Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 01:50:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7feb_31551/04_2023/7feb_31551.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7feb_31551/04_2023/7feb_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_31551/04_2023/7feb_31551.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7feb_31551/04_2023/7feb_31551.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7feb_31551/04_2023/7feb_31551.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7feb_31551/04_2023/7feb_31551.pdb" } resolution = 2.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 14.34, 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: 10.46 Conformation dependent library (CDL) restraints added in 3.6 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: 1.53 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: 7.86 Time building geometry restraints manager: 11.12 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: 4.860 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: 20.820 Check model and map are aligned: 0.360 Set scattering table: 0.190 Process input model: 62.660 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.140 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.935 Fit side-chains outliers start: 8 outliers final: 13 residues processed: 365 average time/residue: 1.6726 time to fit residues: 684.0591 Evaluate side-chains 311 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 298 time to evaluate : 2.716 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 5 residues processed: 8 average time/residue: 0.2089 time to fit residues: 7.2796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B 434 GLN 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 I 434 GLN I 438 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1058 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= 0.135 Angle : 0.488 5.800 33156 Z= 0.242 Chirality : 0.041 0.203 3924 Planarity : 0.004 0.039 4239 Dihedral : 3.595 21.033 3285 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer Outliers : 3.02 % 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: 0.65 (0.16), residues: 3006 helix: 1.88 (0.14), residues: 1413 sheet: -0.74 (0.21), residues: 549 loop : -0.88 (0.19), residues: 1044 *********************** 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 381 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 300 time to evaluate : 3.089 Fit side-chains outliers start: 81 outliers final: 29 residues processed: 371 average time/residue: 1.5316 time to fit residues: 642.1696 Evaluate side-chains 310 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 281 time to evaluate : 3.063 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 28 residues processed: 1 average time/residue: 0.2645 time to fit residues: 4.7838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 0.0770 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: 0.2980 chunk 291 optimal weight: 7.9990 chunk 240 optimal weight: 4.9990 chunk 267 optimal weight: 0.8980 chunk 92 optimal weight: 9.9990 chunk 216 optimal weight: 1.9990 overall best weight: 1.2542 ------------------------------------------------------------------------------- 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 B 438 ASN C 434 GLN D 434 GLN ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 GLN ** F 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 434 GLN ** G 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 434 GLN H 438 ASN H 570 ASN ** H 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 434 GLN I 438 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 24471 Z= 0.191 Angle : 0.544 9.493 33156 Z= 0.264 Chirality : 0.042 0.209 3924 Planarity : 0.004 0.040 4239 Dihedral : 3.774 22.014 3285 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer Outliers : 3.17 % 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: 0.69 (0.15), residues: 3006 helix: 1.92 (0.14), residues: 1413 sheet: -0.75 (0.21), residues: 549 loop : -0.85 (0.19), residues: 1044 *********************** 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 391 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 306 time to evaluate : 3.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 40 residues processed: 368 average time/residue: 1.6097 time to fit residues: 665.6620 Evaluate side-chains 319 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 279 time to evaluate : 2.832 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 30 residues processed: 10 average time/residue: 0.2138 time to fit residues: 8.0817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 0.9980 chunk 203 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 181 optimal weight: 0.0020 chunk 271 optimal weight: 1.9990 chunk 287 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 256 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- 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 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 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 434 GLN ** 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** I 614 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1328 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= 0.162 Angle : 0.516 6.967 33156 Z= 0.254 Chirality : 0.042 0.186 3924 Planarity : 0.004 0.046 4239 Dihedral : 3.679 19.202 3285 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 3.21 % 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: 0.78 (0.16), residues: 3006 helix: 1.99 (0.14), residues: 1413 sheet: -0.73 (0.21), residues: 549 loop : -0.79 (0.19), residues: 1044 *********************** 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 381 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 295 time to evaluate : 3.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 36 residues processed: 367 average time/residue: 1.5316 time to fit residues: 636.6602 Evaluate side-chains 324 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 288 time to evaluate : 2.911 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 32 residues processed: 4 average time/residue: 0.7568 time to fit residues: 7.8730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 4 optimal weight: 1.9990 chunk 213 optimal weight: 0.2980 chunk 118 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 198 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 257 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 434 GLN ** 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 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 434 GLN 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 24471 Z= 0.190 Angle : 0.548 10.684 33156 Z= 0.267 Chirality : 0.043 0.183 3924 Planarity : 0.004 0.036 4239 Dihedral : 3.793 22.863 3285 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer Outliers : 3.39 % 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: 1.97 (0.14), residues: 1413 sheet: -0.74 (0.21), residues: 549 loop : -0.78 (0.19), residues: 1044 *********************** 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 388 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 297 time to evaluate : 3.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 46 residues processed: 364 average time/residue: 1.6306 time to fit residues: 669.3190 Evaluate side-chains 325 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 279 time to evaluate : 2.983 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 34 residues processed: 12 average time/residue: 0.9497 time to fit residues: 17.8444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 4.9990 chunk 258 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 287 optimal weight: 5.9990 chunk 238 optimal weight: 8.9990 chunk 133 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 570 ASN ** F 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 434 GLN 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: 0.8077 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 24471 Z= 0.245 Angle : 0.579 8.708 33156 Z= 0.287 Chirality : 0.044 0.193 3924 Planarity : 0.005 0.041 4239 Dihedral : 3.941 21.685 3285 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 3.09 % 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: 1.85 (0.14), residues: 1413 sheet: -0.75 (0.22), residues: 549 loop : -0.76 (0.19), residues: 1044 *********************** 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 388 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 305 time to evaluate : 3.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 41 residues processed: 373 average time/residue: 1.6242 time to fit residues: 682.2204 Evaluate side-chains 325 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 284 time to evaluate : 2.996 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 37 residues processed: 5 average time/residue: 0.7295 time to fit residues: 9.2416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 163 optimal weight: 8.9990 chunk 209 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 241 optimal weight: 6.9990 chunk 160 optimal weight: 8.9990 chunk 286 optimal weight: 0.4980 chunk 179 optimal weight: 0.9980 chunk 174 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 570 ASN ** F 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 434 GLN G 564 HIS G 570 ASN ** G 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 434 GLN H 508 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 24471 Z= 0.286 Angle : 0.608 8.332 33156 Z= 0.305 Chirality : 0.046 0.209 3924 Planarity : 0.005 0.046 4239 Dihedral : 4.070 21.666 3285 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 3.21 % 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: 0.54 (0.15), residues: 3006 helix: 1.71 (0.14), residues: 1413 sheet: -0.79 (0.21), residues: 549 loop : -0.81 (0.19), residues: 1044 *********************** 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 385 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 299 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 45 residues processed: 360 average time/residue: 1.6694 time to fit residues: 677.0758 Evaluate side-chains 334 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 289 time to evaluate : 2.942 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 37 residues processed: 9 average time/residue: 0.2469 time to fit residues: 8.0754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 170 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 55 optimal weight: 0.0030 chunk 181 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 chunk 141 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 225 optimal weight: 6.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- 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 570 ASN ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 434 GLN G 570 ASN ** G 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 434 GLN H 508 GLN ** 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 24471 Z= 0.173 Angle : 0.551 7.837 33156 Z= 0.275 Chirality : 0.043 0.201 3924 Planarity : 0.005 0.044 4239 Dihedral : 3.834 20.154 3285 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 2.98 % 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: 0.73 (0.16), residues: 3006 helix: 1.92 (0.14), residues: 1413 sheet: -0.71 (0.21), residues: 549 loop : -0.80 (0.19), residues: 1044 *********************** 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 370 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 290 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 39 residues processed: 354 average time/residue: 1.6156 time to fit residues: 643.8102 Evaluate side-chains 315 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 276 time to evaluate : 2.648 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 36 residues processed: 3 average time/residue: 0.6641 time to fit residues: 6.4099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 160 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 209 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 241 optimal weight: 6.9990 chunk 252 optimal weight: 0.7980 chunk 265 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 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 434 GLN G 564 HIS 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 24471 Z= 0.178 Angle : 0.565 8.842 33156 Z= 0.282 Chirality : 0.043 0.202 3924 Planarity : 0.005 0.054 4239 Dihedral : 3.806 19.884 3285 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 2.65 % 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: 0.72 (0.16), residues: 3006 helix: 1.94 (0.14), residues: 1413 sheet: -0.75 (0.21), residues: 549 loop : -0.81 (0.19), residues: 1044 *********************** 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 353 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 282 time to evaluate : 3.089 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: symmetry clash outliers start: 71 outliers final: 41 residues processed: 343 average time/residue: 1.6636 time to fit residues: 641.4112 Evaluate side-chains 318 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 277 time to evaluate : 3.221 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 38 residues processed: 4 average time/residue: 0.6276 time to fit residues: 8.4214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 295 optimal weight: 0.3980 chunk 272 optimal weight: 7.9990 chunk 235 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 434 GLN G 564 HIS 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 24471 Z= 0.223 Angle : 0.592 8.311 33156 Z= 0.297 Chirality : 0.044 0.205 3924 Planarity : 0.005 0.059 4239 Dihedral : 3.912 21.108 3285 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 2.46 % 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: 0.60 (0.15), residues: 3006 helix: 1.83 (0.14), residues: 1413 sheet: -0.86 (0.21), residues: 549 loop : -0.83 (0.19), residues: 1044 ********************** 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 341 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 275 time to evaluate : 3.034 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 outliers start: 66 outliers final: 43 residues processed: 331 average time/residue: 1.7245 time to fit residues: 641.6223 Evaluate side-chains 317 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 274 time to evaluate : 2.652 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 41 residues processed: 3 average time/residue: 0.2376 time to fit residues: 5.0535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 5.9990 chunk 250 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 217 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 235 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 242 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 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 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 GLN F 570 ASN ** F 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 434 GLN G 564 HIS ** G 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 434 GLN H 438 ASN H 508 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.196782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117801 restraints weight = 24164.797| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.06 r_work: 0.3196 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 24471 Z= 0.276 Angle : 0.624 8.216 33156 Z= 0.314 Chirality : 0.046 0.216 3924 Planarity : 0.005 0.060 4239 Dihedral : 4.042 20.160 3285 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 2.80 % 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: 0.44 (0.15), residues: 3006 helix: 1.67 (0.14), residues: 1413 sheet: -0.96 (0.21), residues: 549 loop : -0.85 (0.19), residues: 1044 =============================================================================== Job complete usr+sys time: 11013.28 seconds wall clock time: 194 minutes 59.21 seconds (11699.21 seconds total)