Starting phenix.real_space_refine on Sun Mar 17 09:06:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us2_26722/03_2024/7us2_26722_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us2_26722/03_2024/7us2_26722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us2_26722/03_2024/7us2_26722.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us2_26722/03_2024/7us2_26722.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us2_26722/03_2024/7us2_26722_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us2_26722/03_2024/7us2_26722_updated.pdb" } resolution = 2.76 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= -0.003 sd= 0.067 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: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 60 5.16 5 C 10788 2.51 5 N 3158 2.21 5 O 3170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17200 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2823 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 10, 'TRANS': 336} Chain breaks: 2 Chain: "B" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2823 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 10, 'TRANS': 336} Chain breaks: 2 Chain: "C" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2823 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 10, 'TRANS': 336} Chain breaks: 2 Chain: "D" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2823 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 10, 'TRANS': 336} Chain breaks: 2 Chain: "E" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2823 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 10, 'TRANS': 336} Chain breaks: 2 Chain: "F" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2823 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 10, 'TRANS': 336} Chain breaks: 2 Chain: "P" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.18, per 1000 atoms: 0.53 Number of scatterers: 17200 At special positions: 0 Unit cell: (102.194, 161.634, 152.249, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 18 15.00 Mg 6 11.99 O 3170 8.00 N 3158 7.00 C 10788 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.16 Conformation dependent library (CDL) restraints added in 2.8 seconds 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3952 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 99 helices and 19 sheets defined 52.7% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.23 Creating SS restraints... Processing helix chain 'A' and resid 319 through 336 Processing helix chain 'A' and resid 339 through 346 removed outlier: 3.657A pdb=" N HIS A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 365 Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 417 through 424 removed outlier: 3.816A pdb=" N VAL A 420 " --> pdb=" O ARG A 417 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 421 " --> pdb=" O HIS A 418 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 424 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 444 Processing helix chain 'A' and resid 461 through 472 removed outlier: 3.554A pdb=" N THR A 465 " --> pdb=" O PRO A 461 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N MET A 467 " --> pdb=" O VAL A 463 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLN A 469 " --> pdb=" O THR A 465 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 522 Processing helix chain 'A' and resid 538 through 543 Processing helix chain 'A' and resid 545 through 553 Processing helix chain 'A' and resid 556 through 561 removed outlier: 3.530A pdb=" N ARG A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 593 Processing helix chain 'A' and resid 603 through 611 Processing helix chain 'A' and resid 618 through 639 removed outlier: 3.863A pdb=" N ARG A 629 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL A 630 " --> pdb=" O GLU A 627 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL A 631 " --> pdb=" O ARG A 628 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASN A 632 " --> pdb=" O ARG A 629 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU A 639 " --> pdb=" O ALA A 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 336 removed outlier: 3.571A pdb=" N GLN B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B 324 " --> pdb=" O ALA B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 346 removed outlier: 3.935A pdb=" N HIS B 346 " --> pdb=" O ARG B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 365 Processing helix chain 'B' and resid 387 through 398 Processing helix chain 'B' and resid 411 through 413 No H-bonds generated for 'chain 'B' and resid 411 through 413' Processing helix chain 'B' and resid 417 through 424 removed outlier: 3.689A pdb=" N VAL B 420 " --> pdb=" O ARG B 417 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA B 421 " --> pdb=" O HIS B 418 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE B 424 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 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 461 through 472 removed outlier: 4.101A pdb=" N ILE B 466 " --> pdb=" O ASP B 462 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N MET B 467 " --> pdb=" O VAL B 463 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLN B 469 " --> pdb=" O THR B 465 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 522 Processing helix chain 'B' and resid 538 through 543 Processing helix chain 'B' and resid 545 through 553 Processing helix chain 'B' and resid 556 through 560 Processing helix chain 'B' and resid 573 through 593 Processing helix chain 'B' and resid 603 through 611 Processing helix chain 'B' and resid 618 through 629 removed outlier: 3.581A pdb=" N ARG B 629 " --> pdb=" O VAL B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 639 Processing helix chain 'C' and resid 319 through 336 Processing helix chain 'C' and resid 339 through 346 removed outlier: 3.925A pdb=" N HIS C 346 " --> pdb=" O ARG C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 365 Processing helix chain 'C' and resid 387 through 399 Processing helix chain 'C' and resid 403 through 405 No H-bonds generated for 'chain 'C' and resid 403 through 405' Processing helix chain 'C' and resid 411 through 413 No H-bonds generated for 'chain 'C' and resid 411 through 413' Processing helix chain 'C' and resid 417 through 424 removed outlier: 3.867A pdb=" N VAL C 420 " --> pdb=" O ARG C 417 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA C 421 " --> pdb=" O HIS C 418 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 424 " --> pdb=" O ALA C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 456 through 458 No H-bonds generated for 'chain 'C' and resid 456 through 458' Processing helix chain 'C' and resid 461 through 472 removed outlier: 4.015A pdb=" N ILE C 466 " --> pdb=" O ASP C 462 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N MET C 467 " --> pdb=" O VAL C 463 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU C 468 " --> pdb=" O LEU C 464 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLN C 469 " --> pdb=" O THR C 465 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 522 Processing helix chain 'C' and resid 538 through 543 Processing helix chain 'C' and resid 545 through 553 Processing helix chain 'C' and resid 556 through 560 Processing helix chain 'C' and resid 573 through 594 Processing helix chain 'C' and resid 603 through 612 removed outlier: 3.879A pdb=" N ASP C 611 " --> pdb=" O ASP C 607 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY C 612 " --> pdb=" O VAL C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 629 removed outlier: 3.676A pdb=" N ARG C 629 " --> pdb=" O VAL C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 639 Processing helix chain 'D' and resid 319 through 336 Processing helix chain 'D' and resid 339 through 346 removed outlier: 3.953A pdb=" N HIS D 346 " --> pdb=" O ARG D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 365 Processing helix chain 'D' and resid 387 through 399 Processing helix chain 'D' and resid 403 through 405 No H-bonds generated for 'chain 'D' and resid 403 through 405' Processing helix chain 'D' and resid 411 through 413 No H-bonds generated for 'chain 'D' and resid 411 through 413' Processing helix chain 'D' and resid 417 through 424 removed outlier: 3.803A pdb=" N VAL D 420 " --> pdb=" O ARG D 417 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA D 421 " --> pdb=" O HIS D 418 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE D 424 " --> pdb=" O ALA D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 445 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 461 through 472 removed outlier: 4.004A pdb=" N ILE D 466 " --> pdb=" O ASP D 462 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N MET D 467 " --> pdb=" O VAL D 463 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU D 468 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN D 469 " --> pdb=" O THR D 465 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU D 470 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 522 Processing helix chain 'D' and resid 538 through 543 Processing helix chain 'D' and resid 545 through 553 Processing helix chain 'D' and resid 556 through 561 Processing helix chain 'D' and resid 573 through 593 Processing helix chain 'D' and resid 603 through 612 removed outlier: 3.912A pdb=" N ASP D 611 " --> pdb=" O ASP D 607 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLY D 612 " --> pdb=" O VAL D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 629 removed outlier: 3.805A pdb=" N ARG D 629 " --> pdb=" O VAL D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 639 Processing helix chain 'E' and resid 319 through 336 Processing helix chain 'E' and resid 339 through 346 removed outlier: 3.960A pdb=" N HIS E 346 " --> pdb=" O ARG E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 365 Processing helix chain 'E' and resid 387 through 399 Processing helix chain 'E' and resid 417 through 424 removed outlier: 3.767A pdb=" N VAL E 420 " --> pdb=" O ARG E 417 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA E 421 " --> pdb=" O HIS E 418 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE E 424 " --> pdb=" O ALA E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 445 Processing helix chain 'E' and resid 456 through 458 No H-bonds generated for 'chain 'E' and resid 456 through 458' Processing helix chain 'E' and resid 461 through 472 removed outlier: 4.027A pdb=" N ILE E 466 " --> pdb=" O ASP E 462 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N MET E 467 " --> pdb=" O VAL E 463 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU E 468 " --> pdb=" O LEU E 464 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLN E 469 " --> pdb=" O THR E 465 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU E 470 " --> pdb=" O ILE E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 522 Processing helix chain 'E' and resid 538 through 543 Processing helix chain 'E' and resid 545 through 553 Processing helix chain 'E' and resid 556 through 560 Processing helix chain 'E' and resid 573 through 593 Processing helix chain 'E' and resid 603 through 612 removed outlier: 4.014A pdb=" N ASP E 611 " --> pdb=" O ASP E 607 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY E 612 " --> pdb=" O VAL E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 629 removed outlier: 3.688A pdb=" N ARG E 629 " --> pdb=" O VAL E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 639 Processing helix chain 'F' and resid 319 through 336 Processing helix chain 'F' and resid 339 through 346 removed outlier: 3.715A pdb=" N HIS F 346 " --> pdb=" O ARG F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 365 Processing helix chain 'F' and resid 387 through 398 Processing helix chain 'F' and resid 417 through 424 removed outlier: 3.541A pdb=" N VAL F 420 " --> pdb=" O ARG F 417 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA F 421 " --> pdb=" O HIS F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 445 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 461 through 473 Processing helix chain 'F' and resid 499 through 522 Processing helix chain 'F' and resid 538 through 543 Processing helix chain 'F' and resid 545 through 553 Processing helix chain 'F' and resid 556 through 561 Processing helix chain 'F' and resid 573 through 594 Processing helix chain 'F' and resid 603 through 612 removed outlier: 3.759A pdb=" N ASP F 611 " --> pdb=" O ASP F 607 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY F 612 " --> pdb=" O VAL F 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 629 removed outlier: 3.725A pdb=" N ARG F 629 " --> pdb=" O VAL F 626 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 639 Processing sheet with id= A, first strand: chain 'A' and resid 406 through 410 removed outlier: 6.493A pdb=" N VAL A 450 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU A 409 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU A 452 " --> pdb=" O LEU A 409 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 648 through 653 removed outlier: 3.505A pdb=" N THR A 648 " --> pdb=" O ILE A 683 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A 683 " --> pdb=" O THR A 648 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 377 through 381 removed outlier: 6.986A pdb=" N GLU B 564 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEU B 380 " --> pdb=" O GLU B 564 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL B 566 " --> pdb=" O LEU B 380 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 406 through 410 removed outlier: 6.867A pdb=" N VAL B 450 " --> pdb=" O ILE B 407 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU B 409 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU B 452 " --> pdb=" O LEU B 409 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 597 through 601 removed outlier: 6.505A pdb=" N CYS B 647 " --> pdb=" O THR B 598 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU B 600 " --> pdb=" O CYS B 647 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 649 " --> pdb=" O LEU B 600 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 648 " --> pdb=" O ILE B 683 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 490 through 495 removed outlier: 6.518A pdb=" N LEU C 375 " --> pdb=" O PHE C 491 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N MET C 493 " --> pdb=" O LEU C 375 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N PHE C 377 " --> pdb=" O MET C 493 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N SER C 495 " --> pdb=" O PHE C 377 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE C 379 " --> pdb=" O SER C 495 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLU C 564 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU C 380 " --> pdb=" O GLU C 564 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL C 566 " --> pdb=" O LEU C 380 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 406 through 410 removed outlier: 6.648A pdb=" N VAL C 450 " --> pdb=" O ILE C 407 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU C 409 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU C 452 " --> pdb=" O LEU C 409 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 475 through 477 removed outlier: 3.731A pdb=" N LEU C 476 " --> pdb=" O ILE C 484 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 484 " --> pdb=" O LEU C 476 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 598 through 601 removed outlier: 3.828A pdb=" N THR C 648 " --> pdb=" O ILE C 683 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 490 through 495 removed outlier: 6.464A pdb=" N LEU D 375 " --> pdb=" O PHE D 491 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N MET D 493 " --> pdb=" O LEU D 375 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE D 377 " --> pdb=" O MET D 493 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N SER D 495 " --> pdb=" O PHE D 377 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N PHE D 379 " --> pdb=" O SER D 495 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLU D 564 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU D 380 " --> pdb=" O GLU D 564 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL D 566 " --> pdb=" O LEU D 380 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 406 through 410 removed outlier: 6.637A pdb=" N VAL D 450 " --> pdb=" O ILE D 407 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU D 409 " --> pdb=" O VAL D 450 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU D 452 " --> pdb=" O LEU D 409 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'D' and resid 597 through 600 removed outlier: 6.672A pdb=" N CYS D 647 " --> pdb=" O THR D 598 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N LEU D 600 " --> pdb=" O CYS D 647 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU D 649 " --> pdb=" O LEU D 600 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR D 648 " --> pdb=" O ILE D 683 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 377 through 381 removed outlier: 6.903A pdb=" N GLU E 564 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU E 380 " --> pdb=" O GLU E 564 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL E 566 " --> pdb=" O LEU E 380 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 406 through 410 removed outlier: 6.631A pdb=" N VAL E 450 " --> pdb=" O ILE E 407 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU E 409 " --> pdb=" O VAL E 450 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU E 452 " --> pdb=" O LEU E 409 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ILE E 490 " --> pdb=" O VAL E 451 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N PHE E 453 " --> pdb=" O ILE E 490 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE E 492 " --> pdb=" O PHE E 453 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'E' and resid 598 through 600 removed outlier: 3.887A pdb=" N THR E 648 " --> pdb=" O ILE E 683 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 377 through 381 removed outlier: 7.134A pdb=" N GLU F 564 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LEU F 380 " --> pdb=" O GLU F 564 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL F 566 " --> pdb=" O LEU F 380 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'F' and resid 408 through 410 removed outlier: 6.010A pdb=" N LEU F 452 " --> pdb=" O LEU F 409 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'F' and resid 475 through 477 Processing sheet with id= S, first strand: chain 'F' and resid 648 through 653 removed outlier: 4.127A pdb=" N THR F 648 " --> pdb=" O ILE F 683 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE F 683 " --> pdb=" O THR F 648 " (cutoff:3.500A) 697 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.76 Time building geometry restraints manager: 6.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 5904 1.36 - 1.49: 4088 1.49 - 1.63: 7399 1.63 - 1.76: 3 1.76 - 1.89: 99 Bond restraints: 17493 Sorted by residual: bond pdb=" O3B AGS A 801 " pdb=" PB AGS A 801 " ideal model delta sigma weight residual 1.585 1.871 -0.286 2.70e-02 1.37e+03 1.12e+02 bond pdb=" O3B AGS C 801 " pdb=" PB AGS C 801 " ideal model delta sigma weight residual 1.585 1.859 -0.274 2.70e-02 1.37e+03 1.03e+02 bond pdb=" O3B AGS F 801 " pdb=" PB AGS F 801 " ideal model delta sigma weight residual 1.585 1.856 -0.271 2.70e-02 1.37e+03 1.01e+02 bond pdb=" O3B AGS B 801 " pdb=" PB AGS B 801 " ideal model delta sigma weight residual 1.585 1.856 -0.271 2.70e-02 1.37e+03 1.01e+02 bond pdb=" O3B AGS E 801 " pdb=" PB AGS E 801 " ideal model delta sigma weight residual 1.585 1.854 -0.269 2.70e-02 1.37e+03 9.90e+01 ... (remaining 17488 not shown) Histogram of bond angle deviations from ideal: 89.16 - 99.13: 25 99.13 - 109.10: 1268 109.10 - 119.07: 13509 119.07 - 129.05: 8528 129.05 - 139.02: 189 Bond angle restraints: 23519 Sorted by residual: angle pdb=" PB AGS D 801 " pdb=" O3B AGS D 801 " pdb=" PG AGS D 801 " ideal model delta sigma weight residual 120.12 139.02 -18.90 3.00e+00 1.11e-01 3.97e+01 angle pdb=" PB AGS A 801 " pdb=" O3B AGS A 801 " pdb=" PG AGS A 801 " ideal model delta sigma weight residual 120.12 138.95 -18.83 3.00e+00 1.11e-01 3.94e+01 angle pdb=" PB AGS E 801 " pdb=" O3B AGS E 801 " pdb=" PG AGS E 801 " ideal model delta sigma weight residual 120.12 138.47 -18.35 3.00e+00 1.11e-01 3.74e+01 angle pdb=" O1B AGS F 801 " pdb=" PB AGS F 801 " pdb=" O3B AGS F 801 " ideal model delta sigma weight residual 109.95 91.68 18.27 3.00e+00 1.11e-01 3.71e+01 angle pdb=" O1B AGS B 801 " pdb=" PB AGS B 801 " pdb=" O3B AGS B 801 " ideal model delta sigma weight residual 109.95 91.72 18.23 3.00e+00 1.11e-01 3.69e+01 ... (remaining 23514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 10129 17.60 - 35.21: 488 35.21 - 52.81: 112 52.81 - 70.42: 25 70.42 - 88.02: 3 Dihedral angle restraints: 10757 sinusoidal: 4680 harmonic: 6077 Sorted by residual: dihedral pdb=" CA VAL E 630 " pdb=" C VAL E 630 " pdb=" N VAL E 631 " pdb=" CA VAL E 631 " ideal model delta harmonic sigma weight residual -180.00 -160.77 -19.23 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA VAL F 630 " pdb=" C VAL F 630 " pdb=" N VAL F 631 " pdb=" CA VAL F 631 " ideal model delta harmonic sigma weight residual 180.00 -161.38 -18.62 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA VAL D 630 " pdb=" C VAL D 630 " pdb=" N VAL D 631 " pdb=" CA VAL D 631 " ideal model delta harmonic sigma weight residual -180.00 -163.05 -16.95 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 10754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2191 0.059 - 0.119: 283 0.119 - 0.178: 72 0.178 - 0.238: 5 0.238 - 0.297: 7 Chirality restraints: 2558 Sorted by residual: chirality pdb=" C2' AGS A 801 " pdb=" C1' AGS A 801 " pdb=" C3' AGS A 801 " pdb=" O2' AGS A 801 " both_signs ideal model delta sigma weight residual False -2.67 -2.97 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C2' AGS F 801 " pdb=" C1' AGS F 801 " pdb=" C3' AGS F 801 " pdb=" O2' AGS F 801 " both_signs ideal model delta sigma weight residual False -2.67 -2.96 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C2' AGS E 801 " pdb=" C1' AGS E 801 " pdb=" C3' AGS E 801 " pdb=" O2' AGS E 801 " both_signs ideal model delta sigma weight residual False -2.67 -2.95 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 2555 not shown) Planarity restraints: 3025 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG F 546 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO F 547 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO F 547 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 547 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 546 " 0.040 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO B 547 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 547 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 547 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 546 " -0.034 5.00e-02 4.00e+02 5.05e-02 4.08e+00 pdb=" N PRO E 547 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO E 547 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 547 " -0.029 5.00e-02 4.00e+02 ... (remaining 3022 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 116 2.56 - 3.14: 13456 3.14 - 3.73: 27143 3.73 - 4.31: 38783 4.31 - 4.90: 64160 Nonbonded interactions: 143658 Sorted by model distance: nonbonded pdb=" OG1 THR D 388 " pdb="MG MG D 802 " model vdw 1.974 2.170 nonbonded pdb=" OG1 THR C 388 " pdb="MG MG C 802 " model vdw 1.974 2.170 nonbonded pdb=" OG1 THR E 388 " pdb="MG MG E 802 " model vdw 1.975 2.170 nonbonded pdb=" OG1 THR B 388 " pdb="MG MG B 802 " model vdw 1.984 2.170 nonbonded pdb=" O1B AGS A 801 " pdb="MG MG A 802 " model vdw 1.996 2.170 ... (remaining 143653 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 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: 12.230 Check model and map are aligned: 0.240 Set scattering table: 0.170 Process input model: 44.870 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 : 0.009 0.286 17493 Z= 0.580 Angle : 1.126 23.733 23519 Z= 0.485 Chirality : 0.048 0.297 2558 Planarity : 0.005 0.063 3025 Dihedral : 11.267 88.022 6805 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.84 % Favored : 95.06 % Rotamer: Outliers : 0.56 % Allowed : 3.22 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.15), residues: 2046 helix: -1.02 (0.12), residues: 1064 sheet: -3.97 (0.23), residues: 192 loop : -2.06 (0.19), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 587 HIS 0.006 0.001 HIS C 552 PHE 0.019 0.002 PHE C 423 TYR 0.010 0.001 TYR E 397 ARG 0.003 0.000 ARG C 620 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 218 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 369 TYR cc_start: 0.7934 (p90) cc_final: 0.7699 (p90) REVERT: E 369 TYR cc_start: 0.7693 (p90) cc_final: 0.7142 (p90) outliers start: 10 outliers final: 2 residues processed: 227 average time/residue: 1.9231 time to fit residues: 470.7637 Evaluate side-chains 98 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain E residue 602 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 186 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 624 HIS D 624 HIS E 415 GLN E 455 GLN ** F 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 624 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17493 Z= 0.227 Angle : 0.563 8.902 23519 Z= 0.282 Chirality : 0.039 0.165 2558 Planarity : 0.005 0.080 3025 Dihedral : 8.433 88.191 2423 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.61 % Favored : 98.29 % Rotamer: Outliers : 0.78 % Allowed : 8.56 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.17), residues: 2046 helix: 0.63 (0.14), residues: 1074 sheet: -3.20 (0.27), residues: 207 loop : -1.29 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 587 HIS 0.006 0.001 HIS D 552 PHE 0.009 0.001 PHE D 423 TYR 0.014 0.001 TYR F 369 ARG 0.013 0.001 ARG E 327 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 108 average time/residue: 1.5871 time to fit residues: 189.6121 Evaluate side-chains 83 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain F residue 500 ASP Chi-restraints excluded: chain F residue 556 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 chunk 201 optimal weight: 0.0670 chunk 166 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 563 ASN F 418 HIS F 433 HIS F 552 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17493 Z= 0.267 Angle : 0.505 9.882 23519 Z= 0.256 Chirality : 0.038 0.141 2558 Planarity : 0.003 0.039 3025 Dihedral : 8.021 102.855 2421 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.05 % Favored : 97.85 % Rotamer: Outliers : 1.00 % Allowed : 9.50 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.18), residues: 2046 helix: 1.03 (0.15), residues: 1110 sheet: -3.33 (0.25), residues: 257 loop : -0.55 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 587 HIS 0.006 0.001 HIS D 552 PHE 0.009 0.001 PHE D 423 TYR 0.014 0.001 TYR C 322 ARG 0.010 0.000 ARG B 327 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 617 TYR cc_start: 0.7734 (m-80) cc_final: 0.7362 (m-80) REVERT: D 695 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6530 (ptt90) outliers start: 18 outliers final: 6 residues processed: 92 average time/residue: 1.3580 time to fit residues: 140.3509 Evaluate side-chains 81 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain F residue 486 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 20 optimal weight: 30.0000 chunk 89 optimal weight: 0.5980 chunk 125 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 198 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 177 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 415 GLN E 455 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17493 Z= 0.209 Angle : 0.462 10.619 23519 Z= 0.236 Chirality : 0.037 0.139 2558 Planarity : 0.003 0.035 3025 Dihedral : 7.803 110.332 2421 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.71 % Favored : 98.24 % Rotamer: Outliers : 0.83 % Allowed : 10.00 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.18), residues: 2046 helix: 1.34 (0.15), residues: 1110 sheet: -2.85 (0.25), residues: 274 loop : -0.38 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 587 HIS 0.005 0.001 HIS D 552 PHE 0.008 0.001 PHE D 423 TYR 0.015 0.001 TYR F 369 ARG 0.009 0.000 ARG D 518 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 TYR cc_start: 0.7751 (m-80) cc_final: 0.7451 (m-80) outliers start: 15 outliers final: 6 residues processed: 90 average time/residue: 1.2767 time to fit residues: 131.1019 Evaluate side-chains 81 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain B residue 486 CYS Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain F residue 495 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 169 optimal weight: 0.5980 chunk 136 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 101 optimal weight: 0.3980 chunk 177 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 415 GLN B 595 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17493 Z= 0.178 Angle : 0.456 11.393 23519 Z= 0.232 Chirality : 0.037 0.137 2558 Planarity : 0.003 0.033 3025 Dihedral : 7.700 110.864 2421 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.56 % Favored : 98.39 % Rotamer: Outliers : 0.83 % Allowed : 10.28 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.18), residues: 2046 helix: 1.49 (0.16), residues: 1110 sheet: -2.64 (0.26), residues: 284 loop : -0.19 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 587 HIS 0.006 0.001 HIS E 373 PHE 0.008 0.001 PHE D 423 TYR 0.021 0.001 TYR F 369 ARG 0.005 0.000 ARG D 518 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 617 TYR cc_start: 0.7759 (m-80) cc_final: 0.7441 (m-80) outliers start: 15 outliers final: 6 residues processed: 91 average time/residue: 1.2437 time to fit residues: 128.6264 Evaluate side-chains 78 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain E residue 602 ASP Chi-restraints excluded: chain F residue 495 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 0.0270 chunk 178 optimal weight: 5.9990 chunk 39 optimal weight: 0.4980 chunk 116 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 198 optimal weight: 0.6980 chunk 164 optimal weight: 0.0670 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 65 optimal weight: 0.0980 chunk 104 optimal weight: 0.0970 overall best weight: 0.1574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 399 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17493 Z= 0.123 Angle : 0.450 12.090 23519 Z= 0.229 Chirality : 0.036 0.137 2558 Planarity : 0.003 0.032 3025 Dihedral : 7.481 107.583 2421 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.11 % Allowed : 10.39 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.18), residues: 2046 helix: 1.59 (0.16), residues: 1110 sheet: -2.41 (0.26), residues: 284 loop : -0.16 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 587 HIS 0.005 0.000 HIS D 373 PHE 0.006 0.001 PHE D 423 TYR 0.021 0.001 TYR F 369 ARG 0.012 0.000 ARG D 518 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 76 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 617 TYR cc_start: 0.7704 (m-80) cc_final: 0.7415 (m-80) outliers start: 20 outliers final: 7 residues processed: 93 average time/residue: 1.1648 time to fit residues: 124.7381 Evaluate side-chains 76 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain F residue 495 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 0.0470 chunk 22 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 144 optimal weight: 0.0370 chunk 112 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17493 Z= 0.162 Angle : 0.471 12.395 23519 Z= 0.237 Chirality : 0.037 0.146 2558 Planarity : 0.003 0.031 3025 Dihedral : 7.425 107.762 2421 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.67 % Allowed : 11.06 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.19), residues: 2046 helix: 1.76 (0.16), residues: 1105 sheet: -2.20 (0.27), residues: 282 loop : -0.07 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 587 HIS 0.006 0.001 HIS D 373 PHE 0.007 0.001 PHE D 423 TYR 0.015 0.001 TYR F 369 ARG 0.007 0.000 ARG D 518 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 TYR cc_start: 0.7707 (m-80) cc_final: 0.7440 (m-80) outliers start: 12 outliers final: 7 residues processed: 87 average time/residue: 1.3223 time to fit residues: 130.4884 Evaluate side-chains 78 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 486 CYS Chi-restraints excluded: chain F residue 495 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 118 optimal weight: 0.0060 chunk 59 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 134 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 HIS B 415 GLN E 563 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17493 Z= 0.171 Angle : 0.489 12.870 23519 Z= 0.244 Chirality : 0.037 0.146 2558 Planarity : 0.003 0.030 3025 Dihedral : 7.392 106.592 2421 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.50 % Allowed : 11.06 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.19), residues: 2046 helix: 1.82 (0.16), residues: 1105 sheet: -1.99 (0.27), residues: 282 loop : -0.01 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 587 HIS 0.010 0.001 HIS D 373 PHE 0.008 0.001 PHE D 423 TYR 0.016 0.001 TYR C 322 ARG 0.007 0.000 ARG D 518 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 TYR cc_start: 0.7661 (m-80) cc_final: 0.7413 (m-80) REVERT: D 417 ARG cc_start: 0.8038 (ttp80) cc_final: 0.7804 (ttp80) outliers start: 9 outliers final: 7 residues processed: 79 average time/residue: 1.3837 time to fit residues: 123.5146 Evaluate side-chains 73 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain F residue 486 CYS Chi-restraints excluded: chain F residue 495 SER Chi-restraints excluded: chain F residue 500 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 10.0000 chunk 172 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 56 optimal weight: 0.0980 chunk 166 optimal weight: 0.5980 chunk 174 optimal weight: 0.7980 chunk 183 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17493 Z= 0.176 Angle : 0.509 13.072 23519 Z= 0.250 Chirality : 0.037 0.146 2558 Planarity : 0.003 0.030 3025 Dihedral : 7.369 106.691 2421 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.44 % Allowed : 11.33 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.19), residues: 2046 helix: 1.82 (0.16), residues: 1110 sheet: -1.83 (0.28), residues: 282 loop : 0.08 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 587 HIS 0.011 0.001 HIS D 373 PHE 0.009 0.001 PHE E 414 TYR 0.016 0.001 TYR C 322 ARG 0.006 0.000 ARG D 518 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 TYR cc_start: 0.7700 (m-80) cc_final: 0.7442 (m-80) REVERT: D 417 ARG cc_start: 0.8030 (ttp80) cc_final: 0.7798 (ttp80) outliers start: 8 outliers final: 6 residues processed: 76 average time/residue: 1.3334 time to fit residues: 115.1325 Evaluate side-chains 74 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain F residue 486 CYS Chi-restraints excluded: chain F residue 495 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 0.8980 chunk 118 optimal weight: 0.0980 chunk 92 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 204 optimal weight: 6.9990 chunk 187 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 125 optimal weight: 0.2980 chunk 99 optimal weight: 0.4980 chunk 129 optimal weight: 0.0570 overall best weight: 0.2498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN D 469 GLN E 455 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17493 Z= 0.139 Angle : 0.503 13.199 23519 Z= 0.248 Chirality : 0.036 0.163 2558 Planarity : 0.003 0.030 3025 Dihedral : 7.230 103.550 2421 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.44 % Allowed : 11.39 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.19), residues: 2046 helix: 1.85 (0.16), residues: 1110 sheet: -1.62 (0.29), residues: 282 loop : 0.08 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP D 587 HIS 0.009 0.001 HIS D 373 PHE 0.009 0.001 PHE E 414 TYR 0.017 0.001 TYR C 322 ARG 0.006 0.000 ARG D 518 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 2.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 TYR cc_start: 0.7695 (m-80) cc_final: 0.7473 (m-80) REVERT: D 417 ARG cc_start: 0.7987 (ttp80) cc_final: 0.7758 (ttp80) outliers start: 8 outliers final: 5 residues processed: 75 average time/residue: 1.3882 time to fit residues: 117.8819 Evaluate side-chains 72 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain F residue 486 CYS Chi-restraints excluded: chain F residue 495 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 0.0770 chunk 49 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 0.2980 chunk 162 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 167 optimal weight: 0.6980 chunk 20 optimal weight: 0.1980 chunk 30 optimal weight: 0.2980 chunk 143 optimal weight: 0.9980 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.089170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.062364 restraints weight = 54904.221| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.63 r_work: 0.2826 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17493 Z= 0.143 Angle : 0.501 13.123 23519 Z= 0.246 Chirality : 0.036 0.160 2558 Planarity : 0.003 0.031 3025 Dihedral : 7.158 102.567 2419 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.39 % Allowed : 11.44 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.19), residues: 2046 helix: 1.89 (0.16), residues: 1110 sheet: -1.43 (0.29), residues: 282 loop : 0.11 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP D 587 HIS 0.011 0.001 HIS D 373 PHE 0.007 0.001 PHE E 414 TYR 0.016 0.001 TYR C 322 ARG 0.006 0.000 ARG D 518 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4569.23 seconds wall clock time: 82 minutes 48.33 seconds (4968.33 seconds total)