Starting phenix.real_space_refine (version: dev) on Wed Apr 6 03:26:32 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5e_24187/04_2022/7n5e_24187_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5e_24187/04_2022/7n5e_24187.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5e_24187/04_2022/7n5e_24187.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5e_24187/04_2022/7n5e_24187.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5e_24187/04_2022/7n5e_24187_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5e_24187/04_2022/7n5e_24187_updated.pdb" } resolution = 2.8 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= 0.025 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 611": "OE1" <-> "OE2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 598": "OD1" <-> "OD2" Residue "C PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 625": "OE1" <-> "OE2" Residue "D TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 746": "OE1" <-> "OE2" Residue "E PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 611": "OE1" <-> "OE2" Residue "G PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 695": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 17915 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2579 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 7, 'TRANS': 308} Chain breaks: 2 Chain: "B" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2535 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 7, 'TRANS': 302} Chain breaks: 1 Chain: "C" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2535 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 7, 'TRANS': 302} Chain breaks: 1 Chain: "D" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2535 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 7, 'TRANS': 302} Chain breaks: 1 Chain: "E" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2535 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 7, 'TRANS': 302} Chain breaks: 1 Chain: "F" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2535 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 7, 'TRANS': 302} Chain breaks: 1 Chain: "G" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2535 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 7, 'TRANS': 302} Chain breaks: 1 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.21, per 1000 atoms: 0.57 Number of scatterers: 17915 At special positions: 0 Unit cell: (147.29, 144.2, 140.08, 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 77 16.00 O 3094 8.00 N 2960 7.00 C 11784 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: 6.56 Conformation dependent library (CDL) restraints added in 2.3 seconds 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4224 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 14 sheets defined 56.3% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 295 through 332 removed outlier: 4.266A pdb=" N HIS A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 352 Processing helix chain 'A' and resid 504 through 551 Processing helix chain 'A' and resid 557 through 573 removed outlier: 3.585A pdb=" N PHE A 572 " --> pdb=" O VAL A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 589 Processing helix chain 'A' and resid 631 through 636 removed outlier: 4.907A pdb=" N THR A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 678 Processing helix chain 'A' and resid 715 through 736 Processing helix chain 'B' and resid 296 through 330 removed outlier: 3.906A pdb=" N SER B 329 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 350 removed outlier: 5.032A pdb=" N ASP B 337 " --> pdb=" O ARG B 334 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 349 " --> pdb=" O HIS B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 551 removed outlier: 4.134A pdb=" N ASN B 525 " --> pdb=" O ALA B 521 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS B 526 " --> pdb=" O LEU B 522 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 527 " --> pdb=" O ASN B 523 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ALA B 528 " --> pdb=" O ASP B 524 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL B 529 " --> pdb=" O ASN B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 589 removed outlier: 5.467A pdb=" N ASN B 576 " --> pdb=" O PHE B 572 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N THR B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 636 removed outlier: 4.664A pdb=" N THR B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 677 Processing helix chain 'B' and resid 715 through 735 Processing helix chain 'C' and resid 296 through 330 removed outlier: 3.892A pdb=" N SER C 329 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHE C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 351 removed outlier: 5.010A pdb=" N ASP C 337 " --> pdb=" O ARG C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 551 removed outlier: 4.129A pdb=" N ASN C 525 " --> pdb=" O ALA C 521 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS C 526 " --> pdb=" O LEU C 522 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR C 527 " --> pdb=" O ASN C 523 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ALA C 528 " --> pdb=" O ASP C 524 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N VAL C 529 " --> pdb=" O ASN C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 589 removed outlier: 5.551A pdb=" N ASN C 576 " --> pdb=" O PHE C 572 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N THR C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 636 removed outlier: 4.970A pdb=" N THR C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 677 Processing helix chain 'C' and resid 715 through 736 Processing helix chain 'D' and resid 296 through 330 removed outlier: 3.709A pdb=" N SER D 328 " --> pdb=" O LYS D 324 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER D 329 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 351 removed outlier: 5.086A pdb=" N ASP D 337 " --> pdb=" O ARG D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 551 removed outlier: 4.146A pdb=" N ASN D 525 " --> pdb=" O ALA D 521 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS D 526 " --> pdb=" O LEU D 522 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR D 527 " --> pdb=" O ASN D 523 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA D 528 " --> pdb=" O ASP D 524 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL D 529 " --> pdb=" O ASN D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 589 removed outlier: 5.586A pdb=" N ASN D 576 " --> pdb=" O PHE D 572 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N THR D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 636 removed outlier: 5.031A pdb=" N THR D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 679 Processing helix chain 'D' and resid 715 through 736 Processing helix chain 'E' and resid 296 through 330 removed outlier: 3.648A pdb=" N SER E 328 " --> pdb=" O LYS E 324 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER E 329 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE E 330 " --> pdb=" O LEU E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 351 removed outlier: 5.103A pdb=" N ASP E 337 " --> pdb=" O ARG E 334 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU E 341 " --> pdb=" O ARG E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 523 Processing helix chain 'E' and resid 527 through 551 Processing helix chain 'E' and resid 557 through 589 removed outlier: 5.669A pdb=" N ASN E 576 " --> pdb=" O PHE E 572 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR E 577 " --> pdb=" O ILE E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 636 removed outlier: 4.850A pdb=" N THR E 636 " --> pdb=" O SER E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 662 through 677 Processing helix chain 'E' and resid 715 through 735 Processing helix chain 'F' and resid 296 through 330 removed outlier: 3.985A pdb=" N SER F 329 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE F 330 " --> pdb=" O LEU F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 351 removed outlier: 5.041A pdb=" N ASP F 337 " --> pdb=" O ARG F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 525 removed outlier: 4.147A pdb=" N ASN F 525 " --> pdb=" O ALA F 521 " (cutoff:3.500A) Processing helix chain 'F' and resid 527 through 551 Processing helix chain 'F' and resid 557 through 589 removed outlier: 5.688A pdb=" N ASN F 576 " --> pdb=" O PHE F 572 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR F 577 " --> pdb=" O ILE F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 636 removed outlier: 5.218A pdb=" N THR F 636 " --> pdb=" O SER F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 678 Processing helix chain 'F' and resid 715 through 736 Processing helix chain 'G' and resid 296 through 330 removed outlier: 3.906A pdb=" N SER G 329 " --> pdb=" O ILE G 325 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE G 330 " --> pdb=" O LEU G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 351 removed outlier: 5.016A pdb=" N ASP G 337 " --> pdb=" O ARG G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 508 through 525 removed outlier: 4.328A pdb=" N ASN G 525 " --> pdb=" O ALA G 521 " (cutoff:3.500A) Processing helix chain 'G' and resid 527 through 551 Processing helix chain 'G' and resid 557 through 589 removed outlier: 5.688A pdb=" N ASN G 576 " --> pdb=" O PHE G 572 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N THR G 577 " --> pdb=" O ILE G 573 " (cutoff:3.500A) Processing helix chain 'G' and resid 631 through 636 removed outlier: 5.129A pdb=" N THR G 636 " --> pdb=" O SER G 632 " (cutoff:3.500A) Processing helix chain 'G' and resid 662 through 678 Processing helix chain 'G' and resid 715 through 735 Processing sheet with id= A, first strand: chain 'A' and resid 639 through 641 removed outlier: 6.640A pdb=" N VAL A 618 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N MET A 612 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N THR A 616 " --> pdb=" O MET A 612 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 649 through 657 removed outlier: 6.783A pdb=" N ALA A 703 " --> pdb=" O VAL A 691 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N VAL A 691 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N PHE A 705 " --> pdb=" O MET A 689 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N MET A 689 " --> pdb=" O PHE A 705 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ASN A 707 " --> pdb=" O HIS A 687 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N HIS A 687 " --> pdb=" O ASN A 707 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 639 through 641 removed outlier: 6.843A pdb=" N VAL B 618 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N MET B 612 " --> pdb=" O THR B 616 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N THR B 616 " --> pdb=" O MET B 612 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 649 through 657 removed outlier: 6.749A pdb=" N ALA B 703 " --> pdb=" O VAL B 691 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL B 691 " --> pdb=" O ALA B 703 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE B 705 " --> pdb=" O MET B 689 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N MET B 689 " --> pdb=" O PHE B 705 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 639 through 641 removed outlier: 6.833A pdb=" N VAL C 618 " --> pdb=" O GLU C 610 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N MET C 612 " --> pdb=" O THR C 616 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N THR C 616 " --> pdb=" O MET C 612 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 649 through 657 removed outlier: 6.743A pdb=" N ALA C 703 " --> pdb=" O VAL C 691 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL C 691 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N PHE C 705 " --> pdb=" O MET C 689 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N MET C 689 " --> pdb=" O PHE C 705 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ASN C 707 " --> pdb=" O HIS C 687 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N HIS C 687 " --> pdb=" O ASN C 707 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 639 through 641 removed outlier: 6.513A pdb=" N VAL D 618 " --> pdb=" O GLU D 610 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N MET D 612 " --> pdb=" O THR D 616 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N THR D 616 " --> pdb=" O MET D 612 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 649 through 657 removed outlier: 6.772A pdb=" N ALA D 703 " --> pdb=" O VAL D 691 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL D 691 " --> pdb=" O ALA D 703 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N PHE D 705 " --> pdb=" O MET D 689 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N MET D 689 " --> pdb=" O PHE D 705 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 639 through 641 removed outlier: 6.665A pdb=" N VAL E 618 " --> pdb=" O GLU E 610 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N MET E 612 " --> pdb=" O THR E 616 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR E 616 " --> pdb=" O MET E 612 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 649 through 657 removed outlier: 6.774A pdb=" N ALA E 703 " --> pdb=" O VAL E 691 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N VAL E 691 " --> pdb=" O ALA E 703 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE E 705 " --> pdb=" O MET E 689 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N MET E 689 " --> pdb=" O PHE E 705 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 639 through 641 removed outlier: 6.799A pdb=" N VAL F 618 " --> pdb=" O GLU F 610 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 649 through 657 removed outlier: 6.713A pdb=" N ALA F 703 " --> pdb=" O VAL F 691 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL F 691 " --> pdb=" O ALA F 703 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N PHE F 705 " --> pdb=" O MET F 689 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N MET F 689 " --> pdb=" O PHE F 705 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ASN F 707 " --> pdb=" O HIS F 687 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N HIS F 687 " --> pdb=" O ASN F 707 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 599 through 602 removed outlier: 6.667A pdb=" N VAL G 618 " --> pdb=" O GLU G 610 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N MET G 612 " --> pdb=" O THR G 616 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR G 616 " --> pdb=" O MET G 612 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 649 through 657 removed outlier: 6.782A pdb=" N ALA G 703 " --> pdb=" O VAL G 691 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL G 691 " --> pdb=" O ALA G 703 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N PHE G 705 " --> pdb=" O MET G 689 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N MET G 689 " --> pdb=" O PHE G 705 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASN G 707 " --> pdb=" O HIS G 687 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N HIS G 687 " --> pdb=" O ASN G 707 " (cutoff:3.500A) 1132 hydrogen bonds defined for protein. 3093 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: 5.65 Time building geometry restraints manager: 7.17 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: 3350 1.31 - 1.44: 4632 1.44 - 1.56: 10105 1.56 - 1.69: 59 1.69 - 1.81: 133 Bond restraints: 18279 Sorted by residual: bond pdb=" CB HIS A 331 " pdb=" CG HIS A 331 " ideal model delta sigma weight residual 1.497 1.403 0.094 1.40e-02 5.10e+03 4.47e+01 bond pdb=" CD2 TRP D 507 " pdb=" CE3 TRP D 507 " ideal model delta sigma weight residual 1.398 1.505 -0.107 1.60e-02 3.91e+03 4.46e+01 bond pdb=" CD2 TRP B 507 " pdb=" CE3 TRP B 507 " ideal model delta sigma weight residual 1.398 1.503 -0.105 1.60e-02 3.91e+03 4.28e+01 bond pdb=" CZ2 TRP C 507 " pdb=" CH2 TRP C 507 " ideal model delta sigma weight residual 1.368 1.486 -0.118 1.90e-02 2.77e+03 3.82e+01 bond pdb=" CZ2 TRP E 507 " pdb=" CH2 TRP E 507 " ideal model delta sigma weight residual 1.368 1.483 -0.115 1.90e-02 2.77e+03 3.64e+01 ... (remaining 18274 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.71: 327 105.71 - 112.90: 9671 112.90 - 120.09: 7770 120.09 - 127.27: 6750 127.27 - 134.46: 198 Bond angle restraints: 24716 Sorted by residual: angle pdb=" CA PHE A 335 " pdb=" CB PHE A 335 " pdb=" CG PHE A 335 " ideal model delta sigma weight residual 113.80 122.08 -8.28 1.00e+00 1.00e+00 6.86e+01 angle pdb=" C GLN G 291 " pdb=" N PRO G 292 " pdb=" CA PRO G 292 " ideal model delta sigma weight residual 119.47 128.27 -8.80 1.16e+00 7.43e-01 5.76e+01 angle pdb=" C GLN C 291 " pdb=" N PRO C 292 " pdb=" CA PRO C 292 " ideal model delta sigma weight residual 119.56 127.00 -7.44 1.02e+00 9.61e-01 5.32e+01 angle pdb=" N THR C 557 " pdb=" CA THR C 557 " pdb=" C THR C 557 " ideal model delta sigma weight residual 112.89 121.73 -8.84 1.24e+00 6.50e-01 5.08e+01 angle pdb=" C HIS E 592 " pdb=" N PRO E 593 " pdb=" CA PRO E 593 " ideal model delta sigma weight residual 119.56 126.71 -7.15 1.01e+00 9.80e-01 5.02e+01 ... (remaining 24711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 10586 17.71 - 35.42: 253 35.42 - 53.13: 50 53.13 - 70.84: 30 70.84 - 88.54: 12 Dihedral angle restraints: 10931 sinusoidal: 4511 harmonic: 6420 Sorted by residual: dihedral pdb=" N PHE A 335 " pdb=" C PHE A 335 " pdb=" CA PHE A 335 " pdb=" CB PHE A 335 " ideal model delta harmonic sigma weight residual 122.80 130.99 -8.19 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" N ARG A 296 " pdb=" C ARG A 296 " pdb=" CA ARG A 296 " pdb=" CB ARG A 296 " ideal model delta harmonic sigma weight residual 122.80 114.64 8.16 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" CB GLU A 611 " pdb=" CG GLU A 611 " pdb=" CD GLU A 611 " pdb=" OE1 GLU A 611 " ideal model delta sinusoidal sigma weight residual 0.00 -88.54 88.54 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 10928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2091 0.092 - 0.185: 712 0.185 - 0.277: 110 0.277 - 0.370: 17 0.370 - 0.462: 1 Chirality restraints: 2931 Sorted by residual: chirality pdb=" CA THR C 557 " pdb=" N THR C 557 " pdb=" C THR C 557 " pdb=" CB THR C 557 " both_signs ideal model delta sigma weight residual False 2.53 2.06 0.46 2.00e-01 2.50e+01 5.34e+00 chirality pdb=" CA TRP B 304 " pdb=" N TRP B 304 " pdb=" C TRP B 304 " pdb=" CB TRP B 304 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA THR G 557 " pdb=" N THR G 557 " pdb=" C THR G 557 " pdb=" CB THR G 557 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 2928 not shown) Planarity restraints: 3023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 335 " -0.059 2.00e-02 2.50e+03 3.66e-02 2.35e+01 pdb=" CG PHE A 335 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE A 335 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 335 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE A 335 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 335 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 335 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 291 " 0.022 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C GLN E 291 " -0.074 2.00e-02 2.50e+03 pdb=" O GLN E 291 " 0.028 2.00e-02 2.50e+03 pdb=" N PRO E 292 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 675 " 0.044 2.00e-02 2.50e+03 2.53e-02 1.28e+01 pdb=" CG TYR E 675 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR E 675 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR E 675 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR E 675 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR E 675 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR E 675 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR E 675 " 0.042 2.00e-02 2.50e+03 ... (remaining 3020 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 6744 2.88 - 3.39: 18223 3.39 - 3.89: 30379 3.89 - 4.40: 35025 4.40 - 4.90: 56056 Nonbonded interactions: 146427 Sorted by model distance: nonbonded pdb=" OD1 ASP F 737 " pdb=" NZ LYS F 739 " model vdw 2.378 2.520 nonbonded pdb=" OD1 ASP G 737 " pdb=" NZ LYS G 739 " model vdw 2.385 2.520 nonbonded pdb=" OD1 ASP B 737 " pdb=" NZ LYS B 739 " model vdw 2.386 2.520 nonbonded pdb=" OD1 ASP D 737 " pdb=" NZ LYS D 739 " model vdw 2.399 2.520 nonbonded pdb=" OD1 ASP E 737 " pdb=" NZ LYS E 739 " model vdw 2.399 2.520 ... (remaining 146422 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' and (resid 294 through 354 or resid 507 through 751 or resid 801)) selection = (chain 'B' and (resid 294 through 751 or resid 801)) selection = (chain 'C' and (resid 294 through 751 or resid 801)) selection = (chain 'D' and (resid 294 through 751 or resid 801)) selection = (chain 'E' and (resid 294 through 751 or resid 801)) selection = (chain 'F' and (resid 294 through 751 or resid 801)) selection = (chain 'G' and (resid 294 through 751 or resid 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 77 5.16 5 C 11784 2.51 5 N 2960 2.21 5 O 3094 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.300 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: 0.010 Extract box with map and model: 6.090 Check model and map are aligned: 0.270 Convert atoms to be neutral: 0.160 Process input model: 45.660 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 : 0.023 0.132 18279 Z= 1.471 Angle : 1.544 8.842 24716 Z= 1.056 Chirality : 0.090 0.462 2931 Planarity : 0.008 0.043 3023 Dihedral : 10.255 88.544 6707 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 0.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer Outliers : 0.00 % 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: 1.87 (0.17), residues: 2146 helix: 1.62 (0.13), residues: 1206 sheet: 0.56 (0.31), residues: 290 loop : 1.09 (0.25), residues: 650 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 585 time to evaluate : 2.248 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 585 average time/residue: 1.2828 time to fit residues: 833.8411 Evaluate side-chains 508 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 507 time to evaluate : 1.836 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2506 time to fit residues: 3.0180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 197 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 HIS ** A 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN A 741 ASN C 531 GLN C 648 GLN C 688 ASN C 698 ASN D 533 ASN D 698 ASN D 713 GLN E 531 GLN E 648 GLN E 698 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN F 576 ASN G 719 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 18279 Z= 0.256 Angle : 0.575 7.060 24716 Z= 0.317 Chirality : 0.044 0.187 2931 Planarity : 0.004 0.028 3023 Dihedral : 7.428 58.296 2365 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer Outliers : 2.74 % 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: 2.70 (0.18), residues: 2146 helix: 2.65 (0.14), residues: 1196 sheet: 0.50 (0.27), residues: 329 loop : 0.92 (0.29), residues: 621 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 531 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 20 residues processed: 542 average time/residue: 1.2455 time to fit residues: 754.8070 Evaluate side-chains 536 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 516 time to evaluate : 2.010 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 4 residues processed: 17 average time/residue: 0.6268 time to fit residues: 15.8423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 109 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 197 optimal weight: 0.9990 chunk 213 optimal weight: 0.7980 chunk 175 optimal weight: 2.9990 chunk 195 optimal weight: 0.5980 chunk 67 optimal weight: 9.9990 chunk 158 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN B 698 ASN C 531 GLN ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 686 GLN E 531 GLN E 576 ASN E 648 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 681 ASN G 531 GLN G 681 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 18279 Z= 0.269 Angle : 0.530 7.079 24716 Z= 0.288 Chirality : 0.042 0.139 2931 Planarity : 0.004 0.037 3023 Dihedral : 7.478 56.803 2365 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer Outliers : 3.14 % 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: 2.62 (0.19), residues: 2146 helix: 2.73 (0.14), residues: 1190 sheet: 0.53 (0.28), residues: 324 loop : 0.54 (0.28), residues: 632 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 525 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 26 residues processed: 533 average time/residue: 1.2621 time to fit residues: 751.4014 Evaluate side-chains 530 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 504 time to evaluate : 2.306 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 7 residues processed: 21 average time/residue: 0.5485 time to fit residues: 17.7495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 0.6980 chunk 148 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 198 optimal weight: 0.5980 chunk 209 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 187 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN E 648 GLN G 531 GLN G 681 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 18279 Z= 0.219 Angle : 0.494 11.547 24716 Z= 0.265 Chirality : 0.042 0.375 2931 Planarity : 0.003 0.024 3023 Dihedral : 7.200 58.626 2365 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer Outliers : 3.24 % 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: 2.75 (0.19), residues: 2146 helix: 2.90 (0.14), residues: 1184 sheet: 0.45 (0.27), residues: 329 loop : 0.55 (0.29), residues: 633 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 510 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 32 residues processed: 529 average time/residue: 1.2972 time to fit residues: 764.2534 Evaluate side-chains 536 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 504 time to evaluate : 2.023 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 11 residues processed: 23 average time/residue: 0.5567 time to fit residues: 18.9155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 174 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 86 optimal weight: 0.0020 chunk 178 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 188 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN E 648 GLN G 531 GLN G 681 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 18279 Z= 0.288 Angle : 0.508 8.923 24716 Z= 0.272 Chirality : 0.042 0.137 2931 Planarity : 0.004 0.029 3023 Dihedral : 7.192 59.651 2365 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 3.44 % 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: 2.68 (0.19), residues: 2146 helix: 2.90 (0.14), residues: 1184 sheet: 0.35 (0.27), residues: 329 loop : 0.43 (0.29), residues: 633 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 514 time to evaluate : 2.233 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 39 residues processed: 532 average time/residue: 1.2908 time to fit residues: 765.5731 Evaluate side-chains 544 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 505 time to evaluate : 2.179 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 12 residues processed: 28 average time/residue: 0.4040 time to fit residues: 18.3621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 0.8980 chunk 188 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 209 optimal weight: 1.9990 chunk 174 optimal weight: 0.4980 chunk 97 optimal weight: 6.9990 chunk 17 optimal weight: 0.0770 chunk 69 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN F 698 ASN ** G 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN G 688 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 18279 Z= 0.179 Angle : 0.463 11.941 24716 Z= 0.249 Chirality : 0.040 0.128 2931 Planarity : 0.003 0.027 3023 Dihedral : 6.986 59.482 2365 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer Outliers : 2.99 % 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: 2.82 (0.19), residues: 2146 helix: 3.05 (0.14), residues: 1185 sheet: 0.25 (0.27), residues: 329 loop : 0.49 (0.29), residues: 632 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 522 time to evaluate : 2.615 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 33 residues processed: 543 average time/residue: 1.3569 time to fit residues: 820.6333 Evaluate side-chains 549 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 516 time to evaluate : 2.178 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 10 residues processed: 24 average time/residue: 0.6393 time to fit residues: 21.5994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 153 optimal weight: 0.0970 chunk 118 optimal weight: 0.8980 chunk 176 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 chunk 209 optimal weight: 0.6980 chunk 130 optimal weight: 40.0000 chunk 127 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN E 648 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 18279 Z= 0.192 Angle : 0.479 9.040 24716 Z= 0.256 Chirality : 0.040 0.129 2931 Planarity : 0.003 0.026 3023 Dihedral : 7.019 59.198 2365 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer Outliers : 2.84 % 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: 2.85 (0.19), residues: 2146 helix: 3.07 (0.14), residues: 1185 sheet: 0.27 (0.29), residues: 299 loop : 0.51 (0.28), residues: 662 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 505 time to evaluate : 2.273 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 31 residues processed: 523 average time/residue: 1.2974 time to fit residues: 761.5224 Evaluate side-chains 536 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 505 time to evaluate : 2.244 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 14 residues processed: 20 average time/residue: 0.4762 time to fit residues: 15.6687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 129 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 142 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN B 687 HIS ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 18279 Z= 0.219 Angle : 0.488 9.196 24716 Z= 0.259 Chirality : 0.040 0.126 2931 Planarity : 0.003 0.027 3023 Dihedral : 7.050 58.661 2365 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer Outliers : 2.14 % 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: 2.82 (0.19), residues: 2146 helix: 3.06 (0.14), residues: 1186 sheet: 0.24 (0.29), residues: 299 loop : 0.47 (0.28), residues: 661 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 507 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 28 residues processed: 523 average time/residue: 1.2995 time to fit residues: 757.5078 Evaluate side-chains 535 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 507 time to evaluate : 1.919 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 11 residues processed: 18 average time/residue: 0.5788 time to fit residues: 15.5934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 190 optimal weight: 0.0870 chunk 200 optimal weight: 0.0980 chunk 182 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 184 optimal weight: 0.5980 chunk 127 optimal weight: 4.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN B 515 GLN ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN F 531 GLN ** F 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 698 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 18279 Z= 0.148 Angle : 0.466 9.493 24716 Z= 0.246 Chirality : 0.039 0.130 2931 Planarity : 0.003 0.026 3023 Dihedral : 6.884 59.709 2365 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 2.00 % 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: 2.91 (0.19), residues: 2146 helix: 3.14 (0.14), residues: 1186 sheet: 0.19 (0.29), residues: 299 loop : 0.53 (0.29), residues: 661 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 506 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 22 residues processed: 523 average time/residue: 1.2927 time to fit residues: 753.3330 Evaluate side-chains 522 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 500 time to evaluate : 2.230 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 9 residues processed: 14 average time/residue: 0.3959 time to fit residues: 10.4492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 143 optimal weight: 0.2980 chunk 216 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 132 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 686 GLN B 613 ASN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 GLN ** G 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 613 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 18279 Z= 0.274 Angle : 0.520 10.486 24716 Z= 0.274 Chirality : 0.041 0.135 2931 Planarity : 0.003 0.029 3023 Dihedral : 6.990 59.712 2365 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 1.40 % 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: 2.70 (0.19), residues: 2146 helix: 3.00 (0.14), residues: 1192 sheet: 0.18 (0.29), residues: 299 loop : 0.31 (0.28), residues: 655 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 510 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 17 residues processed: 524 average time/residue: 1.3046 time to fit residues: 762.4229 Evaluate side-chains 525 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 508 time to evaluate : 2.074 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 8 residues processed: 10 average time/residue: 0.4447 time to fit residues: 8.8272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 172 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 chunk 151 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 686 GLN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 531 GLN G 698 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.164297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.129024 restraints weight = 25249.142| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.73 r_work: 0.3553 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 1.55 restraints_weight: 0.2500 r_work: 0.3519 rms_B_bonded: 1.63 restraints_weight: 0.1250 r_work: 0.3500 rms_B_bonded: 1.78 restraints_weight: 0.0625 r_work: 0.3479 rms_B_bonded: 1.99 restraints_weight: 0.0312 r_work: 0.3455 rms_B_bonded: 2.26 restraints_weight: 0.0156 r_work: 0.3428 rms_B_bonded: 2.59 restraints_weight: 0.0078 r_work: 0.3398 rms_B_bonded: 3.00 restraints_weight: 0.0039 r_work: 0.3362 rms_B_bonded: 3.50 restraints_weight: 0.0020 r_work: 0.3321 rms_B_bonded: 4.11 restraints_weight: 0.0010 r_work: 0.3272 rms_B_bonded: 4.84 restraints_weight: 0.0005 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 18279 Z= 0.208 Angle : 0.497 9.076 24716 Z= 0.262 Chirality : 0.040 0.150 2931 Planarity : 0.003 0.028 3023 Dihedral : 6.889 57.869 2365 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 1.10 % 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: 2.79 (0.19), residues: 2146 helix: 3.06 (0.14), residues: 1186 sheet: 0.14 (0.29), residues: 299 loop : 0.43 (0.28), residues: 661 =============================================================================== Job complete usr+sys time: 9663.26 seconds wall clock time: 170 minutes 48.82 seconds (10248.82 seconds total)