints excluded: chain H residue 434 GLN 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 666 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 87 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 434 GLN E 508 GLN A 434 GLN A 508 GLN B 508 GLN B 570 ASN C 434 GLN D 434 GLN D 570 ASN F 434 GLN F 508 GLN G 434 GLN H 508 GLN H 570 ASN I 434 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.196597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117663 restraints weight = 24311.399| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.06 r_work: 0.3206 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 24471 Z= 0.199 Angle : 0.600 7.561 33156 Z= 0.302 Chirality : 0.047 0.213 3924 Planarity : 0.005 0.040 4239 Dihedral : 4.138 26.453 3285 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.32 % Allowed : 16.74 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.15), residues: 3006 helix: 1.71 (0.13), residues: 1413 sheet: -0.88 (0.21), residues: 549 loop : -0.81 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 590 TYR 0.017 0.002 TYR A 405 PHE 0.014 0.002 PHE G 483 TRP 0.010 0.002 TRP B 375 HIS 0.004 0.001 HIS A 564 Details of bonding type rmsd covalent geometry : bond 0.00462 (24471) covalent geometry : angle 0.60028 (33156) hydrogen bonds : bond 0.05061 ( 1188) hydrogen bonds : angle 4.24656 ( 3483) *********************** REFINEMENT MACRO_CYCLE 4 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 405 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 316 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 563 ARG cc_start: 0.7997 (ttm170) cc_final: 0.7074 (pmt-80) REVERT: A 400 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7399 (pt) REVERT: A 423 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7119 (mm) REVERT: A 563 ARG cc_start: 0.7846 (ttm170) cc_final: 0.7005 (pmt-80) REVERT: B 563 ARG cc_start: 0.7906 (ttm170) cc_final: 0.7063 (pmt-80) REVERT: C 563 ARG cc_start: 0.7794 (ttm170) cc_final: 0.7026 (pmt-80) REVERT: C 567 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7038 (tmm160) REVERT: D 453 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.7119 (ptmm) REVERT: D 563 ARG cc_start: 0.7947 (ttm170) cc_final: 0.7079 (pmt-80) REVERT: D 586 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7558 (mt-10) REVERT: F 496 MET cc_start: 0.9215 (mmm) cc_final: 0.8930 (mmm) REVERT: F 563 ARG cc_start: 0.7976 (ttp-170) cc_final: 0.7144 (pmt-80) REVERT: F 586 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7521 (mt-10) REVERT: F 632 VAL cc_start: 0.8431 (t) cc_final: 0.8204 (p) REVERT: G 423 ILE cc_start: 0.7721 (OUTLIER) cc_final: 0.7138 (mm) REVERT: G 563 ARG cc_start: 0.7971 (ttp-170) cc_final: 0.7230 (pmt-80) REVERT: G 567 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7894 (tmt170) REVERT: H 562 ARG cc_start: 0.8680 (ptt90) cc_final: 0.8451 (ptt90) REVERT: H 563 ARG cc_start: 0.7814 (ttm170) cc_final: 0.7003 (pmt-80) REVERT: I 423 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7147 (mm) REVERT: I 496 MET cc_start: 0.9229 (mmm) cc_final: 0.8940 (mmm) REVERT: I 527 ARG cc_start: 0.8721 (mpt180) cc_final: 0.8072 (mtp180) REVERT: I 567 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7676 (tmt170) outliers start: 89 outliers final: 29 residues processed: 378 average time/residue: 0.7535 time to fit residues: 319.0466 Evaluate side-chains 335 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 298 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 353 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 423 ILE 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 666 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 640 LYS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 640 LYS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 453 LYS Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain F residue 453 LYS Chi-restraints excluded: chain F residue 580 ARG Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 567 ARG Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain G residue 585 ILE Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 422 LEU Chi-restraints excluded: chain I residue 423 ILE Chi-restraints excluded: chain I residue 567 ARG Chi-restraints excluded: chain I residue 581 ILE Chi-restraints excluded: chain I residue 666 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 152 optimal weight: 0.9990 chunk 237 optimal weight: 0.9990 chunk 247 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 93 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 434 GLN A 434 GLN A 508 GLN B 434 GLN B 570 ASN C 434 GLN D 434 GLN D 570 ASN F 434 GLN F 508 GLN G 434 GLN G 570 ASN H 434 GLN H 570 ASN I 434 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.197642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.120364 restraints weight = 24160.866| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.00 r_work: 0.3235 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24471 Z= 0.125 Angle : 0.539 7.208 33156 Z= 0.269 Chirality : 0.043 0.184 3924 Planarity : 0.004 0.050 4239 Dihedral : 3.911 25.500 3285 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.43 % Allowed : 17.23 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.15), residues: 3006 helix: 1.93 (0.14), residues: 1413 sheet: -0.80 (0.21), residues: 549 loop : -0.76 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 590 TYR 0.014 0.001 TYR C 405 PHE 0.009 0.001 PHE G 483 TRP 0.006 0.001 TRP I 375 HIS 0.003 0.001 HIS A 564 Details of bonding type rmsd covalent geometry : bond 0.00280 (24471) covalent geometry : angle 0.53945 (33156) hydrogen bonds : bond 0.04053 ( 1188) hydrogen bonds : angle 4.05198 ( 3483) *********************** REFINEMENT MACRO_CYCLE 5 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 407 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 315 time to evaluate : 0.975 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: E 563 ARG cc_start: 0.7960 (ttm170) cc_final: 0.7085 (pmt-80) REVERT: E 662 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6600 (pp) REVERT: A 400 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7396 (pt) REVERT: A 453 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.7117 (ptmm) REVERT: A 563 ARG cc_start: 0.7862 (ttm170) cc_final: 0.7073 (pmt-80) REVERT: A 662 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6535 (pp) REVERT: B 563 ARG cc_start: 0.7893 (ttm170) cc_final: 0.7021 (pmt-80) REVERT: B 578 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7837 (mp) REVERT: B 586 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7458 (mt-10) REVERT: C 563 ARG cc_start: 0.7781 (ttm170) cc_final: 0.7079 (pmt-80) REVERT: C 567 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.6981 (tmm160) REVERT: C 578 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7816 (mp) REVERT: C 662 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6374 (pp) REVERT: D 563 ARG cc_start: 0.7926 (ttm170) cc_final: 0.7068 (pmt-80) REVERT: D 578 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7921 (mp) REVERT: F 400 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7341 (pt) REVERT: F 423 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7084 (mm) REVERT: F 453 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6806 (ptmm) REVERT: F 563 ARG cc_start: 0.7920 (ttp-170) cc_final: 0.7039 (pmt-80) REVERT: F 586 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7516 (mt-10) REVERT: F 632 VAL cc_start: 0.8398 (t) cc_final: 0.8173 (p) REVERT: F 662 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.6276 (pp) REVERT: G 563 ARG cc_start: 0.7919 (ttp-170) cc_final: 0.7200 (pmt-80) REVERT: H 434 GLN cc_start: 0.6679 (OUTLIER) cc_final: 0.6361 (pt0) REVERT: H 442 GLN cc_start: 0.8493 (mm-40) cc_final: 0.7887 (mm-40) REVERT: H 562 ARG cc_start: 0.8625 (ptt90) cc_final: 0.8411 (ptt90) REVERT: H 563 ARG cc_start: 0.7812 (ttm170) cc_final: 0.6984 (pmt-80) REVERT: H 578 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7807 (mp) REVERT: H 662 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6403 (pp) REVERT: I 527 ARG cc_start: 0.8702 (mpt180) cc_final: 0.8094 (mtp180) REVERT: I 567 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7629 (tmt170) REVERT: I 662 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.6411 (pp) outliers start: 92 outliers final: 25 residues processed: 391 average time/residue: 0.7208 time to fit residues: 316.5659 Evaluate side-chains 338 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 295 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 662 LEU 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 A residue 662 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 578 ILE Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 GLN Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 453 LYS Chi-restraints excluded: chain F residue 578 ILE Chi-restraints excluded: chain F residue 580 ARG Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain G residue 585 ILE Chi-restraints excluded: chain H residue 434 GLN Chi-restraints excluded: chain H residue 578 ILE Chi-restraints excluded: chain H residue 580 ARG 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 422 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 Chi-restraints excluded: chain I residue 666 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 139 optimal weight: 9.9990 chunk 272 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 61 optimal weight: 0.0670 chunk 284 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 171 optimal weight: 0.7980 chunk 208 optimal weight: 8.9990 chunk 121 optimal weight: 0.0570 overall best weight: 0.5836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 434 GLN E 508 GLN A 434 GLN B 434 GLN B 508 GLN B 570 ASN C 434 GLN D 434 GLN D 570 ASN F 434 GLN F 508 GLN F 570 ASN G 434 GLN G 570 ASN H 434 GLN H 508 GLN H 570 ASN I 434 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.199276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.120762 restraints weight = 24300.634| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.06 r_work: 0.3248 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24471 Z= 0.102 Angle : 0.522 6.943 33156 Z= 0.262 Chirality : 0.043 0.257 3924 Planarity : 0.004 0.060 4239 Dihedral : 3.718 21.783 3285 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.95 % Allowed : 17.45 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.15), residues: 3006 helix: 2.11 (0.14), residues: 1413 sheet: -0.79 (0.21), residues: 549 loop : -0.74 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 590 TYR 0.011 0.001 TYR G 405 PHE 0.008 0.001 PHE H 378 TRP 0.006 0.001 TRP I 375 HIS 0.003 0.001 HIS A 564 Details of bonding type rmsd covalent geometry : bond 0.00220 (24471) covalent geometry : angle 0.52219 (33156) hydrogen bonds : bond 0.03494 ( 1188) hydrogen bonds : angle 3.90970 ( 3483) *********************** REFINEMENT MACRO_CYCLE 6 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 385 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 306 time to evaluate : 0.951 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: E 453 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.6829 (ptmm) REVERT: E 563 ARG cc_start: 0.7902 (ttm170) cc_final: 0.7076 (pmt-80) REVERT: E 662 LEU cc_start: 0.6295 (OUTLIER) cc_final: 0.6005 (pp) REVERT: A 369 ASP cc_start: 0.7154 (t0) cc_final: 0.6703 (m-30) REVERT: A 400 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7397 (pt) REVERT: A 563 ARG cc_start: 0.7865 (ttm170) cc_final: 0.7081 (pmt-80) REVERT: A 608 HIS cc_start: 0.8284 (m170) cc_final: 0.7936 (m-70) REVERT: A 662 LEU cc_start: 0.6460 (OUTLIER) cc_final: 0.6181 (pp) REVERT: B 527 ARG cc_start: 0.8754 (mpt180) cc_final: 0.8012 (mtp180) REVERT: B 578 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7798 (mp) REVERT: B 586 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7468 (mt-10) REVERT: B 662 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6050 (pp) REVERT: C 563 ARG cc_start: 0.7781 (ttm170) cc_final: 0.7067 (pmt-80) REVERT: C 567 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.6947 (tmm160) REVERT: C 578 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7806 (mp) REVERT: C 662 LEU cc_start: 0.6677 (OUTLIER) cc_final: 0.6358 (pp) REVERT: D 563 ARG cc_start: 0.7898 (ttm170) cc_final: 0.7045 (pmt-80) REVERT: D 578 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7913 (mp) REVERT: D 662 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6529 (pp) REVERT: F 453 LYS cc_start: 0.7277 (OUTLIER) cc_final: 0.6730 (ptmm) REVERT: F 586 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7414 (mt-10) REVERT: F 632 VAL cc_start: 0.8419 (t) cc_final: 0.8178 (p) REVERT: F 662 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6369 (pp) REVERT: G 563 ARG cc_start: 0.7911 (ttp-170) cc_final: 0.7163 (pmt-80) REVERT: G 608 HIS cc_start: 0.8266 (m170) cc_final: 0.8002 (m-70) REVERT: G 662 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6443 (pp) REVERT: H 498 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8232 (pmtt) REVERT: H 562 ARG cc_start: 0.8536 (ptt90) cc_final: 0.8327 (ptt90) REVERT: H 563 ARG cc_start: 0.7799 (ttm170) cc_final: 0.6987 (pmt-80) REVERT: H 578 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7774 (mp) REVERT: H 662 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6342 (pp) REVERT: I 527 ARG cc_start: 0.8709 (mpt180) cc_final: 0.8103 (mtp180) REVERT: I 567 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7652 (tmt170) REVERT: I 578 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7848 (mp) REVERT: I 662 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6578 (pp) outliers start: 79 outliers final: 18 residues processed: 370 average time/residue: 0.7567 time to fit residues: 312.9625 Evaluate side-chains 325 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 287 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 662 LEU Chi-restraints excluded: chain A residue 400 LEU 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 434 GLN Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 578 ILE Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain F residue 453 LYS Chi-restraints excluded: chain F residue 578 ILE Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain G residue 662 LEU Chi-restraints excluded: chain H residue 498 LYS Chi-restraints excluded: chain H residue 578 ILE 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 422 LEU Chi-restraints excluded: chain I residue 567 ARG Chi-restraints excluded: chain I residue 578 ILE Chi-restraints excluded: chain I residue 581 ILE Chi-restraints excluded: chain I residue 662 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 199 optimal weight: 3.9990 chunk 261 optimal weight: 0.6980 chunk 170 optimal weight: 5.9990 chunk 146 optimal weight: 0.0980 chunk 280 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 227 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 177 optimal weight: 3.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 434 GLN E 570 ASN A 434 GLN B 434 GLN B 570 ASN C 434 GLN C 570 ASN D 434 GLN D 570 ASN F 434 GLN F 508 GLN F 570 ASN G 434 GLN G 570 ASN H 434 GLN H 570 ASN I 434 GLN I 570 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.199419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.120837 restraints weight = 24352.436| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.07 r_work: 0.3248 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24471 Z= 0.103 Angle : 0.522 8.422 33156 Z= 0.261 Chirality : 0.042 0.189 3924 Planarity : 0.004 0.044 4239 Dihedral : 3.629 20.250 3285 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.95 % Allowed : 17.79 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.15), residues: 3006 helix: 2.15 (0.14), residues: 1413 sheet: -0.76 (0.21), residues: 549 loop : -0.71 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 590 TYR 0.012 0.001 TYR C 405 PHE 0.008 0.001 PHE H 378 TRP 0.008 0.001 TRP A 375 HIS 0.003 0.001 HIS H 564 Details of bonding type rmsd covalent geometry : bond 0.00222 (24471) covalent geometry : angle 0.52224 (33156) hydrogen bonds : bond 0.03455 ( 1188) hydrogen bonds : angle 3.86870 ( 3483) *********************** REFINEMENT MACRO_CYCLE 7 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 379 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 300 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 453 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.6841 (ptmm) REVERT: E 563 ARG cc_start: 0.7876 (ttm170) cc_final: 0.7079 (pmt-80) REVERT: E 662 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.6088 (pp) REVERT: A 369 ASP cc_start: 0.7162 (t0) cc_final: 0.6717 (m-30) REVERT: A 400 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7410 (pt) REVERT: A 563 ARG cc_start: 0.7848 (ttm170) cc_final: 0.7083 (pmt-80) REVERT: A 608 HIS cc_start: 0.8278 (m170) cc_final: 0.7920 (m-70) REVERT: A 662 LEU cc_start: 0.6693 (OUTLIER) cc_final: 0.6427 (pp) REVERT: B 563 ARG cc_start: 0.7888 (ttm170) cc_final: 0.7052 (pmt-80) REVERT: B 662 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.6375 (pp) REVERT: C 563 ARG cc_start: 0.7830 (ttm170) cc_final: 0.7085 (pmt-80) REVERT: C 567 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.6947 (tmm160) REVERT: C 578 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7752 (mp) REVERT: C 586 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7229 (tt0) REVERT: C 662 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6510 (pp) REVERT: D 563 ARG cc_start: 0.7919 (ttm170) cc_final: 0.7070 (pmt-80) REVERT: D 578 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7898 (mp) REVERT: D 662 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6520 (pp) REVERT: F 400 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7301 (pt) REVERT: F 453 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6757 (ptmm) REVERT: F 586 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7394 (mt-10) REVERT: F 632 VAL cc_start: 0.8388 (t) cc_final: 0.8147 (p) REVERT: F 662 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6434 (pp) REVERT: G 434 GLN cc_start: 0.6740 (OUTLIER) cc_final: 0.6514 (pt0) REVERT: G 563 ARG cc_start: 0.7888 (ttp-170) cc_final: 0.7090 (pmt-80) REVERT: G 567 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7753 (tmt170) REVERT: G 608 HIS cc_start: 0.8253 (m170) cc_final: 0.7964 (m-70) REVERT: G 662 LEU cc_start: 0.6666 (OUTLIER) cc_final: 0.6411 (pp) REVERT: H 562 ARG cc_start: 0.8559 (ptt90) cc_final: 0.8348 (ptt90) REVERT: H 563 ARG cc_start: 0.7842 (ttm170) cc_final: 0.7003 (pmt-80) REVERT: H 614 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8404 (pm20) REVERT: H 662 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6390 (pp) REVERT: I 527 ARG cc_start: 0.8696 (mpt180) cc_final: 0.8082 (mtp180) REVERT: I 567 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7646 (tmt170) REVERT: I 578 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7825 (mp) REVERT: I 662 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6490 (pp) outliers start: 79 outliers final: 18 residues processed: 362 average time/residue: 0.7698 time to fit residues: 311.1796 Evaluate side-chains 324 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 284 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 662 LEU Chi-restraints excluded: chain A residue 400 LEU 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 581 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 578 ILE Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain D residue 434 GLN Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 453 LYS Chi-restraints excluded: chain F residue 578 ILE Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain G residue 434 GLN Chi-restraints excluded: chain G residue 567 ARG Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain G residue 662 LEU Chi-restraints excluded: chain H residue 570 ASN Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain H residue 614 GLN Chi-restraints excluded: chain H residue 662 LEU Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 422 LEU Chi-restraints excluded: chain I residue 567 ARG Chi-restraints excluded: chain I residue 578 ILE Chi-restraints excluded: chain I residue 581 ILE Chi-restraints excluded: chain I residue 662 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 137 optimal weight: 5.9990 chunk 202 optimal weight: 0.1980 chunk 179 optimal weight: 0.8980 chunk 292 optimal weight: 6.9990 chunk 283 optimal weight: 0.5980 chunk 131 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 264 optimal weight: 0.1980 chunk 155 optimal weight: 9.9990 chunk 185 optimal weight: 0.0060 chunk 43 optimal weight: 8.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 434 GLN E 570 ASN A 434 GLN B 434 GLN C 434 GLN C 570 ASN D 434 GLN F 434 GLN F 508 GLN F 570 ASN G 434 GLN G 564 HIS G 570 ASN H 570 ASN I 434 GLN I 570 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.200538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.122430 restraints weight = 24472.054| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.07 r_work: 0.3268 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24471 Z= 0.093 Angle : 0.511 6.379 33156 Z= 0.256 Chirality : 0.042 0.209 3924 Planarity : 0.004 0.049 4239 Dihedral : 3.511 19.097 3285 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.61 % Allowed : 18.49 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.15), residues: 3006 helix: 2.20 (0.14), residues: 1413 sheet: -0.78 (0.21), residues: 549 loop : -0.71 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 590 TYR 0.009 0.001 TYR G 405 PHE 0.006 0.001 PHE H 378 TRP 0.010 0.001 TRP A 375 HIS 0.005 0.001 HIS H 564 Details of bonding type rmsd covalent geometry : bond 0.00197 (24471) covalent geometry : angle 0.51075 (33156) hydrogen bonds : bond 0.03082 ( 1188) hydrogen bonds : angle 3.77675 ( 3483) *********************** REFINEMENT MACRO_CYCLE 8 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 363 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 293 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 400 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7397 (pt) REVERT: E 444 CYS cc_start: 0.7688 (m) cc_final: 0.7392 (t) REVERT: A 369 ASP cc_start: 0.7124 (t0) cc_final: 0.6688 (m-30) REVERT: A 444 CYS cc_start: 0.7735 (m) cc_final: 0.7371 (t) REVERT: A 608 HIS cc_start: 0.8266 (m170) cc_final: 0.7910 (m-70) REVERT: A 614 GLN cc_start: 0.8700 (mt0) cc_final: 0.8460 (mp10) REVERT: B 578 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7736 (mp) REVERT: B 586 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7375 (mt-10) REVERT: B 662 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6489 (pp) REVERT: C 563 ARG cc_start: 0.7825 (ttm170) cc_final: 0.7089 (pmt-80) REVERT: C 567 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.6938 (tmm160) REVERT: C 578 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7753 (mp) REVERT: C 586 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7166 (tt0) REVERT: D 578 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7868 (mp) REVERT: D 662 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6612 (pp) REVERT: F 400 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7386 (pt) REVERT: F 586 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7453 (mt-10) REVERT: F 632 VAL cc_start: 0.8335 (t) cc_final: 0.8094 (p) REVERT: F 662 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.6329 (pp) REVERT: G 563 ARG cc_start: 0.7874 (ttp-170) cc_final: 0.7120 (pmt-80) REVERT: G 608 HIS cc_start: 0.8249 (m170) cc_final: 0.7991 (m-70) REVERT: G 662 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.6303 (pp) REVERT: H 562 ARG cc_start: 0.8494 (ptt90) cc_final: 0.8289 (ptt90) REVERT: H 563 ARG cc_start: 0.7812 (ttm170) cc_final: 0.7012 (pmt-80) REVERT: H 578 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7808 (mp) REVERT: H 614 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8400 (pm20) REVERT: H 662 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6460 (pp) REVERT: I 527 ARG cc_start: 0.8682 (mpt180) cc_final: 0.8080 (mtp180) REVERT: I 567 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7626 (tmt170) REVERT: I 578 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7756 (mp) outliers start: 70 outliers final: 17 residues processed: 352 average time/residue: 0.7751 time to fit residues: 304.9405 Evaluate side-chains 316 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 283 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 614 GLN Chi-restraints excluded: chain E residue 662 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 578 ILE Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 578 ILE Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain G residue 662 LEU Chi-restraints excluded: chain H residue 578 ILE Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain H residue 614 GLN Chi-restraints excluded: chain H residue 662 LEU Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 567 ARG Chi-restraints excluded: chain I residue 578 ILE Chi-restraints excluded: chain I residue 581 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 59 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 215 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 148 optimal weight: 0.9980 chunk 218 optimal weight: 0.6980 chunk 296 optimal weight: 20.0000 chunk 254 optimal weight: 0.6980 chunk 186 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 434 GLN E 570 ASN A 434 GLN A 570 ASN B 434 GLN B 570 ASN C 434 GLN C 570 ASN D 434 GLN F 434 GLN F 508 GLN F 570 ASN G 434 GLN G 564 HIS G 570 ASN I 434 GLN I 570 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.198597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.120199 restraints weight = 24452.736| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.06 r_work: 0.3233 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24471 Z= 0.124 Angle : 0.557 8.456 33156 Z= 0.280 Chirality : 0.043 0.187 3924 Planarity : 0.005 0.054 4239 Dihedral : 3.695 22.622 3285 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.42 % Allowed : 19.13 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.15), residues: 3006 helix: 2.08 (0.14), residues: 1413 sheet: -0.78 (0.21), residues: 549 loop : -0.69 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 590 TYR 0.015 0.002 TYR C 405 PHE 0.008 0.001 PHE G 378 TRP 0.012 0.001 TRP I 375 HIS 0.003 0.001 HIS A 564 Details of bonding type rmsd covalent geometry : bond 0.00276 (24471) covalent geometry : angle 0.55661 (33156) hydrogen bonds : bond 0.03900 ( 1188) hydrogen bonds : angle 3.93904 ( 3483) *********************** REFINEMENT MACRO_CYCLE 9 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 352 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 287 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 563 ARG cc_start: 0.7992 (ttp-170) cc_final: 0.7180 (pmt-80) REVERT: A 369 ASP cc_start: 0.7218 (t0) cc_final: 0.6766 (m-30) REVERT: A 563 ARG cc_start: 0.7898 (ttp-110) cc_final: 0.7187 (pmt-80) REVERT: A 608 HIS cc_start: 0.8289 (m170) cc_final: 0.7925 (m-70) REVERT: A 614 GLN cc_start: 0.8700 (mt0) cc_final: 0.8459 (mp10) REVERT: B 563 ARG cc_start: 0.7900 (ttm170) cc_final: 0.7042 (pmt-80) REVERT: B 578 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7767 (mp) REVERT: B 662 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6661 (pp) REVERT: C 563 ARG cc_start: 0.7885 (ttm170) cc_final: 0.7125 (pmt-80) REVERT: C 567 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.6941 (tmm160) REVERT: C 578 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7707 (mp) REVERT: C 586 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7231 (tt0) REVERT: D 563 ARG cc_start: 0.7892 (ttm170) cc_final: 0.6948 (pmt-80) REVERT: D 662 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6752 (pp) REVERT: F 400 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7290 (pt) REVERT: F 586 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7355 (mt-10) REVERT: F 632 VAL cc_start: 0.8360 (t) cc_final: 0.8126 (p) REVERT: G 563 ARG cc_start: 0.7922 (ttp-170) cc_final: 0.7170 (pmt-80) REVERT: G 567 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7748 (tmt170) REVERT: G 608 HIS cc_start: 0.8267 (m170) cc_final: 0.7980 (m-70) REVERT: G 662 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6270 (pp) REVERT: H 442 GLN cc_start: 0.8554 (mm-40) cc_final: 0.8222 (mm-40) REVERT: H 562 ARG cc_start: 0.8592 (ptt90) cc_final: 0.8384 (ptt90) REVERT: H 563 ARG cc_start: 0.7829 (ttm170) cc_final: 0.6998 (pmt-80) REVERT: H 578 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7759 (mp) REVERT: H 614 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8401 (pm20) REVERT: I 527 ARG cc_start: 0.8685 (mpt180) cc_final: 0.8072 (mtp180) REVERT: I 567 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7607 (tmt170) REVERT: I 578 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7766 (mp) outliers start: 65 outliers final: 24 residues processed: 340 average time/residue: 0.7902 time to fit residues: 299.8634 Evaluate side-chains 316 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 279 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 570 ASN Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 614 GLN Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 578 ILE Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 614 GLN Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 578 ILE Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 640 LYS Chi-restraints excluded: chain G residue 567 ARG Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain G residue 662 LEU Chi-restraints excluded: chain H residue 484 ILE Chi-restraints excluded: chain H residue 578 ILE Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain H residue 614 GLN Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain I residue 412 LEU Chi-restraints excluded: chain I residue 567 ARG Chi-restraints excluded: chain I residue 578 ILE Chi-restraints excluded: chain I residue 581 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 25 optimal weight: 9.9990 chunk 174 optimal weight: 0.0970 chunk 133 optimal weight: 0.2980 chunk 150 optimal weight: 0.6980 chunk 252 optimal weight: 0.8980 chunk 210 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 284 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 171 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 434 GLN E 570 ASN A 434 GLN A 570 ASN B 434 GLN C 434 GLN C 570 ASN D 434 GLN F 434 GLN G 564 HIS I 434 GLN I 570 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.199833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.121448 restraints weight = 24438.286| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.07 r_work: 0.3262 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24471 Z= 0.101 Angle : 0.545 8.677 33156 Z= 0.272 Chirality : 0.042 0.199 3924 Planarity : 0.005 0.066 4239 Dihedral : 3.609 22.387 3285 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.86 % Allowed : 19.84 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.15), residues: 3006 helix: 2.09 (0.14), residues: 1413 sheet: -0.76 (0.21), residues: 549 loop : -0.67 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 590 TYR 0.010 0.001 TYR G 405 PHE 0.007 0.001 PHE A 378 TRP 0.009 0.001 TRP A 375 HIS 0.003 0.001 HIS I 564 Details of bonding type rmsd covalent geometry : bond 0.00215 (24471) covalent geometry : angle 0.54469 (33156) hydrogen bonds : bond 0.03319 ( 1188) hydrogen bonds : angle 3.84649 ( 3483) ********************** REFINEMENT MACRO_CYCLE 10 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 337 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 287 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 563 ARG cc_start: 0.7978 (ttp-170) cc_final: 0.7143 (pmt-80) REVERT: A 369 ASP cc_start: 0.7179 (t0) cc_final: 0.6746 (m-30) REVERT: A 563 ARG cc_start: 0.7901 (ttp-110) cc_final: 0.7187 (pmt-80) REVERT: A 608 HIS cc_start: 0.8252 (m170) cc_final: 0.7893 (m-70) REVERT: A 614 GLN cc_start: 0.8698 (mt0) cc_final: 0.8457 (mp10) REVERT: B 563 ARG cc_start: 0.7889 (ttm170) cc_final: 0.7034 (pmt-80) REVERT: B 578 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7767 (mp) REVERT: B 586 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7363 (mt-10) REVERT: C 563 ARG cc_start: 0.7887 (ttm170) cc_final: 0.7127 (pmt-80) REVERT: C 567 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.6947 (tmm160) REVERT: C 578 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7743 (mp) REVERT: C 586 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7189 (tt0) REVERT: D 563 ARG cc_start: 0.7924 (ttm170) cc_final: 0.6980 (pmt-80) REVERT: F 400 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7392 (pt) REVERT: F 586 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7416 (mt-10) REVERT: F 632 VAL cc_start: 0.8335 (t) cc_final: 0.8098 (p) REVERT: G 563 ARG cc_start: 0.7911 (ttp-170) cc_final: 0.7158 (pmt-80) REVERT: G 608 HIS cc_start: 0.8295 (m170) cc_final: 0.8005 (m-70) REVERT: H 562 ARG cc_start: 0.8541 (ptt90) cc_final: 0.8337 (ptt90) REVERT: H 563 ARG cc_start: 0.7873 (ttm170) cc_final: 0.7010 (pmt-80) REVERT: H 578 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7764 (mp) REVERT: I 527 ARG cc_start: 0.8656 (mpt180) cc_final: 0.8066 (mtp180) REVERT: I 567 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7619 (tmt170) REVERT: I 578 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7750 (mp) outliers start: 50 outliers final: 26 residues processed: 331 average time/residue: 0.7880 time to fit residues: 291.0931 Evaluate side-chains 313 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 279 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 614 GLN Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 578 ILE Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 GLN Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 614 GLN Chi-restraints excluded: chain D residue 669 ILE Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 578 ILE Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain H residue 484 ILE Chi-restraints excluded: chain H residue 578 ILE Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain H residue 614 GLN Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain I residue 567 ARG Chi-restraints excluded: chain I residue 578 ILE Chi-restraints excluded: chain I residue 581 ILE Chi-restraints excluded: chain I residue 614 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 9 optimal weight: 9.9990 chunk 73 optimal weight: 0.0270 chunk 245 optimal weight: 0.5980 chunk 204 optimal weight: 0.7980 chunk 203 optimal weight: 5.9990 chunk 233 optimal weight: 0.9990 chunk 50 optimal weight: 0.0060 chunk 193 optimal weight: 3.9990 chunk 191 optimal weight: 10.0000 chunk 273 optimal weight: 10.0000 chunk 222 optimal weight: 0.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 434 GLN E 570 ASN A 434 GLN A 570 ASN B 434 GLN C 434 GLN C 570 ASN D 434 GLN F 434 GLN F 508 GLN G 564 HIS I 434 GLN I 570 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.200037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.121706 restraints weight = 24355.359| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.08 r_work: 0.3259 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24471 Z= 0.100 Angle : 0.548 8.172 33156 Z= 0.271 Chirality : 0.042 0.179 3924 Planarity : 0.005 0.064 4239 Dihedral : 3.572 21.242 3285 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.79 % Allowed : 19.99 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.15), residues: 3006 helix: 2.10 (0.14), residues: 1413 sheet: -0.76 (0.21), residues: 549 loop : -0.63 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 590 TYR 0.011 0.001 TYR G 405 PHE 0.007 0.001 PHE H 378 TRP 0.010 0.001 TRP A 375 HIS 0.003 0.001 HIS I 564 Details of bonding type rmsd covalent geometry : bond 0.00213 (24471) covalent geometry : angle 0.54762 (33156) hydrogen bonds : bond 0.03291 ( 1188) hydrogen bonds : angle 3.83603 ( 3483) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16568.04 seconds wall clock time: 280 minutes 1.85 seconds (16801.85 seconds total)