Starting phenix.real_space_refine on Tue Mar 19 11:55:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7feb_31551/03_2024/7feb_31551.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7feb_31551/03_2024/7feb_31551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7feb_31551/03_2024/7feb_31551.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7feb_31551/03_2024/7feb_31551.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7feb_31551/03_2024/7feb_31551.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7feb_31551/03_2024/7feb_31551.pdb" } resolution = 2.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 15354 2.51 5 N 4140 2.21 5 O 4473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24075 Number of models: 1 Model: "" Number of chains: 9 Chain: "E" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "A" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "B" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "C" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "D" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "F" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "G" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "H" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "I" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Time building chain proxies: 14.47, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.23 Conformation dependent library (CDL) restraints added in 4.3 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: 2.56 Creating SS restraints... Processing helix chain 'E' and resid 365 through 382 Processing helix chain 'E' and resid 447 through 458 Processing helix chain 'E' and resid 464 through 479 removed outlier: 4.009A pdb=" N ILE E 468 " --> pdb=" O GLY E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 484 removed outlier: 3.807A pdb=" N ILE E 484 " --> pdb=" O GLY E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 485 through 497 Processing helix chain 'E' and resid 500 through 511 Processing helix chain 'E' and resid 512 through 526 removed outlier: 3.609A pdb=" N GLU E 526 " --> pdb=" O ARG E 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 544 Processing helix chain 'E' and resid 549 through 561 Processing helix chain 'E' and resid 561 through 570 Processing helix chain 'E' and resid 582 through 591 Processing helix chain 'E' and resid 605 through 619 Processing helix chain 'E' and resid 631 through 633 No H-bonds generated for 'chain 'E' and resid 631 through 633' Processing helix chain 'E' and resid 634 through 643 Processing helix chain 'E' and resid 655 through 657 No H-bonds generated for 'chain 'E' and resid 655 through 657' Processing helix chain 'A' and resid 365 through 382 Processing helix chain 'A' and resid 447 through 458 Processing helix chain 'A' and resid 464 through 479 removed outlier: 4.009A pdb=" N ILE A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 484 removed outlier: 3.807A pdb=" N ILE A 484 " --> pdb=" O GLY A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 497 Processing helix chain 'A' and resid 500 through 511 Processing helix chain 'A' and resid 512 through 526 removed outlier: 3.609A pdb=" N GLU A 526 " --> pdb=" O ARG A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 544 Processing helix chain 'A' and resid 549 through 561 Processing helix chain 'A' and resid 561 through 570 Processing helix chain 'A' and resid 582 through 591 Processing helix chain 'A' and resid 605 through 619 Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 634 through 643 Processing helix chain 'A' and resid 655 through 657 No H-bonds generated for 'chain 'A' and resid 655 through 657' Processing helix chain 'B' and resid 365 through 382 Processing helix chain 'B' and resid 447 through 458 Processing helix chain 'B' and resid 464 through 479 removed outlier: 4.008A pdb=" N ILE B 468 " --> pdb=" O GLY B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 484 removed outlier: 3.807A pdb=" N ILE B 484 " --> pdb=" O GLY B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 497 Processing helix chain 'B' and resid 500 through 511 Processing helix chain 'B' and resid 512 through 526 removed outlier: 3.609A pdb=" N GLU B 526 " --> pdb=" O ARG B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 544 Processing helix chain 'B' and resid 549 through 561 Processing helix chain 'B' and resid 561 through 570 Processing helix chain 'B' and resid 582 through 591 Processing helix chain 'B' and resid 605 through 619 Processing helix chain 'B' and resid 631 through 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 634 through 643 Processing helix chain 'B' and resid 655 through 657 No H-bonds generated for 'chain 'B' and resid 655 through 657' Processing helix chain 'C' and resid 365 through 382 Processing helix chain 'C' and resid 447 through 458 Processing helix chain 'C' and resid 464 through 479 removed outlier: 4.009A pdb=" N ILE C 468 " --> pdb=" O GLY C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 484 removed outlier: 3.808A pdb=" N ILE C 484 " --> pdb=" O GLY C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 497 Processing helix chain 'C' and resid 500 through 511 Processing helix chain 'C' and resid 512 through 526 removed outlier: 3.608A pdb=" N GLU C 526 " --> pdb=" O ARG C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 544 Processing helix chain 'C' and resid 549 through 561 Processing helix chain 'C' and resid 561 through 570 Processing helix chain 'C' and resid 582 through 591 Processing helix chain 'C' and resid 605 through 619 Processing helix chain 'C' and resid 631 through 633 No H-bonds generated for 'chain 'C' and resid 631 through 633' Processing helix chain 'C' and resid 634 through 643 Processing helix chain 'C' and resid 655 through 657 No H-bonds generated for 'chain 'C' and resid 655 through 657' Processing helix chain 'D' and resid 365 through 382 Processing helix chain 'D' and resid 447 through 458 Processing helix chain 'D' and resid 464 through 479 removed outlier: 4.009A pdb=" N ILE D 468 " --> pdb=" O GLY D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 484 removed outlier: 3.807A pdb=" N ILE D 484 " --> pdb=" O GLY D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 497 Processing helix chain 'D' and resid 500 through 511 Processing helix chain 'D' and resid 512 through 526 removed outlier: 3.608A pdb=" N GLU D 526 " --> pdb=" O ARG D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 544 Processing helix chain 'D' and resid 549 through 561 Processing helix chain 'D' and resid 561 through 570 Processing helix chain 'D' and resid 582 through 591 Processing helix chain 'D' and resid 605 through 619 Processing helix chain 'D' and resid 631 through 633 No H-bonds generated for 'chain 'D' and resid 631 through 633' Processing helix chain 'D' and resid 634 through 643 Processing helix chain 'D' and resid 655 through 657 No H-bonds generated for 'chain 'D' and resid 655 through 657' Processing helix chain 'F' and resid 365 through 382 Processing helix chain 'F' and resid 447 through 458 Processing helix chain 'F' and resid 464 through 479 removed outlier: 4.009A pdb=" N ILE F 468 " --> pdb=" O GLY F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 484 removed outlier: 3.807A pdb=" N ILE F 484 " --> pdb=" O GLY F 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 485 through 497 Processing helix chain 'F' and resid 500 through 511 Processing helix chain 'F' and resid 512 through 526 removed outlier: 3.609A pdb=" N GLU F 526 " --> pdb=" O ARG F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 544 Processing helix chain 'F' and resid 549 through 561 Processing helix chain 'F' and resid 561 through 570 Processing helix chain 'F' and resid 582 through 591 Processing helix chain 'F' and resid 605 through 619 Processing helix chain 'F' and resid 631 through 633 No H-bonds generated for 'chain 'F' and resid 631 through 633' Processing helix chain 'F' and resid 634 through 643 Processing helix chain 'F' and resid 655 through 657 No H-bonds generated for 'chain 'F' and resid 655 through 657' Processing helix chain 'G' and resid 365 through 382 Processing helix chain 'G' and resid 447 through 458 Processing helix chain 'G' and resid 464 through 479 removed outlier: 4.009A pdb=" N ILE G 468 " --> pdb=" O GLY G 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 480 through 484 removed outlier: 3.807A pdb=" N ILE G 484 " --> pdb=" O GLY G 481 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 497 Processing helix chain 'G' and resid 500 through 511 Processing helix chain 'G' and resid 512 through 526 removed outlier: 3.609A pdb=" N GLU G 526 " --> pdb=" O ARG G 522 " (cutoff:3.500A) Processing helix chain 'G' and resid 532 through 544 Processing helix chain 'G' and resid 549 through 561 Processing helix chain 'G' and resid 561 through 570 Processing helix chain 'G' and resid 582 through 591 Processing helix chain 'G' and resid 605 through 619 Processing helix chain 'G' and resid 631 through 633 No H-bonds generated for 'chain 'G' and resid 631 through 633' Processing helix chain 'G' and resid 634 through 643 Processing helix chain 'G' and resid 655 through 657 No H-bonds generated for 'chain 'G' and resid 655 through 657' Processing helix chain 'H' and resid 365 through 382 Processing helix chain 'H' and resid 447 through 458 Processing helix chain 'H' and resid 464 through 479 removed outlier: 4.009A pdb=" N ILE H 468 " --> pdb=" O GLY H 464 " (cutoff:3.500A) Processing helix chain 'H' and resid 480 through 484 removed outlier: 3.807A pdb=" N ILE H 484 " --> pdb=" O GLY H 481 " (cutoff:3.500A) Processing helix chain 'H' and resid 485 through 497 Processing helix chain 'H' and resid 500 through 511 Processing helix chain 'H' and resid 512 through 526 removed outlier: 3.608A pdb=" N GLU H 526 " --> pdb=" O ARG H 522 " (cutoff:3.500A) Processing helix chain 'H' and resid 532 through 544 Processing helix chain 'H' and resid 549 through 561 Processing helix chain 'H' and resid 561 through 570 Processing helix chain 'H' and resid 582 through 591 Processing helix chain 'H' and resid 605 through 619 Processing helix chain 'H' and resid 631 through 633 No H-bonds generated for 'chain 'H' and resid 631 through 633' Processing helix chain 'H' and resid 634 through 643 Processing helix chain 'H' and resid 655 through 657 No H-bonds generated for 'chain 'H' and resid 655 through 657' Processing helix chain 'I' and resid 365 through 382 Processing helix chain 'I' and resid 447 through 458 Processing helix chain 'I' and resid 464 through 479 removed outlier: 4.009A pdb=" N ILE I 468 " --> pdb=" O GLY I 464 " (cutoff:3.500A) Processing helix chain 'I' and resid 480 through 484 removed outlier: 3.808A pdb=" N ILE I 484 " --> pdb=" O GLY I 481 " (cutoff:3.500A) Processing helix chain 'I' and resid 485 through 497 Processing helix chain 'I' and resid 500 through 511 Processing helix chain 'I' and resid 512 through 526 removed outlier: 3.609A pdb=" N GLU I 526 " --> pdb=" O ARG I 522 " (cutoff:3.500A) Processing helix chain 'I' and resid 532 through 544 Processing helix chain 'I' and resid 549 through 561 Processing helix chain 'I' and resid 561 through 570 Processing helix chain 'I' and resid 582 through 591 Processing helix chain 'I' and resid 605 through 619 Processing helix chain 'I' and resid 631 through 633 No H-bonds generated for 'chain 'I' and resid 631 through 633' Processing helix chain 'I' and resid 634 through 643 Processing helix chain 'I' and resid 655 through 657 No H-bonds generated for 'chain 'I' and resid 655 through 657' Processing sheet with id=AA1, first strand: chain 'E' and resid 389 through 392 removed outlier: 6.457A pdb=" N LEU E 404 " --> pdb=" O PRO E 408 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 420 through 423 removed outlier: 3.642A pdb=" N TYR E 420 " --> pdb=" O LEU E 446 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 651 through 653 removed outlier: 6.331A pdb=" N ILE E 628 " --> pdb=" O LEU E 652 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE E 578 " --> pdb=" O VAL E 666 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER E 668 " --> pdb=" O ILE E 578 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG E 580 " --> pdb=" O SER E 668 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 593 through 596 Processing sheet with id=AA5, first strand: chain 'A' and resid 389 through 392 removed outlier: 6.458A pdb=" N LEU A 404 " --> pdb=" O PRO A 408 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 420 through 423 removed outlier: 3.642A pdb=" N TYR A 420 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 651 through 653 removed outlier: 6.331A pdb=" N ILE A 628 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE A 578 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER A 668 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG A 580 " --> pdb=" O SER A 668 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 593 through 596 Processing sheet with id=AA9, first strand: chain 'B' and resid 389 through 392 removed outlier: 6.457A pdb=" N LEU B 404 " --> pdb=" O PRO B 408 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 420 through 423 removed outlier: 3.642A pdb=" N TYR B 420 " --> pdb=" O LEU B 446 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 651 through 653 removed outlier: 6.331A pdb=" N ILE B 628 " --> pdb=" O LEU B 652 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE B 578 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER B 668 " --> pdb=" O ILE B 578 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG B 580 " --> pdb=" O SER B 668 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 593 through 596 Processing sheet with id=AB4, first strand: chain 'C' and resid 389 through 392 removed outlier: 6.457A pdb=" N LEU C 404 " --> pdb=" O PRO C 408 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 420 through 423 removed outlier: 3.642A pdb=" N TYR C 420 " --> pdb=" O LEU C 446 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 651 through 653 removed outlier: 6.331A pdb=" N ILE C 628 " --> pdb=" O LEU C 652 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE C 578 " --> pdb=" O VAL C 666 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER C 668 " --> pdb=" O ILE C 578 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG C 580 " --> pdb=" O SER C 668 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 593 through 596 Processing sheet with id=AB8, first strand: chain 'D' and resid 389 through 392 removed outlier: 6.457A pdb=" N LEU D 404 " --> pdb=" O PRO D 408 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 420 through 423 removed outlier: 3.642A pdb=" N TYR D 420 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 651 through 653 removed outlier: 6.332A pdb=" N ILE D 628 " --> pdb=" O LEU D 652 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE D 578 " --> pdb=" O VAL D 666 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER D 668 " --> pdb=" O ILE D 578 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG D 580 " --> pdb=" O SER D 668 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 593 through 596 Processing sheet with id=AC3, first strand: chain 'F' and resid 389 through 392 removed outlier: 6.457A pdb=" N LEU F 404 " --> pdb=" O PRO F 408 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 420 through 423 removed outlier: 3.641A pdb=" N TYR F 420 " --> pdb=" O LEU F 446 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 651 through 653 removed outlier: 6.332A pdb=" N ILE F 628 " --> pdb=" O LEU F 652 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE F 578 " --> pdb=" O VAL F 666 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER F 668 " --> pdb=" O ILE F 578 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG F 580 " --> pdb=" O SER F 668 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 593 through 596 Processing sheet with id=AC7, first strand: chain 'G' and resid 389 through 392 removed outlier: 6.458A pdb=" N LEU G 404 " --> pdb=" O PRO G 408 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 420 through 423 removed outlier: 3.642A pdb=" N TYR G 420 " --> pdb=" O LEU G 446 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 651 through 653 removed outlier: 6.332A pdb=" N ILE G 628 " --> pdb=" O LEU G 652 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE G 578 " --> pdb=" O VAL G 666 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER G 668 " --> pdb=" O ILE G 578 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG G 580 " --> pdb=" O SER G 668 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 593 through 596 Processing sheet with id=AD2, first strand: chain 'H' and resid 389 through 392 removed outlier: 6.458A pdb=" N LEU H 404 " --> pdb=" O PRO H 408 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 420 through 423 removed outlier: 3.641A pdb=" N TYR H 420 " --> pdb=" O LEU H 446 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 651 through 653 removed outlier: 6.331A pdb=" N ILE H 628 " --> pdb=" O LEU H 652 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE H 578 " --> pdb=" O VAL H 666 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER H 668 " --> pdb=" O ILE H 578 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG H 580 " --> pdb=" O SER H 668 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 593 through 596 Processing sheet with id=AD6, first strand: chain 'I' and resid 389 through 392 removed outlier: 6.458A pdb=" N LEU I 404 " --> pdb=" O PRO I 408 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 420 through 423 removed outlier: 3.642A pdb=" N TYR I 420 " --> pdb=" O LEU I 446 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 651 through 653 removed outlier: 6.331A pdb=" N ILE I 628 " --> pdb=" O LEU I 652 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE I 578 " --> pdb=" O VAL I 666 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER I 668 " --> pdb=" O ILE I 578 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG I 580 " --> pdb=" O SER I 668 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 593 through 596 1188 hydrogen bonds defined for protein. 3483 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.31 Time building geometry restraints manager: 10.99 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: 98.92 - 105.97: 586 105.97 - 113.02: 13629 113.02 - 120.06: 8526 120.06 - 127.11: 10169 127.11 - 134.15: 246 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 2.520 nonbonded pdb=" O LEU B 576 " pdb=" NE2 GLN B 664 " model vdw 2.211 2.520 nonbonded pdb=" O LEU I 576 " pdb=" NE2 GLN I 664 " model vdw 2.211 2.520 nonbonded pdb=" O LEU G 576 " pdb=" NE2 GLN G 664 " model vdw 2.212 2.520 nonbonded pdb=" O LEU D 576 " pdb=" NE2 GLN D 664 " model vdw 2.212 2.520 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' 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: 5.750 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: 21.630 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 64.840 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.160 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:12.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24471 Z= 0.234 Angle : 0.652 7.624 33156 Z= 0.386 Chirality : 0.046 0.230 3924 Planarity : 0.006 0.085 4239 Dihedral : 15.912 79.936 9396 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.30 % Allowed : 16.63 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 3006 helix: 1.22 (0.14), residues: 1395 sheet: -0.73 (0.21), residues: 549 loop : -1.01 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 375 HIS 0.003 0.001 HIS F 564 PHE 0.005 0.001 PHE C 378 TYR 0.011 0.001 TYR D 405 ARG 0.020 0.001 ARG D 590 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 365 time to evaluate : 2.907 Fit side-chains REVERT: A 438 ASN cc_start: 0.8407 (t0) cc_final: 0.8147 (t0) REVERT: A 562 ARG cc_start: 0.8209 (ptt90) cc_final: 0.7987 (ptt90) REVERT: B 438 ASN cc_start: 0.8444 (t0) cc_final: 0.8194 (t0) REVERT: C 632 VAL cc_start: 0.8509 (t) cc_final: 0.8303 (p) REVERT: F 632 VAL cc_start: 0.8369 (t) cc_final: 0.8150 (p) REVERT: G 563 ARG cc_start: 0.7436 (ttp-170) cc_final: 0.7229 (pmt-80) REVERT: H 438 ASN cc_start: 0.8446 (t0) cc_final: 0.8199 (t0) REVERT: H 562 ARG cc_start: 0.8232 (ptt90) cc_final: 0.7849 (ptt90) outliers start: 8 outliers final: 13 residues processed: 365 average time/residue: 1.6078 time to fit residues: 656.7321 Evaluate side-chains 312 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 299 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 610 THR Chi-restraints excluded: chain E residue 633 ASP Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 633 ASP Chi-restraints excluded: chain G residue 610 THR Chi-restraints excluded: chain G residue 633 ASP Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 633 ASP Chi-restraints excluded: chain I residue 610 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 0.9980 chunk 225 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 232 optimal weight: 5.9990 chunk 90 optimal weight: 0.0870 chunk 141 optimal weight: 2.9990 chunk 173 optimal weight: 0.0570 chunk 269 optimal weight: 0.7980 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 434 GLN E 438 ASN A 434 GLN A 438 ASN B 434 GLN B 438 ASN C 434 GLN C 438 ASN D 434 GLN D 438 ASN D 614 GLN F 434 GLN F 438 ASN F 508 GLN G 434 GLN H 434 GLN H 438 ASN I 434 GLN I 438 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 24471 Z= 0.134 Angle : 0.488 5.835 33156 Z= 0.242 Chirality : 0.041 0.203 3924 Planarity : 0.004 0.038 4239 Dihedral : 4.152 100.633 3303 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.87 % Allowed : 15.59 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.16), residues: 3006 helix: 1.87 (0.14), residues: 1413 sheet: -0.74 (0.21), residues: 549 loop : -0.89 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 375 HIS 0.003 0.001 HIS A 564 PHE 0.008 0.001 PHE F 378 TYR 0.011 0.001 TYR C 405 ARG 0.010 0.000 ARG F 590 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 296 time to evaluate : 2.733 Fit side-chains REVERT: E 453 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7010 (ptmm) REVERT: E 662 LEU cc_start: 0.6287 (OUTLIER) cc_final: 0.5987 (pp) REVERT: A 400 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7469 (pt) REVERT: A 453 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7138 (ptmm) REVERT: A 562 ARG cc_start: 0.8238 (ptt90) cc_final: 0.7948 (ptt90) REVERT: A 662 LEU cc_start: 0.6461 (OUTLIER) cc_final: 0.6185 (pp) REVERT: B 662 LEU cc_start: 0.6501 (OUTLIER) cc_final: 0.6190 (pp) REVERT: C 632 VAL cc_start: 0.8479 (t) cc_final: 0.8237 (p) REVERT: C 662 LEU cc_start: 0.6314 (OUTLIER) cc_final: 0.6036 (pp) REVERT: D 662 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.6154 (pp) REVERT: F 400 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7417 (pt) REVERT: F 632 VAL cc_start: 0.8386 (t) cc_final: 0.8154 (p) REVERT: F 662 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5840 (pp) REVERT: G 598 MET cc_start: 0.7018 (mmt) cc_final: 0.6487 (mmt) REVERT: G 662 LEU cc_start: 0.6403 (OUTLIER) cc_final: 0.6126 (pp) REVERT: H 434 GLN cc_start: 0.7067 (OUTLIER) cc_final: 0.6673 (pt0) REVERT: H 562 ARG cc_start: 0.8222 (ptt90) cc_final: 0.7977 (ptt90) REVERT: H 580 ARG cc_start: 0.7660 (ttp-110) cc_final: 0.7441 (ttp-110) REVERT: H 662 LEU cc_start: 0.6217 (OUTLIER) cc_final: 0.5977 (pp) REVERT: I 662 LEU cc_start: 0.6216 (OUTLIER) cc_final: 0.5914 (pp) outliers start: 77 outliers final: 27 residues processed: 363 average time/residue: 1.5236 time to fit residues: 623.6090 Evaluate side-chains 324 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 283 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 630 THR 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 581 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 633 ASP Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 630 THR Chi-restraints excluded: chain F residue 633 ASP Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain G residue 630 THR 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 H residue 630 THR Chi-restraints excluded: chain H residue 662 LEU Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 581 ILE Chi-restraints excluded: chain I residue 630 THR Chi-restraints excluded: chain I residue 633 ASP 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 149 optimal weight: 0.0980 chunk 83 optimal weight: 0.7980 chunk 224 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 74 optimal weight: 30.0000 chunk 270 optimal weight: 0.1980 chunk 291 optimal weight: 7.9990 chunk 240 optimal weight: 0.2980 chunk 267 optimal weight: 0.0770 chunk 92 optimal weight: 0.2980 chunk 216 optimal weight: 1.9990 overall best weight: 0.1938 ------------------------------------------------------------------------------- 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 438 ASN C 434 GLN D 434 GLN F 434 GLN F 508 GLN G 434 GLN H 438 ASN H 570 ASN I 434 GLN I 438 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1291 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= 0.108 Angle : 0.460 6.358 33156 Z= 0.225 Chirality : 0.040 0.157 3924 Planarity : 0.004 0.046 4239 Dihedral : 3.842 97.645 3287 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.76 % Allowed : 16.22 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.15), residues: 3006 helix: 2.08 (0.14), residues: 1404 sheet: -0.70 (0.21), residues: 549 loop : -0.86 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 375 HIS 0.002 0.000 HIS I 564 PHE 0.006 0.001 PHE H 378 TYR 0.007 0.001 TYR C 405 ARG 0.010 0.000 ARG C 590 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 300 time to evaluate : 2.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 400 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7426 (pt) REVERT: E 662 LEU cc_start: 0.6133 (OUTLIER) cc_final: 0.5893 (pp) REVERT: A 400 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7450 (pt) REVERT: A 453 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7092 (ptmm) REVERT: A 662 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.6030 (pp) REVERT: B 662 LEU cc_start: 0.6403 (OUTLIER) cc_final: 0.6160 (pp) REVERT: C 400 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7400 (pt) REVERT: C 632 VAL cc_start: 0.8498 (t) cc_final: 0.8251 (p) REVERT: C 662 LEU cc_start: 0.6193 (OUTLIER) cc_final: 0.5967 (pp) REVERT: D 662 LEU cc_start: 0.6239 (OUTLIER) cc_final: 0.6024 (pp) REVERT: F 400 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7401 (pt) REVERT: F 453 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7301 (pptt) REVERT: G 598 MET cc_start: 0.7027 (mmt) cc_final: 0.6582 (mmt) REVERT: G 662 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.6278 (pp) REVERT: H 562 ARG cc_start: 0.8219 (ptt90) cc_final: 0.7985 (ptt90) REVERT: I 567 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7641 (tmt170) REVERT: I 632 VAL cc_start: 0.8437 (t) cc_final: 0.8226 (p) REVERT: I 662 LEU cc_start: 0.6152 (OUTLIER) cc_final: 0.5922 (pp) outliers start: 74 outliers final: 24 residues processed: 369 average time/residue: 1.5786 time to fit residues: 652.9751 Evaluate side-chains 319 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 281 time to evaluate : 2.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 400 LEU 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 581 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 633 ASP Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 630 THR 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 567 ARG Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 630 THR Chi-restraints excluded: chain F residue 633 ASP Chi-restraints excluded: chain G residue 392 VAL Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain G residue 662 LEU Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain H residue 630 THR Chi-restraints excluded: chain I residue 567 ARG Chi-restraints excluded: chain I residue 581 ILE Chi-restraints excluded: chain I residue 630 THR Chi-restraints excluded: chain I residue 633 ASP Chi-restraints excluded: chain I residue 662 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 181 optimal weight: 0.9980 chunk 271 optimal weight: 9.9990 chunk 287 optimal weight: 6.9990 chunk 141 optimal weight: 0.7980 chunk 256 optimal weight: 0.1980 chunk 77 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 B 434 GLN B 570 ASN C 434 GLN D 434 GLN F 434 GLN ** F 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 434 GLN G 570 ASN H 434 GLN H 570 ASN ** H 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 434 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24471 Z= 0.136 Angle : 0.487 10.203 33156 Z= 0.240 Chirality : 0.041 0.164 3924 Planarity : 0.004 0.036 4239 Dihedral : 3.924 98.592 3287 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.09 % Allowed : 16.11 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.15), residues: 3006 helix: 2.09 (0.14), residues: 1413 sheet: -0.67 (0.22), residues: 549 loop : -0.81 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 375 HIS 0.003 0.000 HIS A 564 PHE 0.007 0.001 PHE D 378 TYR 0.012 0.001 TYR C 405 ARG 0.009 0.001 ARG D 546 *********************** 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 376 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 293 time to evaluate : 3.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 662 LEU cc_start: 0.6148 (OUTLIER) cc_final: 0.5927 (pp) REVERT: A 400 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7447 (pt) REVERT: A 453 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7072 (ptmm) REVERT: B 662 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.6243 (pp) REVERT: C 632 VAL cc_start: 0.8494 (t) cc_final: 0.8247 (p) REVERT: C 662 LEU cc_start: 0.6136 (OUTLIER) cc_final: 0.5922 (pp) REVERT: F 400 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7406 (pt) REVERT: G 662 LEU cc_start: 0.6431 (OUTLIER) cc_final: 0.6203 (pp) REVERT: H 562 ARG cc_start: 0.8258 (ptt90) cc_final: 0.8023 (ptt90) REVERT: I 567 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7659 (tmt170) REVERT: I 662 LEU cc_start: 0.6166 (OUTLIER) cc_final: 0.5926 (pp) outliers start: 83 outliers final: 32 residues processed: 361 average time/residue: 1.5360 time to fit residues: 624.6879 Evaluate side-chains 318 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 277 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 630 THR 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 581 ILE Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 633 ASP Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 580 ARG Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 630 THR Chi-restraints excluded: chain F residue 633 ASP Chi-restraints excluded: chain F residue 640 LYS Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain G residue 630 THR Chi-restraints excluded: chain G residue 662 LEU Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain H residue 630 THR 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 630 THR Chi-restraints excluded: chain I residue 633 ASP Chi-restraints excluded: chain I residue 662 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 213 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 198 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 257 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN B 570 ASN ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 434 GLN D 570 ASN ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 GLN F 570 ASN ** F 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 570 ASN ** G 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 434 GLN H 570 ASN ** H 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 434 GLN I 570 ASN ** I 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24471 Z= 0.179 Angle : 0.520 11.013 33156 Z= 0.257 Chirality : 0.042 0.176 3924 Planarity : 0.004 0.046 4239 Dihedral : 4.043 93.851 3287 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.17 % Allowed : 16.22 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.15), residues: 3006 helix: 2.03 (0.14), residues: 1413 sheet: -0.68 (0.21), residues: 549 loop : -0.79 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 375 HIS 0.003 0.001 HIS C 564 PHE 0.009 0.001 PHE G 483 TYR 0.014 0.002 TYR C 405 ARG 0.013 0.001 ARG C 590 *********************** 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 381 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 296 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 453 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7037 (ptmm) REVERT: E 662 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.6047 (pp) REVERT: A 400 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7428 (pt) REVERT: A 453 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7247 (ptmm) REVERT: B 662 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.6219 (pp) REVERT: C 632 VAL cc_start: 0.8458 (t) cc_final: 0.8241 (p) REVERT: F 453 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.6867 (ptmm) REVERT: G 662 LEU cc_start: 0.6582 (OUTLIER) cc_final: 0.6342 (pp) REVERT: H 562 ARG cc_start: 0.8279 (ptt90) cc_final: 0.8035 (ptt90) REVERT: I 567 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7680 (tmt170) REVERT: I 662 LEU cc_start: 0.6246 (OUTLIER) cc_final: 0.6003 (pp) outliers start: 85 outliers final: 40 residues processed: 361 average time/residue: 1.5538 time to fit residues: 631.7095 Evaluate side-chains 331 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 282 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 610 THR Chi-restraints excluded: chain E residue 630 THR 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 580 ARG Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 633 ASP Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain F residue 453 LYS Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 580 ARG Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 630 THR Chi-restraints excluded: chain F residue 633 ASP Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain G residue 610 THR Chi-restraints excluded: chain G residue 630 THR Chi-restraints excluded: chain G residue 662 LEU Chi-restraints excluded: chain H residue 484 ILE Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain H residue 630 THR 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 630 THR Chi-restraints excluded: chain I residue 633 ASP Chi-restraints excluded: chain I residue 662 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 0.0770 chunk 258 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 70 optimal weight: 0.0870 chunk 287 optimal weight: 6.9990 chunk 238 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 150 optimal weight: 3.9990 overall best weight: 1.5520 ------------------------------------------------------------------------------- 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 ** E 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 GLN ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 ASN ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 434 GLN D 570 ASN ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 GLN F 508 GLN F 570 ASN ** F 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 570 ASN ** G 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 434 GLN H 570 ASN ** H 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 434 GLN ** I 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24471 Z= 0.225 Angle : 0.557 11.441 33156 Z= 0.278 Chirality : 0.044 0.185 3924 Planarity : 0.004 0.048 4239 Dihedral : 4.084 76.600 3287 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.36 % Allowed : 16.89 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 3006 helix: 1.93 (0.14), residues: 1413 sheet: -0.71 (0.21), residues: 549 loop : -0.76 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 375 HIS 0.004 0.001 HIS I 564 PHE 0.011 0.001 PHE G 483 TYR 0.015 0.002 TYR C 405 ARG 0.015 0.001 ARG C 590 *********************** 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 391 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 301 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 453 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7140 (ptmm) REVERT: E 662 LEU cc_start: 0.6405 (OUTLIER) cc_final: 0.6135 (pp) REVERT: A 400 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7416 (pt) REVERT: C 632 VAL cc_start: 0.8465 (t) cc_final: 0.8260 (p) REVERT: D 563 ARG cc_start: 0.7598 (ttm170) cc_final: 0.7113 (pmt-80) REVERT: D 567 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7490 (tmm160) REVERT: F 453 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.6973 (ptmm) REVERT: H 562 ARG cc_start: 0.8294 (ptt90) cc_final: 0.8044 (ptt90) REVERT: H 574 LYS cc_start: 0.7537 (pmtt) cc_final: 0.7320 (pmtt) REVERT: I 567 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7684 (tmt170) outliers start: 90 outliers final: 40 residues processed: 364 average time/residue: 1.5406 time to fit residues: 631.2953 Evaluate side-chains 333 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 287 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 630 THR 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 580 ARG Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 633 ASP Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 434 GLN Chi-restraints excluded: chain D residue 567 ARG Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain F residue 453 LYS Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 580 ARG Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 630 THR Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain G residue 610 THR Chi-restraints excluded: chain G residue 630 THR Chi-restraints excluded: chain H residue 484 ILE Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain H residue 630 THR Chi-restraints excluded: chain H residue 633 ASP 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 630 THR Chi-restraints excluded: chain I residue 633 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 241 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 286 optimal weight: 0.9990 chunk 179 optimal weight: 0.9980 chunk 174 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 ** E 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 GLN ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN B 570 ASN ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN C 570 ASN ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 434 GLN D 570 ASN ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 GLN F 570 ASN ** F 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 570 ASN ** G 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 434 GLN ** H 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 434 GLN I 570 ASN ** I 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24471 Z= 0.232 Angle : 0.579 11.332 33156 Z= 0.287 Chirality : 0.044 0.190 3924 Planarity : 0.005 0.055 4239 Dihedral : 3.912 25.101 3285 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.47 % Allowed : 17.52 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.15), residues: 3006 helix: 1.84 (0.14), residues: 1413 sheet: -0.74 (0.21), residues: 549 loop : -0.76 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 375 HIS 0.004 0.001 HIS I 564 PHE 0.012 0.002 PHE G 483 TYR 0.015 0.002 TYR C 405 ARG 0.017 0.001 ARG C 590 *********************** 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 382 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 289 time to evaluate : 2.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 434 GLN cc_start: 0.6941 (OUTLIER) cc_final: 0.6636 (pt0) REVERT: E 442 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7767 (mm110) REVERT: E 453 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7155 (ptmm) REVERT: A 400 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7440 (pt) REVERT: B 453 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7178 (ptmm) REVERT: C 453 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7489 (ptmm) REVERT: D 453 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.7041 (ptmm) REVERT: D 563 ARG cc_start: 0.7587 (ttm170) cc_final: 0.7127 (pmt-80) REVERT: F 453 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7024 (ptmm) REVERT: H 562 ARG cc_start: 0.8286 (ptt90) cc_final: 0.8040 (ptt90) REVERT: H 574 LYS cc_start: 0.7543 (pmtt) cc_final: 0.7141 (pmtt) REVERT: I 567 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7669 (tmt170) outliers start: 93 outliers final: 49 residues processed: 352 average time/residue: 1.6149 time to fit residues: 635.1901 Evaluate side-chains 337 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 280 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 434 GLN Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 610 THR Chi-restraints excluded: chain E residue 630 THR 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 580 ARG Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain C residue 453 LYS 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 610 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 633 ASP 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 D residue 610 THR Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain F residue 453 LYS Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 580 ARG Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 630 THR Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain G residue 610 THR Chi-restraints excluded: chain G residue 630 THR Chi-restraints excluded: chain G residue 633 ASP Chi-restraints excluded: chain H residue 484 ILE Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 630 THR Chi-restraints excluded: chain H residue 633 ASP Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 567 ARG Chi-restraints excluded: chain I residue 580 ARG Chi-restraints excluded: chain I residue 581 ILE Chi-restraints excluded: chain I residue 630 THR Chi-restraints excluded: chain I residue 633 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 55 optimal weight: 0.0050 chunk 181 optimal weight: 1.9990 chunk 195 optimal weight: 0.6980 chunk 141 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 570 ASN ** E 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 GLN ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN C 570 ASN ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 434 GLN D 570 ASN ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN ** F 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 570 ASN ** G 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 434 GLN H 570 ASN ** H 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 434 GLN I 570 ASN ** I 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24471 Z= 0.187 Angle : 0.566 11.410 33156 Z= 0.278 Chirality : 0.043 0.194 3924 Planarity : 0.005 0.066 4239 Dihedral : 3.838 24.940 3285 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.36 % Allowed : 17.90 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.15), residues: 3006 helix: 1.90 (0.14), residues: 1413 sheet: -0.70 (0.21), residues: 549 loop : -0.76 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 375 HIS 0.003 0.001 HIS I 564 PHE 0.009 0.001 PHE G 483 TYR 0.014 0.002 TYR C 405 ARG 0.018 0.001 ARG C 590 *********************** 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 380 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 290 time to evaluate : 2.750 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: 0.7540 (OUTLIER) cc_final: 0.7050 (ptmm) REVERT: A 400 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7436 (pt) REVERT: C 453 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7387 (ptmm) REVERT: D 453 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7022 (ptmm) REVERT: F 400 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7317 (pt) REVERT: F 453 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.6870 (ptmm) REVERT: G 598 MET cc_start: 0.7153 (mmt) cc_final: 0.6627 (mmt) REVERT: H 562 ARG cc_start: 0.8274 (ptt90) cc_final: 0.8040 (ptt90) REVERT: H 574 LYS cc_start: 0.7507 (pmtt) cc_final: 0.7134 (pmtt) REVERT: I 567 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7651 (tmt170) outliers start: 90 outliers final: 51 residues processed: 353 average time/residue: 1.5999 time to fit residues: 633.3110 Evaluate side-chains 338 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 280 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 610 THR Chi-restraints excluded: chain E residue 630 THR Chi-restraints excluded: chain E residue 633 ASP Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 580 ARG Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 614 GLN Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 453 LYS 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 610 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 633 ASP Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 GLN Chi-restraints excluded: chain D residue 453 LYS Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 453 LYS Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 614 GLN Chi-restraints excluded: chain F residue 630 THR Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain G residue 610 THR Chi-restraints excluded: chain G residue 630 THR Chi-restraints excluded: chain G residue 633 ASP Chi-restraints excluded: chain H residue 484 ILE Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 630 THR Chi-restraints excluded: chain H residue 633 ASP Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 567 ARG Chi-restraints excluded: chain I residue 580 ARG Chi-restraints excluded: chain I residue 581 ILE Chi-restraints excluded: chain I residue 630 THR Chi-restraints excluded: chain I residue 633 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 0.5980 chunk 274 optimal weight: 6.9990 chunk 250 optimal weight: 2.9990 chunk 266 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 209 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 241 optimal weight: 6.9990 chunk 252 optimal weight: 0.5980 chunk 265 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 570 ASN ** E 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 GLN A 570 ASN ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN B 570 ASN ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN C 570 ASN ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 434 GLN ** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN ** F 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 570 ASN ** G 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 434 GLN H 438 ASN ** H 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 434 GLN I 570 ASN ** I 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1596 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= 0.197 Angle : 0.577 10.692 33156 Z= 0.285 Chirality : 0.043 0.202 3924 Planarity : 0.005 0.059 4239 Dihedral : 3.855 22.920 3285 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.09 % Allowed : 18.31 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.15), residues: 3006 helix: 1.86 (0.14), residues: 1413 sheet: -0.70 (0.21), residues: 549 loop : -0.77 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 375 HIS 0.004 0.001 HIS I 564 PHE 0.010 0.001 PHE G 483 TYR 0.014 0.002 TYR A 405 ARG 0.013 0.001 ARG C 590 *********************** 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 369 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 286 time to evaluate : 2.615 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 442 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7779 (mm110) REVERT: E 453 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.6994 (ptmm) REVERT: A 400 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7439 (pt) REVERT: B 453 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.7202 (ptmm) REVERT: C 453 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7448 (ptmm) REVERT: C 567 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.6980 (tmm160) REVERT: C 586 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7587 (tt0) REVERT: D 453 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.6929 (ptmm) REVERT: F 400 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7309 (pt) REVERT: F 453 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.6872 (ptmm) REVERT: G 453 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7186 (ptmm) REVERT: H 562 ARG cc_start: 0.8277 (ptt90) cc_final: 0.8044 (ptt90) REVERT: H 574 LYS cc_start: 0.7495 (pmtt) cc_final: 0.7114 (pmtt) REVERT: H 614 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.8093 (pm20) REVERT: I 567 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7633 (tmt170) outliers start: 83 outliers final: 53 residues processed: 347 average time/residue: 1.6236 time to fit residues: 631.5902 Evaluate side-chains 344 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 280 time to evaluate : 2.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 570 ASN Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 610 THR Chi-restraints excluded: chain E residue 614 GLN Chi-restraints excluded: chain E residue 630 THR Chi-restraints excluded: chain E residue 633 ASP Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 580 ARG Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 614 GLN Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 453 LYS 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 610 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 633 ASP 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 D residue 610 THR Chi-restraints excluded: chain D residue 614 GLN Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 453 LYS Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 614 GLN Chi-restraints excluded: chain F residue 630 THR Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain G residue 453 LYS Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain G residue 610 THR Chi-restraints excluded: chain G residue 630 THR Chi-restraints excluded: chain G residue 633 ASP Chi-restraints excluded: chain H residue 484 ILE Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 614 GLN Chi-restraints excluded: chain H residue 630 THR Chi-restraints excluded: chain H residue 633 ASP Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 567 ARG Chi-restraints excluded: chain I residue 580 ARG Chi-restraints excluded: chain I residue 581 ILE Chi-restraints excluded: chain I residue 630 THR Chi-restraints excluded: chain I residue 633 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 0.9990 chunk 282 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 196 optimal weight: 10.0000 chunk 295 optimal weight: 0.3980 chunk 272 optimal weight: 20.0000 chunk 235 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ** E 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 GLN A 570 ASN ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN C 570 ASN ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 434 GLN ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 508 GLN ** F 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 434 GLN H 438 ASN ** H 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 434 GLN I 570 ASN ** I 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1606 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= 0.160 Angle : 0.556 10.701 33156 Z= 0.275 Chirality : 0.042 0.193 3924 Planarity : 0.005 0.058 4239 Dihedral : 3.757 22.166 3285 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.76 % Allowed : 18.68 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.16), residues: 3006 helix: 1.93 (0.14), residues: 1413 sheet: -0.67 (0.21), residues: 549 loop : -0.76 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 375 HIS 0.003 0.001 HIS I 564 PHE 0.008 0.001 PHE H 378 TYR 0.012 0.001 TYR A 405 ARG 0.014 0.001 ARG B 590 ********************** 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 352 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 278 time to evaluate : 2.725 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 434 GLN cc_start: 0.6854 (OUTLIER) cc_final: 0.6568 (pt0) REVERT: E 442 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7766 (mm110) REVERT: A 400 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7412 (pt) REVERT: C 453 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7344 (ptmm) REVERT: C 586 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7603 (tt0) REVERT: D 453 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.6947 (ptmm) REVERT: F 400 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7325 (pt) REVERT: F 453 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.7291 (pptt) REVERT: H 562 ARG cc_start: 0.8253 (ptt90) cc_final: 0.8025 (ptt90) REVERT: H 614 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8023 (pm20) REVERT: I 567 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7609 (tmt170) outliers start: 74 outliers final: 48 residues processed: 339 average time/residue: 1.6517 time to fit residues: 627.5508 Evaluate side-chains 330 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 274 time to evaluate : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 434 GLN Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 570 ASN Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 610 THR Chi-restraints excluded: chain E residue 630 THR Chi-restraints excluded: chain E residue 633 ASP 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 610 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 614 GLN Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 453 LYS Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 633 ASP 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 D residue 610 THR Chi-restraints excluded: chain D residue 614 GLN Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 453 LYS Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 614 GLN Chi-restraints excluded: chain F residue 630 THR Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain G residue 630 THR Chi-restraints excluded: chain G residue 633 ASP Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 614 GLN Chi-restraints excluded: chain H residue 630 THR Chi-restraints excluded: chain H residue 633 ASP Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 567 ARG Chi-restraints excluded: chain I residue 580 ARG Chi-restraints excluded: chain I residue 581 ILE Chi-restraints excluded: chain I residue 614 GLN Chi-restraints excluded: chain I residue 630 THR Chi-restraints excluded: chain I residue 633 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 4.9990 chunk 250 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 217 optimal weight: 0.0970 chunk 34 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 235 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 242 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 ** E 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 GLN A 570 ASN ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN C 438 ASN C 570 ASN ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 434 GLN ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 508 GLN F 570 ASN ** F 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 570 ASN ** G 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 434 GLN H 438 ASN ** H 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 434 GLN I 570 ASN ** I 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.197207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.119691 restraints weight = 24152.899| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.01 r_work: 0.3205 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 24471 Z= 0.233 Angle : 0.596 10.524 33156 Z= 0.298 Chirality : 0.044 0.197 3924 Planarity : 0.005 0.062 4239 Dihedral : 3.914 21.903 3285 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.02 % Allowed : 18.57 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 3006 helix: 1.78 (0.14), residues: 1413 sheet: -0.69 (0.21), residues: 549 loop : -0.79 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 375 HIS 0.004 0.001 HIS A 564 PHE 0.012 0.002 PHE G 483 TYR 0.015 0.002 TYR A 405 ARG 0.013 0.001 ARG A 590 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11230.16 seconds wall clock time: 198 minutes 2.84 seconds (11882.84 seconds total)