Starting phenix.real_space_refine on Thu Sep 26 02:30:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5is0_8119/09_2024/5is0_8119_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5is0_8119/09_2024/5is0_8119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5is0_8119/09_2024/5is0_8119.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5is0_8119/09_2024/5is0_8119.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5is0_8119/09_2024/5is0_8119_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5is0_8119/09_2024/5is0_8119_trim.cif" } resolution = 3.43 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= 1.000 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 S 76 5.16 5 Cl 4 4.86 5 C 7804 2.51 5 N 1932 2.21 5 O 1992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11808 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 2927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2927 Classifications: {'peptide': 394} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 82} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 339 Unresolved non-hydrogen angles: 438 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 14, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 212 Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'6ET': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, E, D Time building chain proxies: 5.82, per 1000 atoms: 0.49 Number of scatterers: 11808 At special positions: 0 Unit cell: (120.344, 120.344, 98.4636, 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) Cl 4 17.00 S 76 16.00 O 1992 8.00 N 1932 7.00 C 7804 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 - 3.00 Amino acid : True - 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.6 seconds 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2944 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 4 sheets defined 67.3% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 353 removed outlier: 3.736A pdb=" N LEU C 349 " --> pdb=" O LYS C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 411 through 414 Processing helix chain 'C' and resid 415 through 429 removed outlier: 3.936A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN C 423 " --> pdb=" O ASN C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 454 removed outlier: 3.985A pdb=" N ILE C 433 " --> pdb=" O PHE C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 500 removed outlier: 4.300A pdb=" N PHE C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG C 474 " --> pdb=" O GLY C 470 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN C 498 " --> pdb=" O GLN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 513 through 532 removed outlier: 3.555A pdb=" N PHE C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.987A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 557 removed outlier: 3.800A pdb=" N TYR C 555 " --> pdb=" O MET C 552 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 577 removed outlier: 3.636A pdb=" N ILE C 564 " --> pdb=" O GLN C 560 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 597 removed outlier: 3.814A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR C 593 " --> pdb=" O PHE C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 628 removed outlier: 3.638A pdb=" N ASN C 628 " --> pdb=" O GLY C 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 602 through 628' Processing helix chain 'C' and resid 629 through 637 removed outlier: 3.660A pdb=" N THR C 633 " --> pdb=" O SER C 629 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 643 removed outlier: 3.637A pdb=" N ILE C 642 " --> pdb=" O PHE C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 671 Processing helix chain 'C' and resid 673 through 712 removed outlier: 3.946A pdb=" N ILE C 679 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN C 687 " --> pdb=" O GLY C 683 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS C 688 " --> pdb=" O GLU C 684 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU C 692 " --> pdb=" O LYS C 688 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS C 694 " --> pdb=" O ALA C 690 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU C 709 " --> pdb=" O ILE C 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 Processing helix chain 'B' and resid 345 through 353 removed outlier: 3.735A pdb=" N LEU B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 411 through 414 Processing helix chain 'B' and resid 415 through 429 removed outlier: 3.936A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN B 423 " --> pdb=" O ASN B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 454 removed outlier: 3.985A pdb=" N ILE B 433 " --> pdb=" O PHE B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 500 removed outlier: 4.301A pdb=" N PHE B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG B 474 " --> pdb=" O GLY B 470 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN B 498 " --> pdb=" O GLN B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 510 Processing helix chain 'B' and resid 513 through 532 removed outlier: 3.555A pdb=" N PHE B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.987A pdb=" N SER B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.799A pdb=" N TYR B 555 " --> pdb=" O MET B 552 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 577 removed outlier: 3.636A pdb=" N ILE B 564 " --> pdb=" O GLN B 560 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 597 removed outlier: 3.814A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR B 593 " --> pdb=" O PHE B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 628 removed outlier: 3.638A pdb=" N ASN B 628 " --> pdb=" O GLY B 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 602 through 628' Processing helix chain 'B' and resid 629 through 637 removed outlier: 3.659A pdb=" N THR B 633 " --> pdb=" O SER B 629 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 643 removed outlier: 3.637A pdb=" N ILE B 642 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 671 Processing helix chain 'B' and resid 673 through 712 removed outlier: 3.946A pdb=" N ILE B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN B 687 " --> pdb=" O GLY B 683 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS B 688 " --> pdb=" O GLU B 684 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LYS B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU B 709 " --> pdb=" O ILE B 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 344 Processing helix chain 'D' and resid 345 through 353 removed outlier: 3.736A pdb=" N LEU D 349 " --> pdb=" O LYS D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 411 through 414 Processing helix chain 'D' and resid 415 through 429 removed outlier: 3.936A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN D 423 " --> pdb=" O ASN D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 454 removed outlier: 3.984A pdb=" N ILE D 433 " --> pdb=" O PHE D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 500 removed outlier: 4.300A pdb=" N PHE D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG D 474 " --> pdb=" O GLY D 470 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN D 498 " --> pdb=" O GLN D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 510 Processing helix chain 'D' and resid 513 through 532 removed outlier: 3.556A pdb=" N PHE D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 551 removed outlier: 3.987A pdb=" N SER D 540 " --> pdb=" O GLU D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 557 removed outlier: 3.800A pdb=" N TYR D 555 " --> pdb=" O MET D 552 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 577 removed outlier: 3.637A pdb=" N ILE D 564 " --> pdb=" O GLN D 560 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR D 565 " --> pdb=" O GLN D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 597 removed outlier: 3.814A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR D 593 " --> pdb=" O PHE D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 628 removed outlier: 3.638A pdb=" N ASN D 628 " --> pdb=" O GLY D 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 602 through 628' Processing helix chain 'D' and resid 629 through 637 removed outlier: 3.660A pdb=" N THR D 633 " --> pdb=" O SER D 629 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 643 removed outlier: 3.637A pdb=" N ILE D 642 " --> pdb=" O PHE D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 671 Processing helix chain 'D' and resid 673 through 712 removed outlier: 3.946A pdb=" N ILE D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN D 687 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS D 688 " --> pdb=" O GLU D 684 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU D 692 " --> pdb=" O LYS D 688 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LYS D 694 " --> pdb=" O ALA D 690 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU D 709 " --> pdb=" O ILE D 705 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 344 Processing helix chain 'E' and resid 345 through 353 removed outlier: 3.737A pdb=" N LEU E 349 " --> pdb=" O LYS E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 401 Processing helix chain 'E' and resid 411 through 414 Processing helix chain 'E' and resid 415 through 429 removed outlier: 3.937A pdb=" N ARG E 420 " --> pdb=" O GLU E 416 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN E 423 " --> pdb=" O ASN E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 454 removed outlier: 3.984A pdb=" N ILE E 433 " --> pdb=" O PHE E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 500 removed outlier: 4.300A pdb=" N PHE E 473 " --> pdb=" O VAL E 469 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG E 474 " --> pdb=" O GLY E 470 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN E 498 " --> pdb=" O GLN E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 510 Processing helix chain 'E' and resid 513 through 532 removed outlier: 3.556A pdb=" N PHE E 517 " --> pdb=" O GLU E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 551 removed outlier: 3.987A pdb=" N SER E 540 " --> pdb=" O GLU E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 557 removed outlier: 3.800A pdb=" N TYR E 555 " --> pdb=" O MET E 552 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG E 557 " --> pdb=" O TYR E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 577 removed outlier: 3.637A pdb=" N ILE E 564 " --> pdb=" O GLN E 560 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR E 565 " --> pdb=" O GLN E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 597 removed outlier: 3.814A pdb=" N VAL E 583 " --> pdb=" O ARG E 579 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR E 593 " --> pdb=" O PHE E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 602 through 628 removed outlier: 3.638A pdb=" N ASN E 628 " --> pdb=" O GLY E 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 602 through 628' Processing helix chain 'E' and resid 629 through 637 removed outlier: 3.660A pdb=" N THR E 633 " --> pdb=" O SER E 629 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU E 636 " --> pdb=" O SER E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 643 removed outlier: 3.638A pdb=" N ILE E 642 " --> pdb=" O PHE E 638 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 671 Processing helix chain 'E' and resid 673 through 712 removed outlier: 3.947A pdb=" N ILE E 679 " --> pdb=" O LEU E 675 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN E 687 " --> pdb=" O GLY E 683 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS E 688 " --> pdb=" O GLU E 684 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN E 691 " --> pdb=" O ASN E 687 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU E 692 " --> pdb=" O LYS E 688 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS E 694 " --> pdb=" O ALA E 690 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU E 709 " --> pdb=" O ILE E 705 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 368 through 372 removed outlier: 3.808A pdb=" N GLU C 371 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER C 379 " --> pdb=" O GLU C 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 368 through 372 removed outlier: 3.807A pdb=" N GLU B 371 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N SER B 379 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 368 through 372 removed outlier: 3.808A pdb=" N GLU D 371 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER D 379 " --> pdb=" O GLU D 371 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 368 through 372 removed outlier: 3.808A pdb=" N GLU E 371 " --> pdb=" O SER E 379 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER E 379 " --> pdb=" O GLU E 371 " (cutoff:3.500A) 697 hydrogen bonds defined for protein. 2055 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: 3.01 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3514 1.34 - 1.46: 2975 1.46 - 1.57: 5455 1.57 - 1.69: 4 1.69 - 1.81: 128 Bond restraints: 12076 Sorted by residual: bond pdb=" C14 6ET B 801 " pdb=" S15 6ET B 801 " ideal model delta sigma weight residual 1.689 1.588 0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" C14 6ET C 801 " pdb=" S15 6ET C 801 " ideal model delta sigma weight residual 1.689 1.588 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C14 6ET D 801 " pdb=" S15 6ET D 801 " ideal model delta sigma weight residual 1.689 1.588 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C14 6ET E 801 " pdb=" S15 6ET E 801 " ideal model delta sigma weight residual 1.689 1.588 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C14 6ET B 801 " pdb=" N08 6ET B 801 " ideal model delta sigma weight residual 1.348 1.435 -0.087 2.00e-02 2.50e+03 1.89e+01 ... (remaining 12071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 15897 3.08 - 6.15: 435 6.15 - 9.23: 52 9.23 - 12.31: 12 12.31 - 15.38: 8 Bond angle restraints: 16404 Sorted by residual: angle pdb=" N GLU B 513 " pdb=" CA GLU B 513 " pdb=" C GLU B 513 " ideal model delta sigma weight residual 114.56 104.09 10.47 1.27e+00 6.20e-01 6.79e+01 angle pdb=" N GLU C 513 " pdb=" CA GLU C 513 " pdb=" C GLU C 513 " ideal model delta sigma weight residual 114.56 104.10 10.46 1.27e+00 6.20e-01 6.78e+01 angle pdb=" N GLU E 513 " pdb=" CA GLU E 513 " pdb=" C GLU E 513 " ideal model delta sigma weight residual 114.56 104.14 10.42 1.27e+00 6.20e-01 6.73e+01 angle pdb=" N GLU D 513 " pdb=" CA GLU D 513 " pdb=" C GLU D 513 " ideal model delta sigma weight residual 114.56 104.17 10.39 1.27e+00 6.20e-01 6.69e+01 angle pdb=" C07 6ET B 801 " pdb=" N08 6ET B 801 " pdb=" C09 6ET B 801 " ideal model delta sigma weight residual 115.16 130.54 -15.38 3.00e+00 1.11e-01 2.63e+01 ... (remaining 16399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.69: 6828 24.69 - 49.38: 132 49.38 - 74.07: 8 74.07 - 98.76: 4 98.76 - 123.45: 16 Dihedral angle restraints: 6988 sinusoidal: 2376 harmonic: 4612 Sorted by residual: dihedral pdb=" CA GLY C 375 " pdb=" C GLY C 375 " pdb=" N PRO C 376 " pdb=" CA PRO C 376 " ideal model delta harmonic sigma weight residual -180.00 -141.79 -38.21 0 5.00e+00 4.00e-02 5.84e+01 dihedral pdb=" CA GLY E 375 " pdb=" C GLY E 375 " pdb=" N PRO E 376 " pdb=" CA PRO E 376 " ideal model delta harmonic sigma weight residual -180.00 -141.80 -38.20 0 5.00e+00 4.00e-02 5.84e+01 dihedral pdb=" CA GLY B 375 " pdb=" C GLY B 375 " pdb=" N PRO B 376 " pdb=" CA PRO B 376 " ideal model delta harmonic sigma weight residual -180.00 -141.83 -38.17 0 5.00e+00 4.00e-02 5.83e+01 ... (remaining 6985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1058 0.051 - 0.103: 667 0.103 - 0.154: 139 0.154 - 0.206: 19 0.206 - 0.257: 13 Chirality restraints: 1896 Sorted by residual: chirality pdb=" CB VAL B 595 " pdb=" CA VAL B 595 " pdb=" CG1 VAL B 595 " pdb=" CG2 VAL B 595 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB VAL D 595 " pdb=" CA VAL D 595 " pdb=" CG1 VAL D 595 " pdb=" CG2 VAL D 595 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB VAL E 595 " pdb=" CA VAL E 595 " pdb=" CG1 VAL E 595 " pdb=" CG2 VAL E 595 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1893 not shown) Planarity restraints: 2024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY D 375 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.93e+00 pdb=" C GLY D 375 " 0.046 2.00e-02 2.50e+03 pdb=" O GLY D 375 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO D 376 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 375 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.86e+00 pdb=" C GLY E 375 " 0.045 2.00e-02 2.50e+03 pdb=" O GLY E 375 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO E 376 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 375 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.80e+00 pdb=" C GLY B 375 " -0.045 2.00e-02 2.50e+03 pdb=" O GLY B 375 " 0.017 2.00e-02 2.50e+03 pdb=" N PRO B 376 " 0.015 2.00e-02 2.50e+03 ... (remaining 2021 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.01: 4 2.01 - 2.73: 1440 2.73 - 3.45: 16758 3.45 - 4.18: 27400 4.18 - 4.90: 48173 Nonbonded interactions: 93775 Sorted by model distance: nonbonded pdb=" OG SER B 512 " pdb=" O13 6ET B 801 " model vdw 1.283 3.040 nonbonded pdb=" OG SER C 512 " pdb=" O13 6ET C 801 " model vdw 1.302 3.040 nonbonded pdb=" OG SER E 512 " pdb=" O13 6ET E 801 " model vdw 1.314 3.040 nonbonded pdb=" OG SER D 512 " pdb=" O13 6ET D 801 " model vdw 1.330 3.040 nonbonded pdb=" CB SER B 512 " pdb=" O13 6ET B 801 " model vdw 2.094 3.440 ... (remaining 93770 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.350 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: 0.440 Check model and map are aligned: 0.140 Set scattering table: 0.140 Process input model: 25.500 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 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 : 0.015 0.120 12076 Z= 0.902 Angle : 1.237 15.382 16404 Z= 0.646 Chirality : 0.064 0.257 1896 Planarity : 0.006 0.043 2024 Dihedral : 12.935 123.449 4044 Min Nonbonded Distance : 1.283 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.08 % Favored : 89.67 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.26 % 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: -5.27 (0.15), residues: 1568 helix: -3.51 (0.09), residues: 932 sheet: -3.99 (0.60), residues: 64 loop : -3.04 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP E 697 HIS 0.001 0.001 HIS C 410 PHE 0.035 0.004 PHE D 448 TYR 0.016 0.003 TYR D 653 ARG 0.012 0.002 ARG C 743 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 656 LYS cc_start: 0.8352 (tttt) cc_final: 0.8086 (tttm) REVERT: D 656 LYS cc_start: 0.8399 (tttt) cc_final: 0.8143 (tttm) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.2504 time to fit residues: 103.5592 Evaluate side-chains 167 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 HIS C 423 GLN C 700 GLN B 410 HIS B 423 GLN B 700 GLN D 410 HIS D 700 GLN E 410 HIS E 700 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12076 Z= 0.216 Angle : 0.655 9.723 16404 Z= 0.344 Chirality : 0.043 0.168 1896 Planarity : 0.004 0.027 2024 Dihedral : 13.737 117.218 1788 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.25 % Favored : 93.49 % Rotamer: Outliers : 1.12 % Allowed : 9.55 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.44 (0.19), residues: 1568 helix: -0.88 (0.14), residues: 1000 sheet: -2.64 (0.79), residues: 56 loop : -2.83 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 697 HIS 0.001 0.000 HIS C 410 PHE 0.018 0.002 PHE E 489 TYR 0.014 0.001 TYR B 565 ARG 0.004 0.000 ARG B 474 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 284 time to evaluate : 1.411 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 291 average time/residue: 0.2140 time to fit residues: 92.8880 Evaluate side-chains 209 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 202 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain D residue 442 CYS Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain E residue 574 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 141 optimal weight: 0.8980 chunk 153 optimal weight: 40.0000 chunk 126 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 HIS C 423 GLN C 700 GLN B 410 HIS B 423 GLN B 676 ASN D 410 HIS D 423 GLN D 700 GLN E 410 HIS E 423 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12076 Z= 0.231 Angle : 0.597 6.688 16404 Z= 0.315 Chirality : 0.042 0.156 1896 Planarity : 0.003 0.018 2024 Dihedral : 13.137 112.510 1788 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.69 % Allowed : 11.99 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.88 (0.22), residues: 1568 helix: 0.50 (0.17), residues: 972 sheet: -2.83 (0.73), residues: 56 loop : -2.34 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 697 HIS 0.002 0.001 HIS C 410 PHE 0.011 0.001 PHE E 489 TYR 0.014 0.001 TYR C 511 ARG 0.004 0.000 ARG C 474 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 243 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 636 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7557 (mm-30) outliers start: 18 outliers final: 15 residues processed: 258 average time/residue: 0.2351 time to fit residues: 87.8887 Evaluate side-chains 223 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 208 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 442 CYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 442 CYS Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 574 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.7980 chunk 106 optimal weight: 0.3980 chunk 73 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 95 optimal weight: 0.0170 chunk 142 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 700 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12076 Z= 0.146 Angle : 0.543 5.481 16404 Z= 0.290 Chirality : 0.041 0.153 1896 Planarity : 0.003 0.022 2024 Dihedral : 12.657 109.564 1788 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.69 % Allowed : 12.83 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.22), residues: 1568 helix: 0.77 (0.17), residues: 1008 sheet: -2.77 (0.64), residues: 56 loop : -2.40 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 697 HIS 0.001 0.000 HIS E 410 PHE 0.010 0.001 PHE E 489 TYR 0.016 0.001 TYR D 511 ARG 0.006 0.001 ARG B 499 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 245 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 257 average time/residue: 0.2246 time to fit residues: 84.2644 Evaluate side-chains 221 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 211 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 574 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 128 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 40.0000 chunk 135 optimal weight: 2.9990 chunk 38 optimal weight: 40.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 676 ASN E 533 GLN E 676 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12076 Z= 0.190 Angle : 0.577 8.960 16404 Z= 0.299 Chirality : 0.041 0.165 1896 Planarity : 0.002 0.019 2024 Dihedral : 12.510 109.253 1788 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.34 % Allowed : 14.79 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.27 (0.23), residues: 1568 helix: 0.98 (0.17), residues: 1012 sheet: -2.71 (0.62), residues: 56 loop : -2.30 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 697 HIS 0.001 0.000 HIS C 410 PHE 0.011 0.001 PHE D 496 TYR 0.015 0.001 TYR B 511 ARG 0.004 0.000 ARG C 499 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 229 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 699 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8362 (tp) outliers start: 25 outliers final: 22 residues processed: 247 average time/residue: 0.2128 time to fit residues: 79.2287 Evaluate side-chains 226 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 203 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 425 LYS Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 574 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 150 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 12 optimal weight: 0.2980 chunk 49 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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: 0.7217 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12076 Z= 0.211 Angle : 0.589 12.496 16404 Z= 0.305 Chirality : 0.041 0.167 1896 Planarity : 0.003 0.019 2024 Dihedral : 12.400 108.556 1788 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.62 % Allowed : 15.54 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.18 (0.23), residues: 1568 helix: 1.01 (0.17), residues: 1012 sheet: -2.67 (0.59), residues: 56 loop : -2.18 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 697 HIS 0.001 0.000 HIS C 410 PHE 0.011 0.001 PHE B 496 TYR 0.016 0.001 TYR D 511 ARG 0.003 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 222 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 699 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8243 (tp) outliers start: 28 outliers final: 22 residues processed: 243 average time/residue: 0.1993 time to fit residues: 74.1011 Evaluate side-chains 239 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 216 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 574 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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: 0.7167 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12076 Z= 0.169 Angle : 0.587 11.767 16404 Z= 0.302 Chirality : 0.040 0.182 1896 Planarity : 0.002 0.015 2024 Dihedral : 12.046 105.807 1788 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.43 % Allowed : 15.82 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.18 (0.23), residues: 1568 helix: 1.01 (0.17), residues: 1012 sheet: -2.68 (0.56), residues: 56 loop : -2.17 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 697 HIS 0.001 0.000 HIS C 410 PHE 0.010 0.001 PHE C 496 TYR 0.011 0.001 TYR C 565 ARG 0.003 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 240 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 19 residues processed: 258 average time/residue: 0.1880 time to fit residues: 74.1175 Evaluate side-chains 235 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 216 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 425 LYS Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 670 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 102 optimal weight: 0.0270 chunk 74 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 676 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12076 Z= 0.184 Angle : 0.615 14.626 16404 Z= 0.311 Chirality : 0.040 0.135 1896 Planarity : 0.003 0.024 2024 Dihedral : 11.833 104.132 1788 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.72 % Allowed : 16.10 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.05 (0.23), residues: 1568 helix: 1.22 (0.17), residues: 988 sheet: -2.64 (0.55), residues: 56 loop : -2.00 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 697 HIS 0.001 0.000 HIS E 410 PHE 0.010 0.001 PHE B 496 TYR 0.017 0.001 TYR B 511 ARG 0.003 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 239 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 28 residues processed: 259 average time/residue: 0.1843 time to fit residues: 73.9434 Evaluate side-chains 248 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 220 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 425 LYS Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 483 SER Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 673 LEU Chi-restraints excluded: chain E residue 686 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 61 optimal weight: 0.4980 chunk 110 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 GLN ** E 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12076 Z= 0.179 Angle : 0.642 15.304 16404 Z= 0.321 Chirality : 0.041 0.164 1896 Planarity : 0.002 0.015 2024 Dihedral : 11.618 102.367 1788 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.53 % Allowed : 16.76 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.11 (0.22), residues: 1568 helix: 1.04 (0.17), residues: 1016 sheet: -2.67 (0.53), residues: 56 loop : -2.12 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 697 HIS 0.001 0.000 HIS C 410 PHE 0.009 0.001 PHE C 496 TYR 0.018 0.001 TYR D 511 ARG 0.003 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 232 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 26 residues processed: 250 average time/residue: 0.1894 time to fit residues: 73.3038 Evaluate side-chains 247 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 221 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 673 LEU Chi-restraints excluded: chain E residue 686 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 3.9990 chunk 90 optimal weight: 0.0970 chunk 70 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 155 optimal weight: 40.0000 chunk 143 optimal weight: 0.0170 chunk 123 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 75 optimal weight: 0.5980 chunk 98 optimal weight: 0.5980 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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: 0.7138 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12076 Z= 0.179 Angle : 0.652 14.132 16404 Z= 0.326 Chirality : 0.040 0.136 1896 Planarity : 0.003 0.024 2024 Dihedral : 11.491 101.013 1788 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.34 % Allowed : 17.42 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.08 (0.22), residues: 1568 helix: 1.07 (0.17), residues: 1012 sheet: -2.63 (0.52), residues: 56 loop : -2.10 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 697 HIS 0.000 0.000 HIS C 410 PHE 0.010 0.001 PHE B 496 TYR 0.017 0.001 TYR B 511 ARG 0.003 0.000 ARG C 420 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 234 time to evaluate : 1.441 Fit side-chains revert: symmetry clash REVERT: D 682 MET cc_start: 0.7426 (mtt) cc_final: 0.7166 (mtt) outliers start: 25 outliers final: 23 residues processed: 250 average time/residue: 0.1787 time to fit residues: 69.6508 Evaluate side-chains 246 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 223 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 673 LEU Chi-restraints excluded: chain E residue 686 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 37 optimal weight: 40.0000 chunk 114 optimal weight: 30.0000 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.115931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.087110 restraints weight = 27971.433| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.89 r_work: 0.3013 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12076 Z= 0.208 Angle : 0.665 14.178 16404 Z= 0.333 Chirality : 0.041 0.136 1896 Planarity : 0.002 0.019 2024 Dihedral : 11.434 100.212 1788 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.34 % Allowed : 17.98 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.00 (0.22), residues: 1568 helix: 1.14 (0.17), residues: 1012 sheet: -2.67 (0.51), residues: 56 loop : -2.06 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 549 HIS 0.001 0.000 HIS E 410 PHE 0.010 0.001 PHE D 496 TYR 0.016 0.001 TYR E 351 ARG 0.003 0.000 ARG C 420 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2423.13 seconds wall clock time: 45 minutes 23.96 seconds (2723.96 seconds total)