Starting phenix.real_space_refine on Mon Sep 30 01:48:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7feb_31551/09_2024/7feb_31551.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7feb_31551/09_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_31551/09_2024/7feb_31551.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7feb_31551/09_2024/7feb_31551.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7feb_31551/09_2024/7feb_31551.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7feb_31551/09_2024/7feb_31551.cif" } resolution = 2.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 15354 2.51 5 N 4140 2.21 5 O 4473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 14.38, 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.04 Conformation dependent library (CDL) restraints added in 3.0 seconds 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5742 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 36 sheets defined 50.0% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.40 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: 7.49 Time building geometry restraints manager: 6.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4086 1.31 - 1.43: 5715 1.43 - 1.56: 14472 1.56 - 1.68: 9 1.68 - 1.81: 189 Bond restraints: 24471 Sorted by residual: bond pdb=" C TRP D 375 " pdb=" O TRP D 375 " ideal model delta sigma weight residual 1.237 1.193 0.043 1.19e-02 7.06e+03 1.31e+01 bond pdb=" C TRP G 375 " pdb=" O TRP G 375 " ideal model delta sigma weight residual 1.237 1.194 0.042 1.19e-02 7.06e+03 1.27e+01 bond pdb=" C TRP E 375 " pdb=" O TRP E 375 " ideal model delta sigma weight residual 1.237 1.196 0.041 1.17e-02 7.31e+03 1.24e+01 bond pdb=" C PRO C 437 " pdb=" O PRO C 437 " ideal model delta sigma weight residual 1.232 1.186 0.046 1.31e-02 5.83e+03 1.22e+01 bond pdb=" C TRP C 375 " pdb=" O TRP C 375 " ideal model delta sigma weight residual 1.237 1.195 0.041 1.19e-02 7.06e+03 1.21e+01 ... (remaining 24466 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 31920 1.52 - 3.05: 1004 3.05 - 4.57: 133 4.57 - 6.10: 75 6.10 - 7.62: 24 Bond angle restraints: 33156 Sorted by residual: angle pdb=" C ASN D 438 " pdb=" CA ASN D 438 " pdb=" CB ASN D 438 " ideal model delta sigma weight residual 111.51 117.67 -6.16 1.58e+00 4.01e-01 1.52e+01 angle pdb=" C ASN C 438 " pdb=" CA ASN C 438 " pdb=" CB ASN C 438 " ideal model delta sigma weight residual 111.51 117.67 -6.16 1.58e+00 4.01e-01 1.52e+01 angle pdb=" C ASN I 438 " pdb=" CA ASN I 438 " pdb=" CB ASN I 438 " ideal model delta sigma weight residual 111.51 117.66 -6.15 1.58e+00 4.01e-01 1.52e+01 angle pdb=" C ASN E 438 " pdb=" CA ASN E 438 " pdb=" CB ASN E 438 " ideal model delta sigma weight residual 111.51 117.64 -6.13 1.58e+00 4.01e-01 1.50e+01 angle pdb=" C ASN F 438 " pdb=" CA ASN F 438 " pdb=" CB ASN F 438 " ideal model delta sigma weight residual 111.51 117.63 -6.12 1.58e+00 4.01e-01 1.50e+01 ... (remaining 33151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 12989 15.99 - 31.97: 1555 31.97 - 47.96: 477 47.96 - 63.95: 72 63.95 - 79.94: 45 Dihedral angle restraints: 15138 sinusoidal: 6327 harmonic: 8811 Sorted by residual: dihedral pdb=" CA LEU H 662 " pdb=" C LEU H 662 " pdb=" N ILE H 663 " pdb=" CA ILE H 663 " ideal model delta harmonic sigma weight residual -180.00 -156.03 -23.97 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA LEU B 662 " pdb=" C LEU B 662 " pdb=" N ILE B 663 " pdb=" CA ILE B 663 " ideal model delta harmonic sigma weight residual 180.00 -156.05 -23.95 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA LEU C 662 " pdb=" C LEU C 662 " pdb=" N ILE C 663 " pdb=" CA ILE C 663 " ideal model delta harmonic sigma weight residual 180.00 -156.05 -23.95 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 15135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2956 0.046 - 0.092: 699 0.092 - 0.138: 235 0.138 - 0.184: 16 0.184 - 0.230: 18 Chirality restraints: 3924 Sorted by residual: chirality pdb=" CA ASN D 438 " pdb=" N ASN D 438 " pdb=" C ASN D 438 " pdb=" CB ASN D 438 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA ASN C 438 " pdb=" N ASN C 438 " pdb=" C ASN C 438 " pdb=" CB ASN C 438 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ASN H 438 " pdb=" N ASN H 438 " pdb=" C ASN H 438 " pdb=" CB ASN H 438 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 3921 not shown) Planarity restraints: 4239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 590 " -0.189 9.50e-02 1.11e+02 8.52e-02 5.75e+00 pdb=" NE ARG C 590 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG C 590 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG C 590 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C 590 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 590 " 0.188 9.50e-02 1.11e+02 8.50e-02 5.74e+00 pdb=" NE ARG D 590 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG D 590 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG D 590 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG D 590 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 590 " -0.189 9.50e-02 1.11e+02 8.52e-02 5.74e+00 pdb=" NE ARG E 590 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG E 590 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG E 590 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG E 590 " -0.000 2.00e-02 2.50e+03 ... (remaining 4236 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2486 2.75 - 3.29: 23619 3.29 - 3.82: 40810 3.82 - 4.36: 47015 4.36 - 4.90: 78742 Nonbonded interactions: 192672 Sorted by model distance: nonbonded pdb=" O LEU F 576 " pdb=" NE2 GLN F 664 " model vdw 2.211 3.120 nonbonded pdb=" O LEU B 576 " pdb=" NE2 GLN B 664 " model vdw 2.211 3.120 nonbonded pdb=" O LEU I 576 " pdb=" NE2 GLN I 664 " model vdw 2.211 3.120 nonbonded pdb=" O LEU G 576 " pdb=" NE2 GLN G 664 " model vdw 2.212 3.120 nonbonded pdb=" O LEU D 576 " pdb=" NE2 GLN D 664 " model vdw 2.212 3.120 ... (remaining 192667 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 21.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 1.400 Process input model: 51.640 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.860 ------------------------------------------------------------------------------- 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 : 3.006 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: 1.6738 time to fit residues: 683.6128 Evaluate side-chains 312 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 299 time to evaluate : 3.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 610 THR Chi-restraints excluded: chain E residue 633 ASP Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 633 ASP Chi-restraints excluded: chain G residue 610 THR Chi-restraints excluded: chain G residue 633 ASP Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 633 ASP Chi-restraints excluded: chain I residue 610 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 0.7980 chunk 225 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 151 optimal weight: 0.5980 chunk 120 optimal weight: 0.8980 chunk 232 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 173 optimal weight: 0.9980 chunk 269 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 434 GLN E 438 ASN A 434 GLN A 438 ASN B 434 GLN B 438 ASN C 434 GLN C 438 ASN D 434 GLN D 438 ASN D 614 GLN F 434 GLN F 438 ASN F 508 GLN G 434 GLN H 434 GLN H 438 ASN I 434 GLN I 438 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24471 Z= 0.158 Angle : 0.511 6.035 33156 Z= 0.256 Chirality : 0.042 0.218 3924 Planarity : 0.004 0.038 4239 Dihedral : 4.128 82.120 3303 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.57 % Allowed : 15.32 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.15), residues: 3006 helix: 1.84 (0.14), residues: 1413 sheet: -0.75 (0.21), residues: 549 loop : -0.90 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 375 HIS 0.003 0.001 HIS A 564 PHE 0.009 0.001 PHE F 378 TYR 0.014 0.001 TYR C 405 ARG 0.009 0.001 ARG F 590 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 314 time to evaluate : 2.923 Fit side-chains REVERT: E 453 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7103 (ptmm) REVERT: A 400 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7466 (pt) REVERT: A 434 GLN cc_start: 0.6717 (OUTLIER) cc_final: 0.6304 (pt0) REVERT: A 453 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7208 (ptmm) REVERT: A 562 ARG cc_start: 0.8254 (ptt90) cc_final: 0.7995 (ptt90) REVERT: C 632 VAL cc_start: 0.8458 (t) cc_final: 0.8235 (p) REVERT: F 400 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7428 (pt) REVERT: F 453 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7173 (ptmm) REVERT: F 632 VAL cc_start: 0.8383 (t) cc_final: 0.8159 (p) REVERT: G 598 MET cc_start: 0.6968 (mmt) cc_final: 0.6438 (mmt) REVERT: H 434 GLN cc_start: 0.7084 (OUTLIER) cc_final: 0.6737 (pt0) REVERT: H 442 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7808 (mm-40) REVERT: H 562 ARG cc_start: 0.8228 (ptt90) cc_final: 0.7978 (ptt90) REVERT: I 434 GLN cc_start: 0.6882 (OUTLIER) cc_final: 0.6541 (pt0) REVERT: I 442 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7702 (mm-40) REVERT: I 567 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7609 (tmt170) outliers start: 69 outliers final: 17 residues processed: 369 average time/residue: 1.5978 time to fit residues: 664.0220 Evaluate side-chains 320 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 294 time to evaluate : 3.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 669 ILE Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 453 LYS Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 633 ASP Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain H residue 434 GLN Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 434 GLN Chi-restraints excluded: chain I residue 567 ARG Chi-restraints excluded: chain I residue 581 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 224 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 74 optimal weight: 30.0000 chunk 270 optimal weight: 0.7980 chunk 291 optimal weight: 7.9990 chunk 240 optimal weight: 3.9990 chunk 267 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 chunk 216 optimal weight: 0.0970 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 G 434 GLN H 438 ASN H 570 ASN I 434 GLN I 438 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24471 Z= 0.203 Angle : 0.552 7.812 33156 Z= 0.272 Chirality : 0.044 0.211 3924 Planarity : 0.004 0.042 4239 Dihedral : 4.206 84.854 3287 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.31 % Allowed : 16.03 % Favored : 81.66 % 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: 0.67 (0.15), residues: 3006 helix: 1.89 (0.14), residues: 1413 sheet: -0.76 (0.21), residues: 549 loop : -0.85 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 375 HIS 0.003 0.001 HIS A 564 PHE 0.010 0.001 PHE G 483 TYR 0.015 0.002 TYR C 405 ARG 0.011 0.001 ARG C 590 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 317 time to evaluate : 2.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7429 (pt) REVERT: A 562 ARG cc_start: 0.8290 (ptt90) cc_final: 0.8067 (ptt90) REVERT: C 632 VAL cc_start: 0.8450 (t) cc_final: 0.8242 (p) REVERT: F 632 VAL cc_start: 0.8423 (t) cc_final: 0.8214 (p) REVERT: H 562 ARG cc_start: 0.8254 (ptt90) cc_final: 0.8022 (ptt90) REVERT: I 567 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7645 (tmt170) outliers start: 62 outliers final: 20 residues processed: 364 average time/residue: 1.5055 time to fit residues: 614.7147 Evaluate side-chains 311 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 289 time to evaluate : 2.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain D residue 434 GLN Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain F residue 453 LYS Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain H residue 484 ILE Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 567 ARG Chi-restraints excluded: chain I residue 581 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 0.6980 chunk 203 optimal weight: 5.9990 chunk 140 optimal weight: 20.0000 chunk 29 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 271 optimal weight: 0.5980 chunk 287 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 256 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 570 ASN F 434 GLN F 508 GLN G 434 GLN G 570 ASN H 434 GLN H 570 ASN I 434 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24471 Z= 0.156 Angle : 0.514 6.518 33156 Z= 0.256 Chirality : 0.042 0.181 3924 Planarity : 0.004 0.047 4239 Dihedral : 3.776 24.498 3285 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.54 % Allowed : 16.37 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.15), residues: 3006 helix: 2.00 (0.14), residues: 1413 sheet: -0.74 (0.21), residues: 549 loop : -0.83 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 375 HIS 0.003 0.001 HIS A 564 PHE 0.008 0.001 PHE H 378 TYR 0.013 0.001 TYR C 405 ARG 0.013 0.001 ARG C 590 *********************** 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 384 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 316 time to evaluate : 2.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 453 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7128 (ptmm) REVERT: A 400 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7408 (pt) REVERT: A 453 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7137 (ptmm) REVERT: A 562 ARG cc_start: 0.8242 (ptt90) cc_final: 0.7997 (ptt90) REVERT: C 567 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7035 (tmm160) REVERT: F 400 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7328 (pt) REVERT: F 453 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7102 (ptmm) REVERT: G 598 MET cc_start: 0.6677 (mmt) cc_final: 0.6271 (mmt) REVERT: H 562 ARG cc_start: 0.8261 (ptt90) cc_final: 0.8037 (ptt90) REVERT: I 567 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7626 (tmt170) outliers start: 68 outliers final: 20 residues processed: 370 average time/residue: 1.5900 time to fit residues: 661.9771 Evaluate side-chains 324 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 297 time to evaluate : 2.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 669 ILE Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 453 LYS Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 580 ARG Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain H residue 580 ARG Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 567 ARG Chi-restraints excluded: chain I residue 581 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 213 optimal weight: 0.5980 chunk 118 optimal weight: 0.6980 chunk 244 optimal weight: 0.4980 chunk 198 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 146 optimal weight: 0.0980 chunk 257 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 570 ASN C 434 GLN D 434 GLN D 570 ASN F 434 GLN G 434 GLN G 570 ASN H 434 GLN H 570 ASN I 434 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1454 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= 0.133 Angle : 0.497 6.746 33156 Z= 0.247 Chirality : 0.042 0.172 3924 Planarity : 0.004 0.053 4239 Dihedral : 3.629 21.331 3285 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.39 % Allowed : 17.11 % Favored : 80.50 % 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: 0.89 (0.15), residues: 3006 helix: 2.13 (0.14), residues: 1413 sheet: -0.71 (0.21), residues: 549 loop : -0.79 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 375 HIS 0.003 0.001 HIS A 564 PHE 0.007 0.001 PHE H 378 TYR 0.011 0.001 TYR C 405 ARG 0.015 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 374 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 310 time to evaluate : 2.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7418 (pt) REVERT: A 453 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7020 (ptmm) REVERT: F 400 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7414 (pt) REVERT: G 598 MET cc_start: 0.6643 (mmt) cc_final: 0.6237 (mmt) REVERT: H 562 ARG cc_start: 0.8228 (ptt90) cc_final: 0.8012 (ptt90) REVERT: I 567 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7645 (tmt170) outliers start: 64 outliers final: 16 residues processed: 364 average time/residue: 1.5603 time to fit residues: 639.2807 Evaluate side-chains 312 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 292 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain 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 666 VAL Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain H residue 580 ARG Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 567 ARG Chi-restraints excluded: chain I residue 581 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 1.9990 chunk 258 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 287 optimal weight: 5.9990 chunk 238 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 D 570 ASN F 434 GLN F 508 GLN F 570 ASN G 434 GLN G 570 ASN H 434 GLN H 570 ASN I 434 GLN I 570 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 24471 Z= 0.231 Angle : 0.582 9.457 33156 Z= 0.288 Chirality : 0.045 0.189 3924 Planarity : 0.005 0.040 4239 Dihedral : 3.984 27.747 3285 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.61 % Allowed : 18.12 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.15), residues: 3006 helix: 1.95 (0.14), residues: 1413 sheet: -0.73 (0.21), residues: 549 loop : -0.75 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 375 HIS 0.004 0.001 HIS A 564 PHE 0.011 0.001 PHE G 483 TYR 0.016 0.002 TYR A 405 ARG 0.010 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 379 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 309 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 453 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.7052 (ptmm) REVERT: A 400 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7436 (pt) REVERT: B 453 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7346 (ptmm) REVERT: C 453 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7480 (ptmm) REVERT: C 567 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7025 (tmm160) REVERT: C 586 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7534 (tt0) REVERT: F 453 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.6956 (ptmm) REVERT: G 598 MET cc_start: 0.6680 (mmt) cc_final: 0.6212 (mmt) REVERT: H 562 ARG cc_start: 0.8295 (ptt90) cc_final: 0.8062 (ptt90) REVERT: I 567 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7648 (tmt170) outliers start: 70 outliers final: 26 residues processed: 362 average time/residue: 1.6051 time to fit residues: 652.8126 Evaluate side-chains 324 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 290 time to evaluate : 3.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 580 ARG Chi-restraints excluded: chain B residue 581 ILE 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 586 GLU Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 666 VAL 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 666 VAL Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain H residue 484 ILE Chi-restraints excluded: chain H residue 580 ARG Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain H residue 666 VAL Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 567 ARG Chi-restraints excluded: chain I residue 581 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 163 optimal weight: 7.9990 chunk 209 optimal weight: 0.8980 chunk 162 optimal weight: 0.7980 chunk 241 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 chunk 286 optimal weight: 0.1980 chunk 179 optimal weight: 0.9990 chunk 174 optimal weight: 0.4980 chunk 132 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 434 GLN E 570 ASN A 434 GLN B 434 GLN C 434 GLN C 570 ASN D 434 GLN F 508 GLN F 570 ASN G 570 ASN H 434 GLN I 434 GLN I 570 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.002 0.050 24471 Z= 0.138 Angle : 0.531 8.476 33156 Z= 0.260 Chirality : 0.042 0.283 3924 Planarity : 0.004 0.043 4239 Dihedral : 3.710 25.578 3285 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.46 % Allowed : 18.90 % Favored : 78.64 % 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: 0.94 (0.15), residues: 3006 helix: 2.14 (0.14), residues: 1413 sheet: -0.68 (0.21), residues: 549 loop : -0.72 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 375 HIS 0.002 0.001 HIS H 564 PHE 0.007 0.001 PHE D 378 TYR 0.010 0.001 TYR C 405 ARG 0.012 0.001 ARG H 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 367 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 301 time to evaluate : 2.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7404 (pt) REVERT: A 608 HIS cc_start: 0.8008 (m170) cc_final: 0.7761 (m-70) REVERT: C 567 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.6995 (tmm160) REVERT: C 586 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7519 (tt0) REVERT: G 598 MET cc_start: 0.6708 (mmt) cc_final: 0.6266 (mmt) REVERT: G 608 HIS cc_start: 0.7991 (m170) cc_final: 0.7787 (m-70) REVERT: H 562 ARG cc_start: 0.8209 (ptt90) cc_final: 0.7995 (ptt90) REVERT: I 567 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7618 (tmt170) outliers start: 66 outliers final: 17 residues processed: 355 average time/residue: 1.6214 time to fit residues: 646.4538 Evaluate side-chains 305 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 284 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 666 VAL 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 G residue 581 ILE Chi-restraints excluded: chain H residue 580 ARG Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 567 ARG Chi-restraints excluded: chain I residue 581 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 55 optimal weight: 0.0050 chunk 181 optimal weight: 0.9980 chunk 195 optimal weight: 0.8980 chunk 141 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 225 optimal weight: 0.6980 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 570 ASN A 434 GLN B 434 GLN B 570 ASN C 434 GLN C 570 ASN D 434 GLN D 570 ASN F 508 GLN F 570 ASN G 570 ASN H 434 GLN I 434 GLN I 570 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24471 Z= 0.172 Angle : 0.560 10.694 33156 Z= 0.277 Chirality : 0.043 0.292 3924 Planarity : 0.004 0.045 4239 Dihedral : 3.793 26.807 3285 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.35 % Allowed : 19.31 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.88 (0.15), residues: 3006 helix: 2.08 (0.14), residues: 1413 sheet: -0.72 (0.21), residues: 549 loop : -0.71 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 375 HIS 0.003 0.001 HIS I 564 PHE 0.008 0.001 PHE G 483 TYR 0.014 0.001 TYR C 405 ARG 0.013 0.001 ARG B 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 351 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 288 time to evaluate : 2.796 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: A 400 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7422 (pt) REVERT: A 608 HIS cc_start: 0.8006 (m170) cc_final: 0.7737 (m-70) REVERT: C 567 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.6985 (tmm160) REVERT: C 586 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7526 (tt0) REVERT: D 669 ILE cc_start: 0.8337 (mp) cc_final: 0.8079 (mm) REVERT: F 400 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7325 (pt) REVERT: F 453 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7293 (pptt) REVERT: G 598 MET cc_start: 0.6710 (mmt) cc_final: 0.6264 (mmt) REVERT: G 608 HIS cc_start: 0.8013 (m170) cc_final: 0.7809 (m-70) REVERT: H 562 ARG cc_start: 0.8248 (ptt90) cc_final: 0.8030 (ptt90) REVERT: I 567 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7617 (tmt170) outliers start: 63 outliers final: 23 residues processed: 338 average time/residue: 1.5987 time to fit residues: 606.8598 Evaluate side-chains 307 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 278 time to evaluate : 2.767 ------------------------------------------------------------------------------- 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 581 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 614 GLN 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 580 ARG Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 614 GLN Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain H residue 484 ILE Chi-restraints excluded: chain H residue 580 ARG Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 567 ARG Chi-restraints excluded: chain I residue 581 ILE Chi-restraints excluded: chain I residue 614 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 0.7980 chunk 274 optimal weight: 8.9990 chunk 250 optimal weight: 2.9990 chunk 266 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 241 optimal weight: 6.9990 chunk 252 optimal weight: 0.0470 chunk 265 optimal weight: 1.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 570 ASN A 434 GLN B 434 GLN C 434 GLN D 434 GLN F 508 GLN F 570 ASN H 434 GLN H 570 ASN I 434 GLN I 570 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24471 Z= 0.170 Angle : 0.565 10.267 33156 Z= 0.281 Chirality : 0.044 0.293 3924 Planarity : 0.005 0.049 4239 Dihedral : 3.800 26.298 3285 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.86 % Allowed : 19.91 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.86 (0.15), residues: 3006 helix: 2.07 (0.14), residues: 1413 sheet: -0.74 (0.21), residues: 549 loop : -0.72 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 375 HIS 0.003 0.001 HIS C 564 PHE 0.008 0.001 PHE H 378 TYR 0.013 0.001 TYR C 405 ARG 0.013 0.001 ARG B 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 336 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 286 time to evaluate : 2.792 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: A 400 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7414 (pt) REVERT: A 608 HIS cc_start: 0.7998 (m170) cc_final: 0.7729 (m-70) REVERT: C 567 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.6976 (tmm160) REVERT: C 586 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7525 (tt0) REVERT: D 669 ILE cc_start: 0.8355 (mp) cc_final: 0.8130 (mm) REVERT: F 400 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7322 (pt) REVERT: F 453 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.7293 (pptt) REVERT: F 669 ILE cc_start: 0.8456 (mm) cc_final: 0.8228 (mm) REVERT: G 598 MET cc_start: 0.6699 (mmt) cc_final: 0.6266 (mmt) REVERT: G 608 HIS cc_start: 0.8055 (m170) cc_final: 0.7854 (m-70) REVERT: H 434 GLN cc_start: 0.7084 (OUTLIER) cc_final: 0.6864 (pt0) REVERT: H 562 ARG cc_start: 0.8226 (ptt90) cc_final: 0.8007 (ptt90) REVERT: I 567 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7608 (tmt170) outliers start: 50 outliers final: 26 residues processed: 330 average time/residue: 1.6608 time to fit residues: 613.2598 Evaluate side-chains 313 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 280 time to evaluate : 2.869 ------------------------------------------------------------------------------- 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 570 ASN Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 614 GLN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 614 GLN 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 570 ASN Chi-restraints excluded: chain F residue 580 ARG Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 614 GLN Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain H residue 434 GLN Chi-restraints excluded: chain H residue 484 ILE Chi-restraints excluded: chain H residue 570 ASN Chi-restraints excluded: chain H residue 580 ARG Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 567 ARG Chi-restraints excluded: chain I residue 581 ILE Chi-restraints excluded: chain I residue 614 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 0.7980 chunk 282 optimal weight: 0.7980 chunk 172 optimal weight: 5.9990 chunk 133 optimal weight: 0.5980 chunk 196 optimal weight: 0.5980 chunk 295 optimal weight: 5.9990 chunk 272 optimal weight: 7.9990 chunk 235 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 181 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN B 434 GLN C 434 GLN D 434 GLN F 508 GLN G 564 HIS H 434 GLN I 434 GLN I 570 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24471 Z= 0.168 Angle : 0.577 10.870 33156 Z= 0.287 Chirality : 0.044 0.285 3924 Planarity : 0.005 0.058 4239 Dihedral : 3.797 26.788 3285 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.60 % Allowed : 20.17 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.84 (0.16), residues: 3006 helix: 2.03 (0.14), residues: 1413 sheet: -0.74 (0.22), residues: 549 loop : -0.72 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 375 HIS 0.003 0.001 HIS C 564 PHE 0.007 0.001 PHE H 378 TYR 0.012 0.001 TYR C 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 325 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 282 time to evaluate : 2.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7417 (pt) REVERT: C 567 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.6979 (tmm160) REVERT: C 586 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: D 669 ILE cc_start: 0.8333 (mp) cc_final: 0.8120 (mm) REVERT: F 400 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7305 (pt) REVERT: F 453 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7316 (pptt) REVERT: F 669 ILE cc_start: 0.8462 (mm) cc_final: 0.8241 (mm) REVERT: G 598 MET cc_start: 0.6643 (mmt) cc_final: 0.6225 (mmt) REVERT: G 608 HIS cc_start: 0.8073 (m170) cc_final: 0.7871 (m-70) REVERT: H 562 ARG cc_start: 0.8211 (ptt90) cc_final: 0.7990 (ptt90) REVERT: I 567 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7586 (tmt170) outliers start: 43 outliers final: 22 residues processed: 319 average time/residue: 1.7070 time to fit residues: 608.6588 Evaluate side-chains 308 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 280 time to evaluate : 2.881 ------------------------------------------------------------------------------- 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 581 ILE Chi-restraints excluded: chain E residue 614 GLN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 614 GLN 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 580 ARG Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 614 GLN Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain H residue 484 ILE Chi-restraints excluded: chain H residue 580 ARG Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 567 ARG Chi-restraints excluded: chain I residue 581 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 3.9990 chunk 250 optimal weight: 0.3980 chunk 72 optimal weight: 0.8980 chunk 217 optimal weight: 2.9990 chunk 34 optimal weight: 0.0010 chunk 65 optimal weight: 0.6980 chunk 235 optimal weight: 0.0870 chunk 98 optimal weight: 7.9990 chunk 242 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 overall best weight: 0.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN ** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN C 434 GLN D 434 GLN G 564 HIS G 614 GLN I 434 GLN I 570 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.200381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.123870 restraints weight = 24369.180| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.99 r_work: 0.3277 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 24471 Z= 0.145 Angle : 0.556 14.794 33156 Z= 0.276 Chirality : 0.043 0.244 3924 Planarity : 0.005 0.058 4239 Dihedral : 3.651 25.495 3285 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.34 % Allowed : 20.40 % Favored : 78.26 % 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: 0.98 (0.15), residues: 3006 helix: 2.11 (0.14), residues: 1413 sheet: -0.39 (0.23), residues: 495 loop : -0.76 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 375 HIS 0.003 0.001 HIS I 564 PHE 0.007 0.001 PHE H 378 TYR 0.009 0.001 TYR G 405 ARG 0.014 0.001 ARG B 590 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11289.72 seconds wall clock time: 201 minutes 9.21 seconds (12069.21 seconds total)