Starting phenix.real_space_refine on Sat Feb 17 13:40:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8o_10402/02_2024/6t8o_10402_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8o_10402/02_2024/6t8o_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_2024/6t8o_10402.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8o_10402/02_2024/6t8o_10402.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8o_10402/02_2024/6t8o_10402_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8o_10402/02_2024/6t8o_10402_updated.pdb" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 9.77, per 1000 atoms: 0.52 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: 7.18 Conformation dependent library (CDL) restraints added in 3.6 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: 7.97 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: 5.56 Time building geometry restraints manager: 7.76 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: 11567 32.17 - 64.34: 236 64.34 - 96.52: 3 96.52 - 128.69: 5 128.69 - 160.86: 8 Dihedral angle restraints: 11819 sinusoidal: 4997 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 11816 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 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: 0.620 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: 3.820 Check model and map are aligned: 0.270 Set scattering table: 0.200 Process input model: 53.980 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 12.693 160.859 7395 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 % Allowed : 4.34 % Favored : 95.46 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP A 530 HIS 0.008 0.002 HIS D 461 PHE 0.031 0.003 PHE A 597 TYR 0.024 0.003 TYR F 507 ARG 0.006 0.001 ARG B 690 *********************** 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 : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 HIS cc_start: 0.7047 (m-70) cc_final: 0.6485 (m170) REVERT: A 369 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6385 (mt-10) REVERT: A 535 MET cc_start: 0.8674 (ttp) cc_final: 0.8409 (ttt) REVERT: A 587 LEU cc_start: 0.8741 (mt) cc_final: 0.8501 (mt) REVERT: A 596 GLU cc_start: 0.7827 (tp30) cc_final: 0.7308 (tp30) REVERT: A 638 ILE cc_start: 0.7808 (mt) cc_final: 0.7598 (pt) REVERT: B 490 SER cc_start: 0.8103 (p) cc_final: 0.7379 (t) REVERT: B 540 ARG cc_start: 0.8073 (mtm180) cc_final: 0.6890 (mtp85) REVERT: B 702 HIS cc_start: 0.8423 (t70) cc_final: 0.8072 (t-170) REVERT: B 706 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8109 (mm-30) REVERT: C 454 THR cc_start: 0.9421 (p) cc_final: 0.9101 (t) REVERT: C 517 VAL cc_start: 0.8726 (t) cc_final: 0.8019 (t) REVERT: C 522 LYS cc_start: 0.8474 (mmtm) cc_final: 0.8125 (mttt) REVERT: C 595 ASP cc_start: 0.7471 (t0) cc_final: 0.7258 (t0) REVERT: C 648 THR cc_start: 0.9380 (m) cc_final: 0.8978 (p) REVERT: C 706 GLU cc_start: 0.7274 (mm-30) cc_final: 0.7031 (pt0) REVERT: D 321 LEU cc_start: 0.8352 (mt) cc_final: 0.8148 (mt) REVERT: D 328 GLN cc_start: 0.6857 (mp10) cc_final: 0.6648 (mp10) REVERT: D 345 ILE cc_start: 0.8864 (mm) cc_final: 0.8597 (mm) REVERT: D 528 LEU cc_start: 0.9370 (mt) cc_final: 0.9140 (mm) REVERT: D 555 ARG cc_start: 0.8489 (ttp-110) cc_final: 0.8195 (ptp-170) REVERT: D 606 LYS cc_start: 0.8261 (tptp) cc_final: 0.7713 (tppp) REVERT: D 609 GLU cc_start: 0.8309 (tt0) cc_final: 0.7964 (tt0) REVERT: D 650 ILE cc_start: 0.9241 (mm) cc_final: 0.8858 (mt) REVERT: D 657 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8022 (ttmt) REVERT: D 662 THR cc_start: 0.8187 (m) cc_final: 0.7961 (p) REVERT: D 666 GLN cc_start: 0.8532 (pt0) cc_final: 0.8265 (pt0) REVERT: D 672 LEU cc_start: 0.9399 (mt) cc_final: 0.9142 (mt) REVERT: D 675 HIS cc_start: 0.6763 (m-70) cc_final: 0.6484 (m-70) REVERT: D 677 ASP cc_start: 0.8344 (t0) cc_final: 0.8130 (t70) REVERT: D 702 HIS cc_start: 0.7739 (m-70) cc_final: 0.7153 (m90) REVERT: D 719 ASP cc_start: 0.7225 (t0) cc_final: 0.6976 (t70) REVERT: D 720 ILE cc_start: 0.8772 (tt) cc_final: 0.8080 (tt) REVERT: E 432 TYR cc_start: 0.9150 (t80) cc_final: 0.8846 (t80) REVERT: E 438 THR cc_start: 0.8816 (p) cc_final: 0.8609 (m) REVERT: E 504 LEU cc_start: 0.8570 (mt) cc_final: 0.8279 (mt) REVERT: E 604 VAL cc_start: 0.7559 (t) cc_final: 0.6975 (t) REVERT: E 611 LEU cc_start: 0.9251 (mt) cc_final: 0.9032 (mt) REVERT: E 617 GLN cc_start: 0.8102 (tt0) cc_final: 0.7806 (tt0) REVERT: F 422 ARG cc_start: 0.7682 (tpp-160) cc_final: 0.7271 (tpp80) REVERT: F 474 VAL cc_start: 0.9089 (t) cc_final: 0.8863 (t) REVERT: F 612 ILE cc_start: 0.9461 (mm) cc_final: 0.9259 (mt) REVERT: F 617 GLN cc_start: 0.7718 (tt0) cc_final: 0.7316 (tt0) REVERT: F 658 ILE cc_start: 0.8093 (mp) cc_final: 0.7815 (mm) outliers start: 4 outliers final: 0 residues processed: 664 average time/residue: 0.3541 time to fit residues: 336.6078 Evaluate side-chains 375 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 2.214 ------------------------------------------------------------------------------- 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: 2.9990 chunk 120 optimal weight: 0.6980 chunk 95 optimal weight: 0.0870 chunk 184 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 214 optimal weight: 1.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- 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 461 HIS A 512 HIS A 625 HIS A 666 GLN B 631 GLN B 645 ASN C 645 ASN C 666 GLN C 692 HIS C 702 HIS D 383 ASN D 435 HIS D 666 GLN E 383 ASN E 435 HIS F 477 ASN F 549 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 19190 Z= 0.222 Angle : 0.663 8.608 26169 Z= 0.324 Chirality : 0.045 0.183 3128 Planarity : 0.005 0.048 3227 Dihedral : 14.830 174.976 2908 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.89 % Allowed : 14.01 % Favored : 83.10 % 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: -2.43 (0.16), residues: 2350 helix: -0.90 (0.15), residues: 960 sheet: -1.55 (0.23), residues: 403 loop : -2.28 (0.18), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 530 HIS 0.008 0.001 HIS F 702 PHE 0.014 0.002 PHE F 597 TYR 0.018 0.002 TYR C 507 ARG 0.008 0.000 ARG F 661 *********************** 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 479 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 421 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 445 HIS cc_start: 0.8205 (m-70) cc_final: 0.7904 (m-70) REVERT: A 535 MET cc_start: 0.8705 (ttp) cc_final: 0.8465 (ttt) REVERT: A 596 GLU cc_start: 0.7750 (tp30) cc_final: 0.7316 (tp30) REVERT: A 624 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8698 (mp) REVERT: B 540 ARG cc_start: 0.7939 (mtm180) cc_final: 0.6964 (mmt-90) REVERT: B 702 HIS cc_start: 0.8654 (t70) cc_final: 0.8390 (t-90) REVERT: C 521 MET cc_start: 0.7996 (mmt) cc_final: 0.7004 (mmt) REVERT: C 522 LYS cc_start: 0.8488 (mmtm) cc_final: 0.8174 (mttt) REVERT: C 648 THR cc_start: 0.9388 (m) cc_final: 0.9061 (p) REVERT: C 706 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7076 (pt0) REVERT: D 383 ASN cc_start: 0.7407 (m110) cc_final: 0.7138 (m110) REVERT: D 455 ASP cc_start: 0.8358 (t0) cc_final: 0.8008 (m-30) REVERT: D 547 VAL cc_start: 0.8363 (t) cc_final: 0.8036 (p) REVERT: D 555 ARG cc_start: 0.8547 (ttp-110) cc_final: 0.8251 (ptp-170) REVERT: D 599 ASP cc_start: 0.7373 (m-30) cc_final: 0.7141 (m-30) REVERT: D 601 MET cc_start: 0.8946 (mtm) cc_final: 0.8562 (mtm) REVERT: D 609 GLU cc_start: 0.8263 (tt0) cc_final: 0.8019 (tt0) REVERT: D 657 LYS cc_start: 0.8665 (mtpt) cc_final: 0.7932 (ttmt) REVERT: D 662 THR cc_start: 0.8320 (m) cc_final: 0.7968 (p) REVERT: D 675 HIS cc_start: 0.6847 (m-70) cc_final: 0.6577 (m-70) REVERT: D 677 ASP cc_start: 0.8361 (t0) cc_final: 0.8157 (t70) REVERT: D 719 ASP cc_start: 0.7298 (t0) cc_final: 0.6933 (t70) REVERT: E 366 THR cc_start: 0.9427 (m) cc_final: 0.9058 (p) REVERT: E 432 TYR cc_start: 0.9063 (t80) cc_final: 0.8779 (t80) REVERT: F 422 ARG cc_start: 0.7831 (tpp-160) cc_final: 0.7039 (tpp80) REVERT: F 456 LEU cc_start: 0.8999 (tp) cc_final: 0.8783 (tp) REVERT: F 498 ASP cc_start: 0.8696 (t0) cc_final: 0.8461 (t0) REVERT: F 617 GLN cc_start: 0.7845 (tt0) cc_final: 0.7325 (tt0) REVERT: F 658 ILE cc_start: 0.8144 (mp) cc_final: 0.7869 (mm) outliers start: 58 outliers final: 29 residues processed: 455 average time/residue: 0.2922 time to fit residues: 204.2526 Evaluate side-chains 370 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 340 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 600 MET Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 586 THR Chi-restraints excluded: chain E residue 650 ILE Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 481 LEU 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: 20.0000 chunk 178 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 214 optimal weight: 0.0170 chunk 231 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 172 optimal weight: 3.9990 overall best weight: 1.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 666 GLN B 360 HIS C 653 GLN ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 GLN ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 702 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 19190 Z= 0.248 Angle : 0.659 7.799 26169 Z= 0.318 Chirality : 0.045 0.185 3128 Planarity : 0.004 0.063 3227 Dihedral : 14.489 171.406 2908 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.79 % Allowed : 15.75 % Favored : 80.46 % 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: -1.67 (0.17), residues: 2350 helix: -0.16 (0.17), residues: 962 sheet: -1.14 (0.24), residues: 410 loop : -2.01 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 530 HIS 0.009 0.001 HIS F 702 PHE 0.019 0.002 PHE F 597 TYR 0.016 0.002 TYR C 507 ARG 0.005 0.000 ARG E 540 *********************** 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 437 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 361 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 539 TYR cc_start: 0.8558 (m-80) cc_final: 0.8330 (m-80) REVERT: A 587 LEU cc_start: 0.8623 (mt) cc_final: 0.8231 (mt) REVERT: A 638 ILE cc_start: 0.7783 (mp) cc_final: 0.7288 (pt) REVERT: B 419 GLN cc_start: 0.7785 (tt0) cc_final: 0.7068 (mt0) REVERT: B 477 ASN cc_start: 0.8790 (m-40) cc_final: 0.8575 (t0) REVERT: B 540 ARG cc_start: 0.7924 (mtm180) cc_final: 0.6806 (mtp85) REVERT: B 650 ILE cc_start: 0.7682 (mm) cc_final: 0.7472 (mm) REVERT: C 455 ASP cc_start: 0.8358 (t0) cc_final: 0.7750 (t0) REVERT: C 521 MET cc_start: 0.7918 (mmt) cc_final: 0.6857 (mmt) REVERT: C 522 LYS cc_start: 0.8461 (mmtm) cc_final: 0.8225 (mttt) REVERT: C 648 THR cc_start: 0.9408 (m) cc_final: 0.9123 (p) REVERT: C 650 ILE cc_start: 0.9291 (mm) cc_final: 0.9011 (mt) REVERT: D 455 ASP cc_start: 0.8108 (t0) cc_final: 0.7840 (m-30) REVERT: D 459 MET cc_start: 0.8228 (mmm) cc_final: 0.7981 (mmm) REVERT: D 496 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8250 (mmt) REVERT: D 547 VAL cc_start: 0.8469 (t) cc_final: 0.8053 (p) REVERT: D 555 ARG cc_start: 0.8565 (ttp-110) cc_final: 0.8264 (ptp-170) REVERT: D 601 MET cc_start: 0.8864 (mtm) cc_final: 0.8570 (mtm) REVERT: D 609 GLU cc_start: 0.8256 (tt0) cc_final: 0.8010 (tt0) REVERT: D 662 THR cc_start: 0.8266 (m) cc_final: 0.7978 (p) REVERT: D 719 ASP cc_start: 0.7130 (t0) cc_final: 0.6840 (t70) REVERT: E 366 THR cc_start: 0.9441 (m) cc_final: 0.9051 (p) REVERT: E 432 TYR cc_start: 0.9042 (t80) cc_final: 0.8803 (t80) REVERT: F 420 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6840 (mtp) REVERT: F 484 LEU cc_start: 0.9583 (mt) cc_final: 0.9294 (mt) REVERT: F 535 MET cc_start: 0.8976 (ttp) cc_final: 0.8693 (ttp) REVERT: F 602 MET cc_start: 0.7727 (tmm) cc_final: 0.7373 (mmp) outliers start: 76 outliers final: 51 residues processed: 412 average time/residue: 0.2724 time to fit residues: 176.0754 Evaluate side-chains 383 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 330 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 600 MET Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 530 TRP Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain E residue 586 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 526 ASN Chi-restraints excluded: chain F residue 601 MET Chi-restraints excluded: chain F residue 612 ILE Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain F residue 709 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 chunk 215 optimal weight: 0.3980 chunk 228 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 C 435 HIS D 383 ASN D 526 ASN ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 GLN E 371 GLN ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 702 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19190 Z= 0.203 Angle : 0.626 7.462 26169 Z= 0.299 Chirality : 0.045 0.170 3128 Planarity : 0.004 0.049 3227 Dihedral : 14.198 166.781 2908 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.69 % Allowed : 17.20 % Favored : 79.11 % 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: -1.24 (0.17), residues: 2350 helix: 0.19 (0.17), residues: 956 sheet: -0.95 (0.24), residues: 415 loop : -1.74 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 708 HIS 0.009 0.001 HIS F 702 PHE 0.016 0.001 PHE F 597 TYR 0.012 0.001 TYR D 432 ARG 0.007 0.000 ARG A 538 *********************** 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 437 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 363 time to evaluate : 1.987 Fit side-chains REVERT: A 461 HIS cc_start: 0.8270 (m-70) cc_final: 0.7979 (m-70) REVERT: A 638 ILE cc_start: 0.7707 (mp) cc_final: 0.7262 (pt) REVERT: A 701 VAL cc_start: 0.9182 (t) cc_final: 0.8847 (p) REVERT: B 419 GLN cc_start: 0.7797 (tt0) cc_final: 0.7087 (mt0) REVERT: B 521 MET cc_start: 0.6240 (tpt) cc_final: 0.5889 (tpt) REVERT: B 540 ARG cc_start: 0.7818 (mtm180) cc_final: 0.6752 (mtp85) REVERT: C 455 ASP cc_start: 0.8210 (t0) cc_final: 0.7701 (t0) REVERT: C 459 MET cc_start: 0.8569 (mmm) cc_final: 0.8359 (mmm) REVERT: C 521 MET cc_start: 0.7933 (mmt) cc_final: 0.7461 (mmt) REVERT: C 522 LYS cc_start: 0.8454 (mmtm) cc_final: 0.8230 (mttt) REVERT: C 618 LYS cc_start: 0.8759 (tttt) cc_final: 0.8360 (mttm) REVERT: C 650 ILE cc_start: 0.9362 (mm) cc_final: 0.9096 (mt) REVERT: C 672 LEU cc_start: 0.9216 (mt) cc_final: 0.8831 (mt) REVERT: C 717 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7361 (mp) REVERT: D 455 ASP cc_start: 0.8056 (t0) cc_final: 0.7820 (m-30) REVERT: D 496 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8258 (mmt) REVERT: D 547 VAL cc_start: 0.8446 (t) cc_final: 0.8111 (p) REVERT: D 555 ARG cc_start: 0.8562 (ttp-110) cc_final: 0.8247 (ptp-170) REVERT: D 662 THR cc_start: 0.8288 (m) cc_final: 0.8019 (p) REVERT: D 719 ASP cc_start: 0.7109 (t0) cc_final: 0.6648 (t70) REVERT: E 366 THR cc_start: 0.9422 (m) cc_final: 0.9060 (p) REVERT: E 432 TYR cc_start: 0.8985 (t80) cc_final: 0.8771 (t80) REVERT: F 339 MET cc_start: 0.8448 (tpp) cc_final: 0.8182 (tpp) REVERT: F 459 MET cc_start: 0.8420 (mtp) cc_final: 0.8017 (mmm) REVERT: F 484 LEU cc_start: 0.9572 (mt) cc_final: 0.9292 (mt) REVERT: F 498 ASP cc_start: 0.8658 (t0) cc_final: 0.8320 (t0) REVERT: F 535 MET cc_start: 0.8983 (ttp) cc_final: 0.8659 (ttp) REVERT: F 602 MET cc_start: 0.7615 (tmm) cc_final: 0.7216 (mmp) outliers start: 74 outliers final: 52 residues processed: 410 average time/residue: 0.2838 time to fit residues: 184.0068 Evaluate side-chains 376 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 322 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 530 TRP Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 530 TRP Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain E residue 586 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 526 ASN Chi-restraints excluded: chain F residue 612 ILE Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 659 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 204 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 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 419 GLN A 435 HIS ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 GLN D 435 HIS D 477 ASN ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 GLN E 383 ASN ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 617 GLN F 702 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3707 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= 0.245 Angle : 0.641 8.260 26169 Z= 0.308 Chirality : 0.045 0.156 3128 Planarity : 0.004 0.045 3227 Dihedral : 13.983 172.857 2908 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.44 % Allowed : 17.30 % Favored : 78.27 % 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: -0.93 (0.17), residues: 2350 helix: 0.44 (0.17), residues: 952 sheet: -0.76 (0.25), residues: 406 loop : -1.56 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 708 HIS 0.008 0.001 HIS F 702 PHE 0.024 0.002 PHE E 553 TYR 0.011 0.001 TYR D 680 ARG 0.005 0.000 ARG B 690 *********************** 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 423 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 334 time to evaluate : 2.364 Fit side-chains REVERT: A 360 HIS cc_start: 0.7230 (m90) cc_final: 0.6777 (m170) REVERT: A 461 HIS cc_start: 0.8280 (m-70) cc_final: 0.7964 (m-70) REVERT: A 535 MET cc_start: 0.8519 (ttt) cc_final: 0.7652 (ttt) REVERT: A 539 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.8338 (m-80) REVERT: A 638 ILE cc_start: 0.7757 (mp) cc_final: 0.7336 (pt) REVERT: A 701 VAL cc_start: 0.9288 (t) cc_final: 0.8998 (p) REVERT: B 419 GLN cc_start: 0.7780 (tt0) cc_final: 0.7065 (mt0) REVERT: B 540 ARG cc_start: 0.7778 (mtm180) cc_final: 0.6746 (mtp85) REVERT: B 550 LEU cc_start: 0.7842 (mt) cc_final: 0.7631 (mp) REVERT: C 455 ASP cc_start: 0.8182 (t0) cc_final: 0.7747 (t0) REVERT: C 521 MET cc_start: 0.8013 (mmt) cc_final: 0.6773 (mmt) REVERT: C 522 LYS cc_start: 0.8522 (mmtm) cc_final: 0.8276 (mttt) REVERT: C 595 ASP cc_start: 0.7103 (t0) cc_final: 0.6809 (t0) REVERT: C 618 LYS cc_start: 0.8716 (tttt) cc_final: 0.8513 (tttt) REVERT: C 650 ILE cc_start: 0.9405 (mm) cc_final: 0.9109 (mt) REVERT: C 672 LEU cc_start: 0.9084 (mt) cc_final: 0.8867 (mt) REVERT: C 717 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7453 (mp) REVERT: D 496 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8270 (mmt) REVERT: D 501 MET cc_start: 0.7809 (ttp) cc_final: 0.7562 (ttp) REVERT: D 542 MET cc_start: 0.8274 (ptp) cc_final: 0.7949 (ptm) REVERT: D 547 VAL cc_start: 0.8400 (t) cc_final: 0.7560 (p) REVERT: D 555 ARG cc_start: 0.8556 (ttp-110) cc_final: 0.8270 (ptp-170) REVERT: D 609 GLU cc_start: 0.8010 (tt0) cc_final: 0.7802 (tt0) REVERT: D 612 ILE cc_start: 0.9155 (mm) cc_final: 0.8926 (mt) REVERT: D 657 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8077 (ttmt) REVERT: D 716 TYR cc_start: 0.7896 (m-10) cc_final: 0.7566 (m-10) REVERT: D 719 ASP cc_start: 0.7064 (t0) cc_final: 0.6677 (t70) REVERT: E 366 THR cc_start: 0.9384 (m) cc_final: 0.9002 (p) REVERT: F 339 MET cc_start: 0.8411 (tpp) cc_final: 0.8074 (tpp) REVERT: F 459 MET cc_start: 0.8488 (mtp) cc_final: 0.8112 (mmm) REVERT: F 484 LEU cc_start: 0.9591 (mt) cc_final: 0.9304 (mt) REVERT: F 535 MET cc_start: 0.9023 (ttp) cc_final: 0.8682 (ttp) REVERT: F 602 MET cc_start: 0.7514 (tmm) cc_final: 0.7172 (mmp) outliers start: 89 outliers final: 60 residues processed: 395 average time/residue: 0.2665 time to fit residues: 167.2274 Evaluate side-chains 382 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 319 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 539 TYR Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 530 TRP Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 530 TRP Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 586 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 526 ASN Chi-restraints excluded: chain F residue 612 ILE Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 659 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 0.8980 chunk 205 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 228 optimal weight: 1.9990 chunk 189 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 75 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN C 435 HIS D 435 HIS ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 GLN ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 702 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 19190 Z= 0.166 Angle : 0.619 10.483 26169 Z= 0.293 Chirality : 0.044 0.184 3128 Planarity : 0.004 0.047 3227 Dihedral : 13.668 174.847 2908 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.24 % Allowed : 18.84 % Favored : 77.92 % 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: -0.64 (0.18), residues: 2350 helix: 0.66 (0.18), residues: 956 sheet: -0.56 (0.25), residues: 404 loop : -1.40 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 530 HIS 0.008 0.001 HIS F 702 PHE 0.020 0.001 PHE D 553 TYR 0.021 0.001 TYR E 432 ARG 0.004 0.000 ARG B 690 *********************** 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 420 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 355 time to evaluate : 2.048 Fit side-chains REVERT: A 432 TYR cc_start: 0.8916 (t80) cc_final: 0.8530 (t80) REVERT: A 535 MET cc_start: 0.8579 (ttt) cc_final: 0.7888 (ttt) REVERT: A 638 ILE cc_start: 0.7635 (mp) cc_final: 0.7184 (pt) REVERT: A 701 VAL cc_start: 0.9303 (t) cc_final: 0.8997 (p) REVERT: B 419 GLN cc_start: 0.7682 (tt0) cc_final: 0.6953 (mt0) REVERT: B 481 LEU cc_start: 0.9173 (mp) cc_final: 0.8771 (tt) REVERT: B 540 ARG cc_start: 0.7709 (mtm180) cc_final: 0.6782 (mmt-90) REVERT: C 521 MET cc_start: 0.8037 (mmt) cc_final: 0.6951 (mmt) REVERT: C 522 LYS cc_start: 0.8456 (mmtm) cc_final: 0.8222 (mttt) REVERT: C 595 ASP cc_start: 0.7008 (t0) cc_final: 0.6423 (t0) REVERT: C 618 LYS cc_start: 0.8740 (tttt) cc_final: 0.8348 (pttt) REVERT: C 650 ILE cc_start: 0.9352 (mm) cc_final: 0.9029 (mt) REVERT: C 717 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7385 (mp) REVERT: D 547 VAL cc_start: 0.8460 (t) cc_final: 0.8090 (p) REVERT: D 555 ARG cc_start: 0.8518 (ttp-110) cc_final: 0.8220 (ptp-170) REVERT: D 609 GLU cc_start: 0.8077 (tt0) cc_final: 0.7823 (tt0) REVERT: D 612 ILE cc_start: 0.9135 (mm) cc_final: 0.8896 (mt) REVERT: D 657 LYS cc_start: 0.8702 (mtmt) cc_final: 0.8171 (ttmt) REVERT: D 662 THR cc_start: 0.8719 (m) cc_final: 0.8281 (p) REVERT: D 716 TYR cc_start: 0.7686 (m-10) cc_final: 0.7260 (m-10) REVERT: D 719 ASP cc_start: 0.7096 (t0) cc_final: 0.6861 (t70) REVERT: E 366 THR cc_start: 0.9312 (m) cc_final: 0.8967 (p) REVERT: E 558 LYS cc_start: 0.8526 (tmtt) cc_final: 0.7990 (ttmm) REVERT: E 628 LEU cc_start: 0.9485 (mt) cc_final: 0.9263 (mt) REVERT: F 339 MET cc_start: 0.8391 (tpp) cc_final: 0.8126 (tpp) REVERT: F 484 LEU cc_start: 0.9564 (mt) cc_final: 0.9290 (mt) REVERT: F 535 MET cc_start: 0.9037 (ttp) cc_final: 0.8671 (ttp) REVERT: F 602 MET cc_start: 0.7389 (tmm) cc_final: 0.7018 (mmp) outliers start: 65 outliers final: 46 residues processed: 395 average time/residue: 0.2730 time to fit residues: 169.8993 Evaluate side-chains 368 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 321 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 530 TRP Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 539 TYR Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 526 ASN Chi-restraints excluded: chain F residue 612 ILE Chi-restraints excluded: chain F residue 637 VAL Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 659 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 227 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN B 617 GLN ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 GLN D 671 GLN E 583 GLN ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 702 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 19190 Z= 0.451 Angle : 0.763 11.126 26169 Z= 0.371 Chirality : 0.048 0.188 3128 Planarity : 0.005 0.054 3227 Dihedral : 13.949 178.402 2908 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.79 % Allowed : 18.34 % Favored : 76.87 % 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: -0.74 (0.17), residues: 2350 helix: 0.50 (0.17), residues: 954 sheet: -0.43 (0.25), residues: 411 loop : -1.48 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 708 HIS 0.008 0.001 HIS E 461 PHE 0.026 0.002 PHE E 553 TYR 0.031 0.002 TYR B 539 ARG 0.004 0.001 ARG E 538 *********************** 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 414 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 318 time to evaluate : 2.036 Fit side-chains REVERT: A 638 ILE cc_start: 0.7909 (mp) cc_final: 0.7427 (pt) REVERT: A 701 VAL cc_start: 0.9413 (t) cc_final: 0.9125 (p) REVERT: B 419 GLN cc_start: 0.7762 (tt0) cc_final: 0.6984 (mt0) REVERT: B 540 ARG cc_start: 0.7919 (mtm180) cc_final: 0.6839 (mtp85) REVERT: C 354 VAL cc_start: 0.9010 (p) cc_final: 0.8757 (m) REVERT: C 455 ASP cc_start: 0.8192 (t0) cc_final: 0.7781 (t0) REVERT: C 522 LYS cc_start: 0.8674 (mmtm) cc_final: 0.8430 (mttt) REVERT: C 618 LYS cc_start: 0.8736 (tttt) cc_final: 0.8437 (pttt) REVERT: C 650 ILE cc_start: 0.9456 (mm) cc_final: 0.9197 (mt) REVERT: C 717 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7606 (mp) REVERT: D 547 VAL cc_start: 0.8468 (t) cc_final: 0.8146 (p) REVERT: D 555 ARG cc_start: 0.8606 (ttp-110) cc_final: 0.8233 (ptp-170) REVERT: D 609 GLU cc_start: 0.8063 (tt0) cc_final: 0.7846 (tt0) REVERT: D 612 ILE cc_start: 0.9211 (mm) cc_final: 0.8980 (mt) REVERT: D 657 LYS cc_start: 0.8810 (mtmt) cc_final: 0.8052 (ttmt) REVERT: D 662 THR cc_start: 0.8922 (m) cc_final: 0.8403 (p) REVERT: D 716 TYR cc_start: 0.7928 (m-10) cc_final: 0.7640 (m-10) REVERT: D 719 ASP cc_start: 0.7176 (t0) cc_final: 0.6803 (t70) REVERT: E 366 THR cc_start: 0.9472 (m) cc_final: 0.9065 (p) REVERT: F 339 MET cc_start: 0.8483 (tpp) cc_final: 0.8095 (tpp) REVERT: F 459 MET cc_start: 0.8558 (mtp) cc_final: 0.8120 (mmm) REVERT: F 484 LEU cc_start: 0.9638 (mt) cc_final: 0.9370 (mt) REVERT: F 653 GLN cc_start: 0.8622 (tt0) cc_final: 0.8346 (tt0) outliers start: 96 outliers final: 71 residues processed: 385 average time/residue: 0.2651 time to fit residues: 162.7142 Evaluate side-chains 376 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 304 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 653 GLN Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 530 TRP Chi-restraints excluded: chain B residue 600 MET Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 530 TRP Chi-restraints excluded: chain D residue 539 TYR Chi-restraints excluded: chain D residue 601 MET Chi-restraints excluded: chain D residue 615 ILE Chi-restraints excluded: chain D residue 666 GLN Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 586 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 396 SER Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 483 ILE Chi-restraints excluded: chain F residue 526 ASN Chi-restraints excluded: chain F residue 612 ILE Chi-restraints excluded: chain F residue 637 VAL Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 696 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 178 optimal weight: 0.8980 chunk 206 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** ** D 645 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19190 Z= 0.176 Angle : 0.650 9.668 26169 Z= 0.307 Chirality : 0.045 0.165 3128 Planarity : 0.004 0.054 3227 Dihedral : 13.710 174.580 2908 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.19 % Allowed : 20.44 % Favored : 76.37 % 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: 0.77 (0.18), residues: 950 sheet: -0.58 (0.25), residues: 399 loop : -1.18 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 708 HIS 0.003 0.001 HIS C 445 PHE 0.034 0.002 PHE E 553 TYR 0.027 0.001 TYR B 539 ARG 0.005 0.000 ARG E 548 *********************** 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 394 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 330 time to evaluate : 2.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7983 (tm-30) REVERT: A 638 ILE cc_start: 0.7653 (mp) cc_final: 0.7289 (pt) REVERT: A 701 VAL cc_start: 0.9384 (t) cc_final: 0.9086 (p) REVERT: B 419 GLN cc_start: 0.7687 (tt0) cc_final: 0.6895 (mt0) REVERT: B 447 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.8025 (mt) REVERT: B 479 MET cc_start: 0.8784 (mmt) cc_final: 0.8567 (mmp) REVERT: B 481 LEU cc_start: 0.9180 (mp) cc_final: 0.8846 (tt) REVERT: B 540 ARG cc_start: 0.7697 (mtm180) cc_final: 0.6877 (mtt-85) REVERT: C 521 MET cc_start: 0.7805 (mmt) cc_final: 0.6620 (mmt) REVERT: C 522 LYS cc_start: 0.8415 (mmtm) cc_final: 0.8208 (mttt) REVERT: C 595 ASP cc_start: 0.7091 (t0) cc_final: 0.6766 (t0) REVERT: C 618 LYS cc_start: 0.8727 (tttt) cc_final: 0.8462 (pttt) REVERT: C 650 ILE cc_start: 0.9380 (mm) cc_final: 0.9093 (mt) REVERT: D 542 MET cc_start: 0.8296 (ptp) cc_final: 0.8066 (ptm) REVERT: D 547 VAL cc_start: 0.8524 (t) cc_final: 0.7695 (p) REVERT: D 609 GLU cc_start: 0.8042 (tt0) cc_final: 0.7838 (tt0) REVERT: D 645 ASN cc_start: 0.8550 (m-40) cc_final: 0.8270 (t0) REVERT: D 657 LYS cc_start: 0.8767 (mtmt) cc_final: 0.8116 (ttmt) REVERT: D 662 THR cc_start: 0.8748 (m) cc_final: 0.8274 (p) REVERT: D 719 ASP cc_start: 0.7182 (t0) cc_final: 0.6892 (t70) REVERT: E 366 THR cc_start: 0.9368 (m) cc_final: 0.8991 (p) REVERT: E 628 LEU cc_start: 0.9481 (mt) cc_final: 0.9217 (mt) REVERT: F 339 MET cc_start: 0.8429 (tpp) cc_final: 0.8137 (tpp) REVERT: F 459 MET cc_start: 0.8400 (mtp) cc_final: 0.7995 (mmm) REVERT: F 484 LEU cc_start: 0.9589 (mt) cc_final: 0.9291 (mp) REVERT: F 535 MET cc_start: 0.9030 (ttp) cc_final: 0.8716 (ttp) REVERT: F 602 MET cc_start: 0.7515 (tmm) cc_final: 0.7141 (mmm) outliers start: 64 outliers final: 54 residues processed: 373 average time/residue: 0.2731 time to fit residues: 162.3138 Evaluate side-chains 367 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 312 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 539 TYR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 530 TRP Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 530 TRP Chi-restraints excluded: chain D residue 539 TYR Chi-restraints excluded: chain D residue 666 GLN Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 396 SER Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 526 ASN Chi-restraints excluded: chain F residue 637 VAL Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 696 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 211 optimal weight: 0.8980 chunk 127 optimal weight: 0.0060 chunk 92 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 191 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 224 optimal weight: 0.0170 overall best weight: 0.5434 ------------------------------------------------------------------------------- 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** ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 GLN F 419 GLN F 702 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19190 Z= 0.161 Angle : 0.643 11.258 26169 Z= 0.301 Chirality : 0.044 0.167 3128 Planarity : 0.004 0.052 3227 Dihedral : 13.512 171.568 2908 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.94 % Allowed : 20.44 % Favored : 76.62 % 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: -0.29 (0.18), residues: 2350 helix: 0.87 (0.18), residues: 951 sheet: -0.35 (0.25), residues: 396 loop : -1.12 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 708 HIS 0.009 0.001 HIS F 702 PHE 0.038 0.001 PHE E 553 TYR 0.025 0.001 TYR B 539 ARG 0.004 0.000 ARG E 548 *********************** 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 391 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 332 time to evaluate : 2.060 Fit side-chains REVERT: A 638 ILE cc_start: 0.7603 (mp) cc_final: 0.7180 (pt) REVERT: A 701 VAL cc_start: 0.9405 (t) cc_final: 0.9098 (p) REVERT: B 419 GLN cc_start: 0.7696 (tt0) cc_final: 0.6896 (mt0) REVERT: B 441 LEU cc_start: 0.8622 (mm) cc_final: 0.8272 (mm) REVERT: B 447 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.8004 (mt) REVERT: B 479 MET cc_start: 0.8792 (mmt) cc_final: 0.8411 (mmp) REVERT: B 481 LEU cc_start: 0.9241 (mp) cc_final: 0.8962 (tt) REVERT: B 502 LEU cc_start: 0.7332 (pt) cc_final: 0.6497 (pp) REVERT: B 540 ARG cc_start: 0.7751 (mtm180) cc_final: 0.6879 (mtt-85) REVERT: C 521 MET cc_start: 0.7764 (mmt) cc_final: 0.6547 (mmt) REVERT: C 522 LYS cc_start: 0.8417 (mmtm) cc_final: 0.8177 (mttt) REVERT: C 618 LYS cc_start: 0.8684 (tttt) cc_final: 0.8478 (pttt) REVERT: C 650 ILE cc_start: 0.9337 (mm) cc_final: 0.9066 (mt) REVERT: D 542 MET cc_start: 0.8333 (ptp) cc_final: 0.8111 (ptm) REVERT: D 547 VAL cc_start: 0.8510 (t) cc_final: 0.7687 (p) REVERT: D 645 ASN cc_start: 0.8323 (m-40) cc_final: 0.8050 (t0) REVERT: D 662 THR cc_start: 0.8774 (m) cc_final: 0.8316 (p) REVERT: D 719 ASP cc_start: 0.7049 (t0) cc_final: 0.6836 (t70) REVERT: E 366 THR cc_start: 0.9348 (m) cc_final: 0.9007 (p) REVERT: E 628 LEU cc_start: 0.9484 (mt) cc_final: 0.9203 (mt) REVERT: F 339 MET cc_start: 0.8375 (tpp) cc_final: 0.8093 (tpp) REVERT: F 484 LEU cc_start: 0.9552 (mt) cc_final: 0.9280 (mt) REVERT: F 535 MET cc_start: 0.9024 (ttp) cc_final: 0.8684 (ttp) REVERT: F 602 MET cc_start: 0.7551 (tmm) cc_final: 0.7153 (mmm) REVERT: F 645 ASN cc_start: 0.7980 (m-40) cc_final: 0.7541 (t0) outliers start: 59 outliers final: 47 residues processed: 374 average time/residue: 0.2646 time to fit residues: 158.0284 Evaluate side-chains 368 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 320 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 530 TRP Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 530 TRP Chi-restraints excluded: chain D residue 539 TYR Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 396 SER Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 419 GLN Chi-restraints excluded: chain F residue 526 ASN Chi-restraints excluded: chain F residue 637 VAL Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain F residue 696 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 chunk 155 optimal weight: 0.0010 chunk 235 optimal weight: 10.0000 chunk 216 optimal weight: 7.9990 chunk 187 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 114 optimal weight: 0.0010 chunk 148 optimal weight: 6.9990 chunk 199 optimal weight: 0.7980 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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** D 671 GLN E 383 ASN F 419 GLN F 702 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19190 Z= 0.157 Angle : 0.649 13.732 26169 Z= 0.301 Chirality : 0.044 0.168 3128 Planarity : 0.004 0.048 3227 Dihedral : 13.354 168.751 2908 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.69 % Allowed : 21.14 % Favored : 76.17 % 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: -0.16 (0.18), residues: 2350 helix: 0.95 (0.18), residues: 950 sheet: -0.16 (0.26), residues: 401 loop : -1.07 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 530 HIS 0.009 0.001 HIS F 702 PHE 0.039 0.001 PHE E 553 TYR 0.022 0.001 TYR B 539 ARG 0.004 0.000 ARG E 548 ********************** 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 402 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 348 time to evaluate : 2.133 Fit side-chains REVERT: A 610 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7974 (tm-30) REVERT: A 638 ILE cc_start: 0.7485 (mp) cc_final: 0.7046 (pt) REVERT: A 701 VAL cc_start: 0.9401 (t) cc_final: 0.9108 (p) REVERT: B 419 GLN cc_start: 0.7698 (tt0) cc_final: 0.6836 (mt0) REVERT: B 441 LEU cc_start: 0.8533 (mm) cc_final: 0.8222 (mm) REVERT: B 447 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.8010 (mt) REVERT: B 479 MET cc_start: 0.8765 (mmt) cc_final: 0.8478 (mmp) REVERT: B 481 LEU cc_start: 0.9274 (mp) cc_final: 0.8957 (tt) REVERT: B 540 ARG cc_start: 0.7745 (mtm180) cc_final: 0.6887 (mtt-85) REVERT: C 521 MET cc_start: 0.7753 (mmt) cc_final: 0.6583 (mmt) REVERT: C 522 LYS cc_start: 0.8461 (mmtm) cc_final: 0.8229 (mttt) REVERT: C 618 LYS cc_start: 0.8704 (tttt) cc_final: 0.8481 (pttt) REVERT: C 650 ILE cc_start: 0.9333 (mm) cc_final: 0.9076 (mt) REVERT: C 680 TYR cc_start: 0.8966 (t80) cc_final: 0.8751 (t80) REVERT: D 459 MET cc_start: 0.8480 (mmt) cc_final: 0.8257 (mmt) REVERT: D 542 MET cc_start: 0.8351 (ptp) cc_final: 0.8115 (ptm) REVERT: D 547 VAL cc_start: 0.8557 (t) cc_final: 0.7722 (p) REVERT: D 600 MET cc_start: 0.8135 (ttt) cc_final: 0.7806 (ttt) REVERT: D 602 MET cc_start: 0.7676 (ppp) cc_final: 0.7359 (mmm) REVERT: D 612 ILE cc_start: 0.9205 (tp) cc_final: 0.8991 (tp) REVERT: D 645 ASN cc_start: 0.8187 (m-40) cc_final: 0.7961 (t0) REVERT: D 662 THR cc_start: 0.8713 (m) cc_final: 0.8286 (p) REVERT: D 719 ASP cc_start: 0.7054 (t0) cc_final: 0.6702 (t70) REVERT: E 366 THR cc_start: 0.9333 (m) cc_final: 0.8979 (p) REVERT: E 617 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7637 (tm-30) REVERT: E 628 LEU cc_start: 0.9487 (mt) cc_final: 0.9259 (mt) REVERT: F 339 MET cc_start: 0.8362 (tpp) cc_final: 0.8086 (tpp) REVERT: F 484 LEU cc_start: 0.9529 (mt) cc_final: 0.9274 (mt) REVERT: F 535 MET cc_start: 0.9027 (ttp) cc_final: 0.8687 (ttp) REVERT: F 602 MET cc_start: 0.7460 (tmm) cc_final: 0.7205 (mmm) REVERT: F 645 ASN cc_start: 0.7958 (m-40) cc_final: 0.7538 (t0) outliers start: 54 outliers final: 49 residues processed: 387 average time/residue: 0.2598 time to fit residues: 160.7198 Evaluate side-chains 381 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 331 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 530 TRP Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 539 TYR Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 396 SER Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 419 GLN Chi-restraints excluded: chain F residue 526 ASN Chi-restraints excluded: chain F residue 637 VAL Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain F residue 696 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 0.0000 chunk 172 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 52 optimal weight: 6.9990 chunk 187 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 192 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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** D 671 GLN F 419 GLN F 702 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.122149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.098593 restraints weight = 36619.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.099894 restraints weight = 23347.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.100547 restraints weight = 17735.603| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4569 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= 0.164 Angle : 0.654 13.794 26169 Z= 0.303 Chirality : 0.044 0.172 3128 Planarity : 0.004 0.046 3227 Dihedral : 13.271 166.472 2908 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.94 % Allowed : 21.34 % Favored : 75.72 % 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: -0.15 (0.18), residues: 2350 helix: 0.91 (0.18), residues: 955 sheet: -0.14 (0.25), residues: 407 loop : -1.05 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 530 HIS 0.009 0.001 HIS F 702 PHE 0.039 0.001 PHE E 553 TYR 0.018 0.001 TYR C 432 ARG 0.004 0.000 ARG E 548 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4025.89 seconds wall clock time: 73 minutes 51.07 seconds (4431.07 seconds total)