Starting phenix.real_space_refine (version: dev) on Thu Feb 23 00:03:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8o_10402/02_2023/6t8o_10402_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8o_10402/02_2023/6t8o_10402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8o_10402/02_2023/6t8o_10402.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8o_10402/02_2023/6t8o_10402.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8o_10402/02_2023/6t8o_10402_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8o_10402/02_2023/6t8o_10402_updated.pdb" } resolution = 3.99 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= 0.000 sd= 0.004 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 Process input model Symmetric amino acids flipped Residue "A ARG 341": "NH1" <-> "NH2" Residue "A ARG 367": "NH1" <-> "NH2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A ARG 398": "NH1" <-> "NH2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "A ARG 493": "NH1" <-> "NH2" Residue "A ARG 529": "NH1" <-> "NH2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A ARG 538": "NH1" <-> "NH2" Residue "A ARG 540": "NH1" <-> "NH2" Residue "A ARG 548": "NH1" <-> "NH2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A ARG 620": "NH1" <-> "NH2" Residue "A ARG 632": "NH1" <-> "NH2" Residue "A ARG 649": "NH1" <-> "NH2" Residue "A ARG 661": "NH1" <-> "NH2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A ARG 703": "NH1" <-> "NH2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "B ARG 341": "NH1" <-> "NH2" Residue "B ARG 367": "NH1" <-> "NH2" Residue "B ARG 380": "NH1" <-> "NH2" Residue "B ARG 390": "NH1" <-> "NH2" Residue "B ARG 398": "NH1" <-> "NH2" Residue "B ARG 418": "NH1" <-> "NH2" Residue "B ARG 422": "NH1" <-> "NH2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "B ARG 493": "NH1" <-> "NH2" Residue "B ARG 529": "NH1" <-> "NH2" Residue "B ARG 537": "NH1" <-> "NH2" Residue "B ARG 538": "NH1" <-> "NH2" Residue "B ARG 540": "NH1" <-> "NH2" Residue "B ARG 548": "NH1" <-> "NH2" Residue "B ARG 555": "NH1" <-> "NH2" Residue "B ARG 614": "NH1" <-> "NH2" Residue "B ARG 620": "NH1" <-> "NH2" Residue "B ARG 632": "NH1" <-> "NH2" Residue "B ARG 649": "NH1" <-> "NH2" Residue "B ARG 661": "NH1" <-> "NH2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B ARG 703": "NH1" <-> "NH2" Residue "B ARG 711": "NH1" <-> "NH2" Residue "C ARG 341": "NH1" <-> "NH2" Residue "C ARG 367": "NH1" <-> "NH2" Residue "C ARG 380": "NH1" <-> "NH2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "C ARG 398": "NH1" <-> "NH2" Residue "C ARG 418": "NH1" <-> "NH2" Residue "C ARG 422": "NH1" <-> "NH2" Residue "C ARG 450": "NH1" <-> "NH2" Residue "C ARG 493": "NH1" <-> "NH2" Residue "C ARG 529": "NH1" <-> "NH2" Residue "C ARG 537": "NH1" <-> "NH2" Residue "C ARG 538": "NH1" <-> "NH2" Residue "C ARG 540": "NH1" <-> "NH2" Residue "C ARG 548": "NH1" <-> "NH2" Residue "C ARG 555": "NH1" <-> "NH2" Residue "C ARG 614": "NH1" <-> "NH2" Residue "C ARG 620": "NH1" <-> "NH2" Residue "C ARG 632": "NH1" <-> "NH2" Residue "C ARG 649": "NH1" <-> "NH2" Residue "C ARG 661": "NH1" <-> "NH2" Residue "C ARG 690": "NH1" <-> "NH2" Residue "C ARG 703": "NH1" <-> "NH2" Residue "C ARG 711": "NH1" <-> "NH2" Residue "D ARG 341": "NH1" <-> "NH2" Residue "D ARG 367": "NH1" <-> "NH2" Residue "D ARG 380": "NH1" <-> "NH2" Residue "D ARG 390": "NH1" <-> "NH2" Residue "D ARG 398": "NH1" <-> "NH2" Residue "D ARG 418": "NH1" <-> "NH2" Residue "D ARG 422": "NH1" <-> "NH2" Residue "D ARG 450": "NH1" <-> "NH2" Residue "D ARG 493": "NH1" <-> "NH2" Residue "D ARG 529": "NH1" <-> "NH2" Residue "D ARG 537": "NH1" <-> "NH2" Residue "D ARG 538": "NH1" <-> "NH2" Residue "D ARG 540": "NH1" <-> "NH2" Residue "D ARG 548": "NH1" <-> "NH2" Residue "D ARG 555": "NH1" <-> "NH2" Residue "D ARG 614": "NH1" <-> "NH2" Residue "D ARG 620": "NH1" <-> "NH2" Residue "D ARG 632": "NH1" <-> "NH2" Residue "D ARG 649": "NH1" <-> "NH2" Residue "D ARG 661": "NH1" <-> "NH2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D ARG 703": "NH1" <-> "NH2" Residue "D ARG 711": "NH1" <-> "NH2" Residue "E ARG 341": "NH1" <-> "NH2" Residue "E ARG 367": "NH1" <-> "NH2" Residue "E ARG 380": "NH1" <-> "NH2" Residue "E ARG 390": "NH1" <-> "NH2" Residue "E ARG 398": "NH1" <-> "NH2" Residue "E ARG 418": "NH1" <-> "NH2" Residue "E ARG 422": "NH1" <-> "NH2" Residue "E ARG 450": "NH1" <-> "NH2" Residue "E ARG 493": "NH1" <-> "NH2" Residue "E ARG 529": "NH1" <-> "NH2" Residue "E ARG 537": "NH1" <-> "NH2" Residue "E ARG 538": "NH1" <-> "NH2" Residue "E ARG 540": "NH1" <-> "NH2" Residue "E ARG 548": "NH1" <-> "NH2" Residue "E ARG 555": "NH1" <-> "NH2" Residue "E ARG 614": "NH1" <-> "NH2" Residue "E ARG 620": "NH1" <-> "NH2" Residue "E ARG 632": "NH1" <-> "NH2" Residue "E ARG 649": "NH1" <-> "NH2" Residue "E ARG 661": "NH1" <-> "NH2" Residue "E ARG 690": "NH1" <-> "NH2" Residue "E ARG 703": "NH1" <-> "NH2" Residue "E ARG 711": "NH1" <-> "NH2" Residue "F ARG 341": "NH1" <-> "NH2" Residue "F ARG 367": "NH1" <-> "NH2" Residue "F ARG 380": "NH1" <-> "NH2" Residue "F ARG 390": "NH1" <-> "NH2" Residue "F ARG 398": "NH1" <-> "NH2" Residue "F ARG 418": "NH1" <-> "NH2" Residue "F ARG 422": "NH1" <-> "NH2" Residue "F ARG 450": "NH1" <-> "NH2" Residue "F ARG 493": "NH1" <-> "NH2" Residue "F ARG 529": "NH1" <-> "NH2" Residue "F ARG 537": "NH1" <-> "NH2" Residue "F ARG 538": "NH1" <-> "NH2" Residue "F ARG 540": "NH1" <-> "NH2" Residue "F ARG 548": "NH1" <-> "NH2" Residue "F ARG 555": "NH1" <-> "NH2" Residue "F ARG 614": "NH1" <-> "NH2" Residue "F ARG 620": "NH1" <-> "NH2" Residue "F ARG 632": "NH1" <-> "NH2" Residue "F ARG 649": "NH1" <-> "NH2" Residue "F ARG 661": "NH1" <-> "NH2" Residue "F ARG 690": "NH1" <-> "NH2" Residue "F ARG 703": "NH1" <-> "NH2" Residue "F ARG 711": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 18806 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3014 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 368} Chain breaks: 1 Chain: "B" Number of atoms: 2991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2991 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 365} Chain breaks: 1 Chain: "C" Number of atoms: 3038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3038 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 371} Chain breaks: 1 Chain: "D" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3018 Classifications: {'peptide': 396} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 369} Chain breaks: 1 Chain: "E" Number of atoms: 3021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3021 Classifications: {'peptide': 396} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 368} Chain breaks: 1 Chain: "F" Number of atoms: 3029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3029 Classifications: {'peptide': 397} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 369} Chain breaks: 1 Chain: "G" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "H" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 266 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.38, per 1000 atoms: 0.55 Number of scatterers: 18806 At special positions: 0 Unit cell: (140.432, 103.752, 132.048, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 P 38 15.00 O 3583 8.00 N 3249 7.00 C 11846 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: 7.03 Conformation dependent library (CDL) restraints added in 2.9 seconds 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4424 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 93 helices and 21 sheets defined 36.5% alpha, 13.9% beta 13 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 5.67 Creating SS restraints... Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'A' and resid 333 through 349 removed outlier: 3.778A pdb=" N MET A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 391 removed outlier: 5.057A pdb=" N LYS A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ASP A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 427 No H-bonds generated for 'chain 'A' and resid 424 through 427' Processing helix chain 'A' and resid 430 through 433 No H-bonds generated for 'chain 'A' and resid 430 through 433' Processing helix chain 'A' and resid 473 through 484 Processing helix chain 'A' and resid 504 through 507 removed outlier: 3.706A pdb=" N TYR A 507 " --> pdb=" O LEU A 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 504 through 507' Processing helix chain 'A' and resid 521 through 545 Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 568 through 583 No H-bonds generated for 'chain 'A' and resid 568 through 583' Processing helix chain 'A' and resid 597 through 603 Processing helix chain 'A' and resid 607 through 616 Processing helix chain 'A' and resid 619 through 621 No H-bonds generated for 'chain 'A' and resid 619 through 621' Processing helix chain 'A' and resid 657 through 663 Processing helix chain 'A' and resid 698 through 709 Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'B' and resid 318 through 320 No H-bonds generated for 'chain 'B' and resid 318 through 320' Processing helix chain 'B' and resid 333 through 349 Processing helix chain 'B' and resid 378 through 391 removed outlier: 4.096A pdb=" N LEU B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA B 385 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LYS B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASP B 387 " --> pdb=" O ASN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 427 Processing helix chain 'B' and resid 430 through 433 No H-bonds generated for 'chain 'B' and resid 430 through 433' Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 472 through 486 removed outlier: 4.134A pdb=" N LYS B 486 " --> pdb=" O SER B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 507 removed outlier: 4.089A pdb=" N ILE B 506 " --> pdb=" O GLU B 503 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR B 507 " --> pdb=" O LEU B 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 503 through 507' Processing helix chain 'B' and resid 521 through 545 Processing helix chain 'B' and resid 550 through 562 Processing helix chain 'B' and resid 597 through 603 removed outlier: 3.757A pdb=" N MET B 602 " --> pdb=" O ALA B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 620 removed outlier: 3.652A pdb=" N GLU B 610 " --> pdb=" O LYS B 607 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 617 " --> pdb=" O ARG B 614 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS B 618 " --> pdb=" O ILE B 615 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ALA B 619 " --> pdb=" O ALA B 616 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG B 620 " --> pdb=" O GLN B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 645 removed outlier: 4.643A pdb=" N ASN B 645 " --> pdb=" O LEU B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 662 No H-bonds generated for 'chain 'B' and resid 660 through 662' Processing helix chain 'B' and resid 698 through 709 Processing helix chain 'C' and resid 333 through 348 Processing helix chain 'C' and resid 379 through 392 removed outlier: 5.546A pdb=" N LEU C 384 " --> pdb=" O ARG C 380 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA C 385 " --> pdb=" O ILE C 381 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS C 386 " --> pdb=" O SER C 382 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP C 387 " --> pdb=" O ASN C 383 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 392 " --> pdb=" O LEU C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 427 Processing helix chain 'C' and resid 430 through 433 No H-bonds generated for 'chain 'C' and resid 430 through 433' Processing helix chain 'C' and resid 473 through 484 Processing helix chain 'C' and resid 504 through 507 Processing helix chain 'C' and resid 521 through 545 Processing helix chain 'C' and resid 550 through 562 Processing helix chain 'C' and resid 597 through 603 Processing helix chain 'C' and resid 606 through 616 Processing helix chain 'C' and resid 642 through 645 No H-bonds generated for 'chain 'C' and resid 642 through 645' Processing helix chain 'C' and resid 657 through 663 Processing helix chain 'C' and resid 669 through 671 No H-bonds generated for 'chain 'C' and resid 669 through 671' Processing helix chain 'C' and resid 698 through 709 Processing helix chain 'C' and resid 718 through 720 No H-bonds generated for 'chain 'C' and resid 718 through 720' Processing helix chain 'D' and resid 318 through 320 No H-bonds generated for 'chain 'D' and resid 318 through 320' Processing helix chain 'D' and resid 333 through 349 Processing helix chain 'D' and resid 379 through 391 removed outlier: 5.248A pdb=" N LEU D 384 " --> pdb=" O ARG D 380 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA D 385 " --> pdb=" O ILE D 381 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N LYS D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASP D 387 " --> pdb=" O ASN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 427 Processing helix chain 'D' and resid 430 through 433 No H-bonds generated for 'chain 'D' and resid 430 through 433' Processing helix chain 'D' and resid 456 through 458 No H-bonds generated for 'chain 'D' and resid 456 through 458' Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 504 through 507 removed outlier: 3.628A pdb=" N TYR D 507 " --> pdb=" O LEU D 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 504 through 507' Processing helix chain 'D' and resid 522 through 545 Processing helix chain 'D' and resid 550 through 562 removed outlier: 3.557A pdb=" N GLU D 561 " --> pdb=" O VAL D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 603 Processing helix chain 'D' and resid 606 through 616 Processing helix chain 'D' and resid 640 through 645 removed outlier: 3.836A pdb=" N ASN D 645 " --> pdb=" O LEU D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 663 Processing helix chain 'D' and resid 669 through 671 No H-bonds generated for 'chain 'D' and resid 669 through 671' Processing helix chain 'D' and resid 698 through 711 removed outlier: 3.703A pdb=" N ARG D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 720 No H-bonds generated for 'chain 'D' and resid 718 through 720' Processing helix chain 'E' and resid 318 through 320 No H-bonds generated for 'chain 'E' and resid 318 through 320' Processing helix chain 'E' and resid 333 through 349 Processing helix chain 'E' and resid 379 through 392 removed outlier: 5.787A pdb=" N LEU E 384 " --> pdb=" O ARG E 380 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA E 385 " --> pdb=" O ILE E 381 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LYS E 386 " --> pdb=" O SER E 382 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASP E 387 " --> pdb=" O ASN E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 427 Processing helix chain 'E' and resid 430 through 433 No H-bonds generated for 'chain 'E' and resid 430 through 433' Processing helix chain 'E' and resid 473 through 484 Processing helix chain 'E' and resid 521 through 545 Processing helix chain 'E' and resid 550 through 562 Processing helix chain 'E' and resid 597 through 603 Processing helix chain 'E' and resid 606 through 618 removed outlier: 4.294A pdb=" N LYS E 618 " --> pdb=" O ARG E 614 " (cutoff:3.500A) Processing helix chain 'E' and resid 640 through 643 No H-bonds generated for 'chain 'E' and resid 640 through 643' Processing helix chain 'E' and resid 657 through 663 Processing helix chain 'E' and resid 669 through 671 No H-bonds generated for 'chain 'E' and resid 669 through 671' Processing helix chain 'E' and resid 698 through 709 Processing helix chain 'F' and resid 318 through 320 No H-bonds generated for 'chain 'F' and resid 318 through 320' Processing helix chain 'F' and resid 333 through 349 Processing helix chain 'F' and resid 379 through 391 removed outlier: 5.183A pdb=" N LEU F 384 " --> pdb=" O ARG F 380 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA F 385 " --> pdb=" O ILE F 381 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LYS F 386 " --> pdb=" O SER F 382 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASP F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 427 Processing helix chain 'F' and resid 430 through 433 No H-bonds generated for 'chain 'F' and resid 430 through 433' Processing helix chain 'F' and resid 456 through 458 No H-bonds generated for 'chain 'F' and resid 456 through 458' Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'F' and resid 504 through 507 removed outlier: 3.633A pdb=" N TYR F 507 " --> pdb=" O LEU F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 504 through 507' Processing helix chain 'F' and resid 521 through 545 Processing helix chain 'F' and resid 550 through 562 Processing helix chain 'F' and resid 597 through 604 Processing helix chain 'F' and resid 606 through 618 Processing helix chain 'F' and resid 640 through 645 removed outlier: 3.921A pdb=" N ASN F 645 " --> pdb=" O LEU F 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 657 through 664 Processing helix chain 'F' and resid 698 through 711 Processing helix chain 'F' and resid 718 through 720 No H-bonds generated for 'chain 'F' and resid 718 through 720' Processing sheet with id= A, first strand: chain 'A' and resid 398 through 400 removed outlier: 5.854A pdb=" N GLN A 371 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N VAL A 356 " --> pdb=" O GLN A 371 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 688 through 691 removed outlier: 3.656A pdb=" N ALA A 651 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A 649 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LEU A 463 " --> pdb=" O ILE A 650 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE A 590 " --> pdb=" O HIS A 625 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ILE A 627 " --> pdb=" O ILE A 590 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 592 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ALA A 629 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL A 594 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 591 " --> pdb=" O ARG A 493 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 495 " --> pdb=" O VAL A 591 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 440 through 445 removed outlier: 3.633A pdb=" N LEU A 443 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ILE A 452 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 398 through 400 removed outlier: 5.745A pdb=" N GLN B 371 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL B 356 " --> pdb=" O GLN B 371 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 649 through 651 removed outlier: 7.304A pdb=" N ILE B 650 " --> pdb=" O HIS B 461 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LEU B 463 " --> pdb=" O ILE B 650 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N LEU B 462 " --> pdb=" O ILE B 624 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU B 626 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL B 464 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU B 628 " --> pdb=" O VAL B 464 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE B 590 " --> pdb=" O HIS B 625 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE B 627 " --> pdb=" O ILE B 590 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL B 592 " --> pdb=" O ILE B 627 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA B 629 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL B 594 " --> pdb=" O ALA B 629 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 591 " --> pdb=" O ARG B 493 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 677 through 680 Processing sheet with id= G, first strand: chain 'B' and resid 440 through 445 removed outlier: 3.622A pdb=" N LEU B 441 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 443 " --> pdb=" O ILE B 452 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE B 452 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 398 through 400 removed outlier: 5.971A pdb=" N GLN C 371 " --> pdb=" O VAL C 356 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VAL C 356 " --> pdb=" O GLN C 371 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 689 through 692 removed outlier: 3.728A pdb=" N ALA C 651 " --> pdb=" O LEU C 679 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU C 463 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE C 590 " --> pdb=" O HIS C 625 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ILE C 627 " --> pdb=" O ILE C 590 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL C 592 " --> pdb=" O ILE C 627 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ALA C 629 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL C 594 " --> pdb=" O ALA C 629 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 440 through 445 removed outlier: 6.937A pdb=" N ILE C 452 " --> pdb=" O LEU C 443 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 398 through 400 removed outlier: 6.169A pdb=" N GLN D 371 " --> pdb=" O VAL D 356 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL D 356 " --> pdb=" O GLN D 371 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 689 through 692 removed outlier: 3.784A pdb=" N ARG D 649 " --> pdb=" O LEU D 681 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ILE D 650 " --> pdb=" O HIS D 461 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU D 463 " --> pdb=" O ILE D 650 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N LEU D 462 " --> pdb=" O ILE D 624 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU D 626 " --> pdb=" O LEU D 462 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL D 464 " --> pdb=" O LEU D 626 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU D 628 " --> pdb=" O VAL D 464 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE D 590 " --> pdb=" O HIS D 625 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ILE D 627 " --> pdb=" O ILE D 590 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL D 592 " --> pdb=" O ILE D 627 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ALA D 629 " --> pdb=" O VAL D 592 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL D 594 " --> pdb=" O ALA D 629 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 440 through 445 removed outlier: 7.070A pdb=" N ILE D 452 " --> pdb=" O LEU D 443 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 398 through 400 removed outlier: 5.959A pdb=" N GLN E 371 " --> pdb=" O VAL E 356 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL E 356 " --> pdb=" O GLN E 371 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 461 through 464 removed outlier: 6.377A pdb=" N LEU E 626 " --> pdb=" O LEU E 462 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N VAL E 464 " --> pdb=" O LEU E 626 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU E 628 " --> pdb=" O VAL E 464 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 649 through 651 removed outlier: 3.667A pdb=" N ARG E 649 " --> pdb=" O LEU E 681 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 440 through 445 removed outlier: 6.914A pdb=" N ILE E 452 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 398 through 400 removed outlier: 5.977A pdb=" N GLN F 371 " --> pdb=" O VAL F 356 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N VAL F 356 " --> pdb=" O GLN F 371 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 463 through 465 Processing sheet with id= T, first strand: chain 'F' and resid 494 through 497 removed outlier: 6.192A pdb=" N VAL F 591 " --> pdb=" O ILE F 495 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ILE F 497 " --> pdb=" O VAL F 591 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL F 593 " --> pdb=" O ILE F 497 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N HIS F 625 " --> pdb=" O VAL F 592 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL F 594 " --> pdb=" O HIS F 625 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE F 627 " --> pdb=" O VAL F 594 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 440 through 445 removed outlier: 6.770A pdb=" N ILE F 452 " --> pdb=" O LEU F 443 " (cutoff:3.500A) 648 hydrogen bonds defined for protein. 1851 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 5.52 Time building geometry restraints manager: 7.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5388 1.33 - 1.45: 2468 1.45 - 1.57: 11092 1.57 - 1.69: 68 1.69 - 1.81: 174 Bond restraints: 19190 Sorted by residual: bond pdb=" C SER A 332 " pdb=" N PRO A 333 " ideal model delta sigma weight residual 1.335 1.363 -0.029 1.28e-02 6.10e+03 5.03e+00 bond pdb=" C LEU E 514 " pdb=" N CYS E 515 " ideal model delta sigma weight residual 1.339 1.217 0.122 5.57e-02 3.22e+02 4.80e+00 bond pdb=" C ALA A 713 " pdb=" N PRO A 714 " ideal model delta sigma weight residual 1.333 1.351 -0.017 1.01e-02 9.80e+03 3.00e+00 bond pdb=" C ALA D 713 " pdb=" N PRO D 714 " ideal model delta sigma weight residual 1.332 1.350 -0.018 1.12e-02 7.97e+03 2.67e+00 bond pdb=" CG LEU D 384 " pdb=" CD2 LEU D 384 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.19e+00 ... (remaining 19185 not shown) Histogram of bond angle deviations from ideal: 98.19 - 106.29: 949 106.29 - 114.40: 11761 114.40 - 122.50: 11007 122.50 - 130.61: 2354 130.61 - 138.71: 98 Bond angle restraints: 26169 Sorted by residual: angle pdb=" N VAL F 378 " pdb=" CA VAL F 378 " pdb=" C VAL F 378 " ideal model delta sigma weight residual 113.42 107.55 5.87 1.17e+00 7.31e-01 2.52e+01 angle pdb=" N GLY A 605 " pdb=" CA GLY A 605 " pdb=" C GLY A 605 " ideal model delta sigma weight residual 111.56 116.63 -5.07 1.01e+00 9.80e-01 2.52e+01 angle pdb=" C MET E 459 " pdb=" N PRO E 460 " pdb=" CA PRO E 460 " ideal model delta sigma weight residual 127.00 138.71 -11.71 2.40e+00 1.74e-01 2.38e+01 angle pdb=" C MET D 459 " pdb=" N PRO D 460 " pdb=" CD PRO D 460 " ideal model delta sigma weight residual 120.60 109.99 10.61 2.20e+00 2.07e-01 2.33e+01 angle pdb=" C MET E 459 " pdb=" N PRO E 460 " pdb=" CD PRO E 460 " ideal model delta sigma weight residual 120.60 110.06 10.54 2.20e+00 2.07e-01 2.30e+01 ... (remaining 26164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.17: 11529 32.17 - 64.34: 222 64.34 - 96.52: 3 96.52 - 128.69: 5 128.69 - 160.86: 8 Dihedral angle restraints: 11767 sinusoidal: 4945 harmonic: 6822 Sorted by residual: dihedral pdb=" O1B ADP F 801 " pdb=" O3A ADP F 801 " pdb=" PB ADP F 801 " pdb=" PA ADP F 801 " ideal model delta sinusoidal sigma weight residual -60.00 100.86 -160.86 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" O2A ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PA ADP A 801 " pdb=" PB ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 98.36 -158.36 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" O2A ADP E 801 " pdb=" O3A ADP E 801 " pdb=" PA ADP E 801 " pdb=" PB ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 95.75 -155.75 1 2.00e+01 2.50e-03 4.59e+01 ... (remaining 11764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2225 0.052 - 0.104: 683 0.104 - 0.156: 189 0.156 - 0.208: 23 0.208 - 0.260: 8 Chirality restraints: 3128 Sorted by residual: chirality pdb=" CB ILE C 395 " pdb=" CA ILE C 395 " pdb=" CG1 ILE C 395 " pdb=" CG2 ILE C 395 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB ILE F 395 " pdb=" CA ILE F 395 " pdb=" CG1 ILE F 395 " pdb=" CG2 ILE F 395 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB ILE B 663 " pdb=" CA ILE B 663 " pdb=" CG1 ILE B 663 " pdb=" CG2 ILE B 663 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 3125 not shown) Planarity restraints: 3227 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 632 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.24e+00 pdb=" N PRO E 633 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO E 633 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 633 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 488 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO A 489 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 489 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 489 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 488 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO C 489 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 489 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 489 " 0.029 5.00e-02 4.00e+02 ... (remaining 3224 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4374 2.80 - 3.32: 16696 3.32 - 3.85: 31266 3.85 - 4.37: 35135 4.37 - 4.90: 60072 Nonbonded interactions: 147543 Sorted by model distance: nonbonded pdb=" O THR B 438 " pdb=" OG SER B 487 " model vdw 2.270 2.440 nonbonded pdb=" O THR A 438 " pdb=" OG SER A 487 " model vdw 2.271 2.440 nonbonded pdb=" OE2 GLU A 609 " pdb=" OG1 THR A 639 " model vdw 2.277 2.440 nonbonded pdb=" O THR E 438 " pdb=" OG SER E 487 " model vdw 2.298 2.440 nonbonded pdb=" OH TYR F 331 " pdb=" OD1 ASP F 417 " model vdw 2.309 2.440 ... (remaining 147538 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 315 through 570 or resid 586 through 721 or resid 801)) selection = chain 'B' selection = (chain 'C' and (resid 315 through 570 or resid 586 through 721 or resid 801)) selection = (chain 'D' and (resid 315 through 570 or resid 586 through 721 or resid 801)) selection = (chain 'E' and (resid 315 through 570 or resid 586 through 721 or resid 801)) selection = (chain 'F' and (resid 315 through 570 or resid 586 through 721 or resid 801)) } ncs_group { reference = (chain 'G' and resid 1 through 12) selection = (chain 'H' and resid 2 through 13) } 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: 5 Type Number sf(0) Gaussians P 38 5.49 5 S 90 5.16 5 C 11846 2.51 5 N 3249 2.21 5 O 3583 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 group one per residue 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: 0.570 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: 0.020 Extract box with map and model: 4.900 Check model and map are aligned: 0.290 Process input model: 50.640 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.170 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 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 : 0.006 0.122 19190 Z= 0.374 Angle : 0.913 12.819 26169 Z= 0.475 Chirality : 0.055 0.260 3128 Planarity : 0.007 0.062 3227 Dihedral : 12.495 160.859 7343 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -4.05 (0.14), residues: 2350 helix: -2.62 (0.12), residues: 960 sheet: -2.08 (0.23), residues: 399 loop : -2.87 (0.16), residues: 991 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 661 time to evaluate : 1.956 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: 4 outliers final: 0 residues processed: 664 average time/residue: 0.3527 time to fit residues: 336.3716 Evaluate side-chains 356 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 2.043 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 95 optimal weight: 0.0870 chunk 184 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 137 optimal weight: 0.2980 chunk 214 optimal weight: 1.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS A 419 GLN A 435 HIS A 461 HIS A 512 HIS A 666 GLN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 631 GLN B 645 ASN C 645 ASN C 666 GLN C 692 HIS D 383 ASN D 435 HIS ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 383 ASN E 435 HIS E 617 GLN F 477 ASN F 549 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 19190 Z= 0.190 Angle : 0.665 7.957 26169 Z= 0.325 Chirality : 0.045 0.188 3128 Planarity : 0.005 0.046 3227 Dihedral : 14.674 171.458 2856 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 2.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.45 (0.16), residues: 2350 helix: -0.99 (0.15), residues: 969 sheet: -1.36 (0.24), residues: 394 loop : -2.32 (0.17), residues: 987 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 418 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 31 residues processed: 450 average time/residue: 0.3062 time to fit residues: 209.6511 Evaluate side-chains 358 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 327 time to evaluate : 2.085 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1978 time to fit residues: 14.0488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 214 optimal weight: 4.9990 chunk 231 optimal weight: 0.3980 chunk 191 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A 625 HIS ** A 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS D 477 ASN D 666 GLN E 371 GLN ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 645 ASN F 666 GLN F 702 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.087 19190 Z= 0.412 Angle : 0.761 8.082 26169 Z= 0.372 Chirality : 0.048 0.160 3128 Planarity : 0.005 0.066 3227 Dihedral : 14.579 172.913 2856 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer Outliers : 3.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.84 (0.16), residues: 2350 helix: -0.34 (0.16), residues: 965 sheet: -1.15 (0.24), residues: 410 loop : -2.08 (0.19), residues: 975 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 349 time to evaluate : 2.203 Fit side-chains revert: symmetry clash outliers start: 66 outliers final: 38 residues processed: 389 average time/residue: 0.2893 time to fit residues: 178.7197 Evaluate side-chains 336 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 298 time to evaluate : 2.289 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.2127 time to fit residues: 17.8723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 215 optimal weight: 0.0980 chunk 228 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 435 HIS ** A 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN ** D 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 GLN E 383 ASN ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 617 GLN F 645 ASN F 702 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 19190 Z= 0.237 Angle : 0.657 8.182 26169 Z= 0.317 Chirality : 0.045 0.193 3128 Planarity : 0.004 0.050 3227 Dihedral : 14.258 168.141 2856 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.36 (0.17), residues: 2350 helix: 0.09 (0.17), residues: 957 sheet: -1.05 (0.25), residues: 388 loop : -1.77 (0.19), residues: 1005 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 348 time to evaluate : 2.171 Fit side-chains outliers start: 42 outliers final: 25 residues processed: 374 average time/residue: 0.2811 time to fit residues: 166.6603 Evaluate side-chains 334 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 309 time to evaluate : 2.179 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1788 time to fit residues: 11.2920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 0.3980 chunk 129 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 169 optimal weight: 0.0170 chunk 94 optimal weight: 0.9980 chunk 194 optimal weight: 0.0370 chunk 157 optimal weight: 0.0030 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.2906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 GLN ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 666 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 19190 Z= 0.156 Angle : 0.623 8.766 26169 Z= 0.298 Chirality : 0.044 0.161 3128 Planarity : 0.004 0.045 3227 Dihedral : 13.772 168.057 2856 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.97 (0.17), residues: 2350 helix: 0.40 (0.17), residues: 958 sheet: -0.89 (0.26), residues: 372 loop : -1.52 (0.19), residues: 1020 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 369 time to evaluate : 2.207 Fit side-chains outliers start: 37 outliers final: 14 residues processed: 394 average time/residue: 0.2757 time to fit residues: 170.6235 Evaluate side-chains 332 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 318 time to evaluate : 1.954 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1715 time to fit residues: 7.0265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 228 optimal weight: 6.9990 chunk 189 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS ** A 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 GLN ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 19190 Z= 0.266 Angle : 0.672 9.078 26169 Z= 0.320 Chirality : 0.045 0.162 3128 Planarity : 0.004 0.048 3227 Dihedral : 13.696 174.200 2856 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.79 (0.17), residues: 2350 helix: 0.47 (0.17), residues: 957 sheet: -0.45 (0.26), residues: 398 loop : -1.51 (0.19), residues: 995 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 316 time to evaluate : 2.338 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 18 residues processed: 336 average time/residue: 0.2724 time to fit residues: 146.9592 Evaluate side-chains 324 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 306 time to evaluate : 2.263 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1818 time to fit residues: 9.1306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 9.9990 chunk 25 optimal weight: 0.0050 chunk 130 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 227 optimal weight: 0.8980 chunk 142 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS ** A 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 GLN ** C 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 GLN ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 702 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 19190 Z= 0.217 Angle : 0.660 9.769 26169 Z= 0.313 Chirality : 0.045 0.178 3128 Planarity : 0.004 0.051 3227 Dihedral : 13.587 176.390 2856 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.66 (0.17), residues: 2350 helix: 0.60 (0.17), residues: 951 sheet: -0.42 (0.26), residues: 399 loop : -1.43 (0.19), residues: 1000 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 320 time to evaluate : 2.273 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 16 residues processed: 333 average time/residue: 0.2749 time to fit residues: 145.7778 Evaluate side-chains 318 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 302 time to evaluate : 2.191 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1992 time to fit residues: 8.5830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 154 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 702 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 19190 Z= 0.248 Angle : 0.689 11.943 26169 Z= 0.325 Chirality : 0.046 0.153 3128 Planarity : 0.004 0.055 3227 Dihedral : 13.550 179.722 2856 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.52 (0.18), residues: 2350 helix: 0.69 (0.17), residues: 946 sheet: -0.39 (0.26), residues: 399 loop : -1.30 (0.20), residues: 1005 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 312 time to evaluate : 2.339 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 319 average time/residue: 0.2730 time to fit residues: 139.3887 Evaluate side-chains 310 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 298 time to evaluate : 2.400 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1926 time to fit residues: 7.2770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 211 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 191 optimal weight: 0.9990 chunk 200 optimal weight: 0.6980 chunk 139 optimal weight: 0.7980 chunk 224 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 GLN ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 702 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 19190 Z= 0.180 Angle : 0.668 12.488 26169 Z= 0.312 Chirality : 0.045 0.177 3128 Planarity : 0.004 0.054 3227 Dihedral : 13.408 177.067 2856 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.53 (0.18), residues: 2350 helix: 0.65 (0.17), residues: 959 sheet: -0.41 (0.25), residues: 398 loop : -1.28 (0.20), residues: 993 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 323 time to evaluate : 2.386 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 328 average time/residue: 0.2857 time to fit residues: 150.3842 Evaluate side-chains 316 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 305 time to evaluate : 3.063 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2317 time to fit residues: 8.0167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 216 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 144 optimal weight: 7.9990 chunk 114 optimal weight: 0.1980 chunk 148 optimal weight: 0.5980 chunk 199 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 383 ASN ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 702 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 19190 Z= 0.181 Angle : 0.674 12.908 26169 Z= 0.313 Chirality : 0.045 0.157 3128 Planarity : 0.004 0.053 3227 Dihedral : 13.287 174.162 2856 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.46 (0.18), residues: 2350 helix: 0.72 (0.18), residues: 956 sheet: -0.30 (0.25), residues: 405 loop : -1.28 (0.20), residues: 989 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 316 time to evaluate : 2.403 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 319 average time/residue: 0.2717 time to fit residues: 138.5340 Evaluate side-chains 306 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 303 time to evaluate : 1.992 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2039 time to fit residues: 4.2773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 8.9990 chunk 172 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 52 optimal weight: 0.0050 chunk 187 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 192 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 GLN ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 702 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.119663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.095109 restraints weight = 36667.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.097279 restraints weight = 23753.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.098790 restraints weight = 17501.371| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 19190 Z= 0.237 Angle : 0.693 13.087 26169 Z= 0.322 Chirality : 0.045 0.157 3128 Planarity : 0.004 0.052 3227 Dihedral : 13.306 178.043 2856 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.43 (0.18), residues: 2350 helix: 0.72 (0.17), residues: 951 sheet: -0.24 (0.25), residues: 413 loop : -1.26 (0.20), residues: 986 =============================================================================== Job complete usr+sys time: 3721.60 seconds wall clock time: 68 minutes 13.38 seconds (4093.38 seconds total)