Starting phenix.real_space_refine on Fri Feb 16 07:07:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2n_23134/02_2024/7l2n_23134_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2n_23134/02_2024/7l2n_23134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2n_23134/02_2024/7l2n_23134.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2n_23134/02_2024/7l2n_23134.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2n_23134/02_2024/7l2n_23134_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2n_23134/02_2024/7l2n_23134_updated.pdb" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 9696 2.51 5 N 2328 2.21 5 O 2608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 534": "NH1" <-> "NH2" Residue "C ARG 367": "NH1" <-> "NH2" Residue "C ARG 534": "NH1" <-> "NH2" Residue "C ARG 557": "NH1" <-> "NH2" Residue "D ARG 367": "NH1" <-> "NH2" Residue "D ARG 534": "NH1" <-> "NH2" Residue "B ARG 367": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14724 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3635 Classifications: {'peptide': 445} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 433} Chain breaks: 1 Chain: "C" Number of atoms: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3635 Classifications: {'peptide': 445} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 433} Chain breaks: 1 Chain: "D" Number of atoms: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3635 Classifications: {'peptide': 445} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 433} Chain breaks: 1 Chain: "B" Number of atoms: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3635 Classifications: {'peptide': 445} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 433} Chain breaks: 1 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.88, per 1000 atoms: 0.54 Number of scatterers: 14724 At special positions: 0 Unit cell: (123.84, 122.808, 100.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 2608 8.00 N 2328 7.00 C 9696 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: 5.44 Conformation dependent library (CDL) restraints added in 2.5 seconds 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 4 sheets defined 61.2% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 287 through 293 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 336 through 342 Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 409 through 414 removed outlier: 4.199A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU A 414 " --> pdb=" O HIS A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 409 through 414' Processing helix chain 'A' and resid 416 through 428 Processing helix chain 'A' and resid 430 through 453 Processing helix chain 'A' and resid 469 through 499 Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 511 through 531 Processing helix chain 'A' and resid 535 through 556 removed outlier: 4.073A pdb=" N VAL A 542 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TRP A 549 " --> pdb=" O ALA A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 598 removed outlier: 3.943A pdb=" N TYR A 565 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 567 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE A 573 " --> pdb=" O GLU A 570 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG A 575 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASP A 576 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU A 577 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N CYS A 578 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 579 " --> pdb=" O ASP A 576 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 580 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 584 " --> pdb=" O MET A 581 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 589 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 591 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 593 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 596 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 removed outlier: 3.855A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 670 Processing helix chain 'A' and resid 674 through 711 removed outlier: 5.592A pdb=" N GLN A 691 " --> pdb=" O ASN A 687 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLU A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN A 695 " --> pdb=" O GLN A 691 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LYS A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 293 Processing helix chain 'C' and resid 299 through 319 Processing helix chain 'C' and resid 336 through 342 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 409 through 414 removed outlier: 4.143A pdb=" N LEU C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LEU C 414 " --> pdb=" O HIS C 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 409 through 414' Processing helix chain 'C' and resid 416 through 428 Processing helix chain 'C' and resid 430 through 453 Processing helix chain 'C' and resid 469 through 499 Processing helix chain 'C' and resid 503 through 505 No H-bonds generated for 'chain 'C' and resid 503 through 505' Processing helix chain 'C' and resid 511 through 531 Processing helix chain 'C' and resid 535 through 556 removed outlier: 4.038A pdb=" N VAL C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TRP C 549 " --> pdb=" O ALA C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 598 removed outlier: 3.969A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 removed outlier: 3.874A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 Processing helix chain 'C' and resid 674 through 711 removed outlier: 5.621A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLU C 692 " --> pdb=" O LYS C 688 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN C 695 " --> pdb=" O GLN C 691 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 293 Processing helix chain 'D' and resid 299 through 319 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 346 through 353 Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 409 through 414 removed outlier: 4.167A pdb=" N LEU D 413 " --> pdb=" O ARG D 409 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LEU D 414 " --> pdb=" O HIS D 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 409 through 414' Processing helix chain 'D' and resid 416 through 428 Processing helix chain 'D' and resid 430 through 453 Processing helix chain 'D' and resid 469 through 499 Processing helix chain 'D' and resid 503 through 505 No H-bonds generated for 'chain 'D' and resid 503 through 505' Processing helix chain 'D' and resid 511 through 531 Processing helix chain 'D' and resid 535 through 556 removed outlier: 4.077A pdb=" N VAL D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN D 551 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 575 Processing helix chain 'D' and resid 577 through 598 Processing helix chain 'D' and resid 630 through 641 removed outlier: 3.824A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 670 Processing helix chain 'D' and resid 674 through 711 removed outlier: 5.609A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLU D 692 " --> pdb=" O LYS D 688 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN D 695 " --> pdb=" O GLN D 691 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LYS D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 299 through 319 Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 409 through 414 removed outlier: 3.998A pdb=" N LEU B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEU B 414 " --> pdb=" O HIS B 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 409 through 414' Processing helix chain 'B' and resid 416 through 428 Processing helix chain 'B' and resid 430 through 453 Processing helix chain 'B' and resid 469 through 499 Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 511 through 531 Processing helix chain 'B' and resid 535 through 556 removed outlier: 4.159A pdb=" N VAL B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 575 Processing helix chain 'B' and resid 577 through 598 Processing helix chain 'B' and resid 630 through 641 removed outlier: 3.796A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 674 through 711 removed outlier: 5.482A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN B 695 " --> pdb=" O GLN B 691 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 368 through 370 Processing sheet with id= B, first strand: chain 'C' and resid 368 through 370 Processing sheet with id= C, first strand: chain 'D' and resid 368 through 370 Processing sheet with id= D, first strand: chain 'B' and resid 368 through 370 799 hydrogen bonds defined for protein. 2118 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: 4.34 Time building geometry restraints manager: 5.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2268 1.31 - 1.43: 4284 1.43 - 1.56: 8368 1.56 - 1.69: 20 1.69 - 1.81: 152 Bond restraints: 15092 Sorted by residual: bond pdb=" CAM 6EU D 901 " pdb=" OAC 6EU D 901 " ideal model delta sigma weight residual 1.422 1.203 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" CAM 6EU B 901 " pdb=" OAC 6EU B 901 " ideal model delta sigma weight residual 1.422 1.204 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" CAM 6EU C 901 " pdb=" OAC 6EU C 901 " ideal model delta sigma weight residual 1.422 1.204 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" CAM 6EU A 901 " pdb=" OAC 6EU A 901 " ideal model delta sigma weight residual 1.422 1.204 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" CAV 6EU D 901 " pdb=" CBB 6EU D 901 " ideal model delta sigma weight residual 1.330 1.516 -0.186 2.00e-02 2.50e+03 8.67e+01 ... (remaining 15087 not shown) Histogram of bond angle deviations from ideal: 96.80 - 104.24: 168 104.24 - 111.69: 6943 111.69 - 119.14: 5198 119.14 - 126.58: 7993 126.58 - 134.03: 158 Bond angle restraints: 20460 Sorted by residual: angle pdb=" CAN 6EU C 901 " pdb=" CAJ 6EU C 901 " pdb=" CAO 6EU C 901 " ideal model delta sigma weight residual 115.38 129.83 -14.45 3.00e+00 1.11e-01 2.32e+01 angle pdb=" CAN 6EU B 901 " pdb=" CAJ 6EU B 901 " pdb=" CAO 6EU B 901 " ideal model delta sigma weight residual 115.38 129.82 -14.44 3.00e+00 1.11e-01 2.32e+01 angle pdb=" CAN 6EU A 901 " pdb=" CAJ 6EU A 901 " pdb=" CAO 6EU A 901 " ideal model delta sigma weight residual 115.38 129.72 -14.34 3.00e+00 1.11e-01 2.28e+01 angle pdb=" CAN 6EU D 901 " pdb=" CAJ 6EU D 901 " pdb=" CAO 6EU D 901 " ideal model delta sigma weight residual 115.38 129.68 -14.30 3.00e+00 1.11e-01 2.27e+01 angle pdb=" CAN 6EU D 901 " pdb=" CAJ 6EU D 901 " pdb=" OAA 6EU D 901 " ideal model delta sigma weight residual 110.99 96.80 14.19 3.00e+00 1.11e-01 2.24e+01 ... (remaining 20455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.19: 8537 16.19 - 32.37: 483 32.37 - 48.56: 100 48.56 - 64.74: 22 64.74 - 80.93: 14 Dihedral angle restraints: 9156 sinusoidal: 3892 harmonic: 5264 Sorted by residual: dihedral pdb=" CA LEU C 647 " pdb=" C LEU C 647 " pdb=" N GLU C 648 " pdb=" CA GLU C 648 " ideal model delta harmonic sigma weight residual 180.00 156.34 23.66 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA LEU A 647 " pdb=" C LEU A 647 " pdb=" N GLU A 648 " pdb=" CA GLU A 648 " ideal model delta harmonic sigma weight residual 180.00 156.35 23.65 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA LEU B 647 " pdb=" C LEU B 647 " pdb=" N GLU B 648 " pdb=" CA GLU B 648 " ideal model delta harmonic sigma weight residual 180.00 156.66 23.34 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 9153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 2280 0.137 - 0.273: 8 0.273 - 0.410: 4 0.410 - 0.546: 8 0.546 - 0.683: 4 Chirality restraints: 2304 Sorted by residual: chirality pdb=" CAJ 6EU B 901 " pdb=" CAK 6EU B 901 " pdb=" CAN 6EU B 901 " pdb=" CAO 6EU B 901 " both_signs ideal model delta sigma weight residual False 2.66 1.97 0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" CAJ 6EU D 901 " pdb=" CAK 6EU D 901 " pdb=" CAN 6EU D 901 " pdb=" CAO 6EU D 901 " both_signs ideal model delta sigma weight residual False 2.66 1.98 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CAJ 6EU C 901 " pdb=" CAK 6EU C 901 " pdb=" CAN 6EU C 901 " pdb=" CAO 6EU C 901 " both_signs ideal model delta sigma weight residual False 2.66 1.99 0.67 2.00e-01 2.50e+01 1.12e+01 ... (remaining 2301 not shown) Planarity restraints: 2500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAM 6EU C 901 " -0.108 2.00e-02 2.50e+03 1.91e-01 3.64e+02 pdb=" CAV 6EU C 901 " 0.330 2.00e-02 2.50e+03 pdb=" CBB 6EU C 901 " -0.112 2.00e-02 2.50e+03 pdb=" CBD 6EU C 901 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM 6EU D 901 " -0.108 2.00e-02 2.50e+03 1.89e-01 3.57e+02 pdb=" CAV 6EU D 901 " 0.327 2.00e-02 2.50e+03 pdb=" CBB 6EU D 901 " -0.111 2.00e-02 2.50e+03 pdb=" CBD 6EU D 901 " -0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM 6EU B 901 " 0.107 2.00e-02 2.50e+03 1.89e-01 3.56e+02 pdb=" CAV 6EU B 901 " -0.327 2.00e-02 2.50e+03 pdb=" CBB 6EU B 901 " 0.111 2.00e-02 2.50e+03 pdb=" CBD 6EU B 901 " 0.109 2.00e-02 2.50e+03 ... (remaining 2497 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 604 2.71 - 3.26: 15641 3.26 - 3.81: 24800 3.81 - 4.35: 30499 4.35 - 4.90: 51554 Nonbonded interactions: 123098 Sorted by model distance: nonbonded pdb=" NH1 ARG B 557 " pdb=" OE1 GLU B 570 " model vdw 2.167 2.520 nonbonded pdb=" NH1 ARG A 557 " pdb=" OE1 GLU A 570 " model vdw 2.168 2.520 nonbonded pdb=" NH1 ARG D 557 " pdb=" OE1 GLU D 570 " model vdw 2.179 2.520 nonbonded pdb=" N GLU A 458 " pdb=" OE1 GLU A 458 " model vdw 2.288 2.520 nonbonded pdb=" N GLU C 458 " pdb=" OE1 GLU C 458 " model vdw 2.313 2.520 ... (remaining 123093 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' } 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: 1.370 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: 5.900 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 40.570 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 : 0.011 0.219 15092 Z= 0.719 Angle : 0.858 14.452 20460 Z= 0.411 Chirality : 0.057 0.683 2304 Planarity : 0.008 0.191 2500 Dihedral : 11.270 80.929 5772 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.25 % Allowed : 1.69 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.30 (0.20), residues: 1764 helix: 1.26 (0.15), residues: 1164 sheet: -2.81 (0.54), residues: 68 loop : -1.78 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 549 HIS 0.006 0.001 HIS B 289 PHE 0.023 0.002 PHE C 304 TYR 0.013 0.002 TYR C 351 ARG 0.004 0.001 ARG B 331 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 752 time to evaluate : 1.710 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.7934 (mmm) cc_final: 0.7432 (mmm) REVERT: A 313 LEU cc_start: 0.8937 (mt) cc_final: 0.8619 (mt) REVERT: A 356 GLU cc_start: 0.6596 (tt0) cc_final: 0.6352 (tt0) REVERT: A 379 SER cc_start: 0.7939 (m) cc_final: 0.7623 (t) REVERT: A 428 ARG cc_start: 0.7764 (ttm-80) cc_final: 0.7461 (mtp-110) REVERT: A 432 ARG cc_start: 0.7987 (mtt90) cc_final: 0.7658 (mmt90) REVERT: A 471 ASP cc_start: 0.7322 (m-30) cc_final: 0.7028 (m-30) REVERT: A 472 TYR cc_start: 0.7732 (m-80) cc_final: 0.7524 (m-80) REVERT: A 627 TYR cc_start: 0.6531 (m-80) cc_final: 0.6127 (m-80) REVERT: A 636 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8448 (mm-30) REVERT: A 644 MET cc_start: 0.8896 (mmm) cc_final: 0.8554 (mmm) REVERT: A 653 TYR cc_start: 0.8691 (p90) cc_final: 0.8360 (p90) REVERT: A 682 MET cc_start: 0.7356 (mtp) cc_final: 0.6542 (mtm) REVERT: A 696 ILE cc_start: 0.8518 (tt) cc_final: 0.8102 (mm) REVERT: C 352 ILE cc_start: 0.8696 (mt) cc_final: 0.8488 (mt) REVERT: C 358 HIS cc_start: 0.6356 (p90) cc_final: 0.5516 (t-90) REVERT: C 379 SER cc_start: 0.7946 (m) cc_final: 0.7716 (t) REVERT: C 393 ASN cc_start: 0.8224 (m-40) cc_final: 0.7506 (m-40) REVERT: C 427 ASP cc_start: 0.8718 (m-30) cc_final: 0.8469 (m-30) REVERT: C 432 ARG cc_start: 0.8027 (mtt90) cc_final: 0.7568 (mmt90) REVERT: C 438 PHE cc_start: 0.9161 (t80) cc_final: 0.8932 (t80) REVERT: C 471 ASP cc_start: 0.7423 (m-30) cc_final: 0.7179 (m-30) REVERT: C 561 GLN cc_start: 0.7383 (mt0) cc_final: 0.6802 (tt0) REVERT: C 571 LYS cc_start: 0.8312 (mtpp) cc_final: 0.8071 (mtpp) REVERT: C 639 LYS cc_start: 0.8509 (mttt) cc_final: 0.8300 (mttm) REVERT: C 644 MET cc_start: 0.8944 (mmm) cc_final: 0.8468 (mmm) REVERT: C 653 TYR cc_start: 0.8697 (p90) cc_final: 0.8353 (p90) REVERT: C 656 LYS cc_start: 0.8730 (tttt) cc_final: 0.8486 (ttpp) REVERT: C 697 TRP cc_start: 0.8272 (t60) cc_final: 0.8071 (t60) REVERT: D 308 MET cc_start: 0.7912 (mmm) cc_final: 0.7484 (mmm) REVERT: D 313 LEU cc_start: 0.8913 (mt) cc_final: 0.8490 (mt) REVERT: D 388 ASP cc_start: 0.6728 (p0) cc_final: 0.6494 (p0) REVERT: D 411 ASP cc_start: 0.8267 (m-30) cc_final: 0.7545 (m-30) REVERT: D 432 ARG cc_start: 0.8035 (mtt90) cc_final: 0.7612 (mmt180) REVERT: D 561 GLN cc_start: 0.7320 (mt0) cc_final: 0.6971 (tt0) REVERT: D 644 MET cc_start: 0.8982 (mmm) cc_final: 0.8580 (mmm) REVERT: D 696 ILE cc_start: 0.8586 (tt) cc_final: 0.8213 (mm) REVERT: D 697 TRP cc_start: 0.7898 (t60) cc_final: 0.7686 (t60) REVERT: D 698 LYS cc_start: 0.8832 (mttm) cc_final: 0.8595 (mttp) REVERT: B 288 LEU cc_start: 0.8975 (mt) cc_final: 0.8644 (mt) REVERT: B 308 MET cc_start: 0.8277 (mmm) cc_final: 0.7744 (mmm) REVERT: B 313 LEU cc_start: 0.9036 (tp) cc_final: 0.8828 (tp) REVERT: B 324 LYS cc_start: 0.7974 (mttt) cc_final: 0.7554 (ptpp) REVERT: B 363 ARG cc_start: 0.7245 (ttt90) cc_final: 0.6668 (mtt90) REVERT: B 379 SER cc_start: 0.7901 (m) cc_final: 0.7596 (t) REVERT: B 381 LEU cc_start: 0.7344 (mp) cc_final: 0.7097 (mp) REVERT: B 408 ASN cc_start: 0.7853 (m-40) cc_final: 0.7603 (t0) REVERT: B 420 ARG cc_start: 0.8385 (tpp80) cc_final: 0.8051 (tpp80) REVERT: B 432 ARG cc_start: 0.8051 (mtt90) cc_final: 0.7587 (mmt180) REVERT: B 471 ASP cc_start: 0.7664 (m-30) cc_final: 0.7447 (m-30) REVERT: B 589 PHE cc_start: 0.8687 (t80) cc_final: 0.8474 (t80) REVERT: B 627 TYR cc_start: 0.6636 (m-80) cc_final: 0.6081 (m-80) REVERT: B 644 MET cc_start: 0.8858 (mmm) cc_final: 0.8437 (mmm) REVERT: B 695 ASN cc_start: 0.7699 (m-40) cc_final: 0.7159 (m-40) outliers start: 4 outliers final: 4 residues processed: 754 average time/residue: 0.2878 time to fit residues: 304.9539 Evaluate side-chains 572 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 568 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 137 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN A 393 ASN A 687 ASN C 354 GLN C 652 ASN D 354 GLN D 393 ASN B 354 GLN B 393 ASN B 687 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15092 Z= 0.209 Angle : 0.561 12.352 20460 Z= 0.291 Chirality : 0.038 0.162 2304 Planarity : 0.003 0.024 2500 Dihedral : 7.572 59.955 2352 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.56 % Allowed : 12.12 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.20), residues: 1764 helix: 1.33 (0.15), residues: 1152 sheet: -2.50 (0.54), residues: 72 loop : -1.92 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 697 HIS 0.008 0.001 HIS C 289 PHE 0.021 0.001 PHE A 304 TYR 0.017 0.001 TYR C 463 ARG 0.008 0.000 ARG D 721 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 618 time to evaluate : 1.821 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: A 308 MET cc_start: 0.7909 (mmm) cc_final: 0.7399 (mmm) REVERT: A 313 LEU cc_start: 0.8982 (mt) cc_final: 0.8686 (mt) REVERT: A 356 GLU cc_start: 0.6549 (tt0) cc_final: 0.6278 (tt0) REVERT: A 379 SER cc_start: 0.7825 (m) cc_final: 0.7566 (t) REVERT: A 425 LYS cc_start: 0.7984 (tptt) cc_final: 0.7682 (tptt) REVERT: A 427 ASP cc_start: 0.8504 (m-30) cc_final: 0.8303 (m-30) REVERT: A 432 ARG cc_start: 0.8012 (mtt90) cc_final: 0.7635 (mmt90) REVERT: A 472 TYR cc_start: 0.7903 (m-80) cc_final: 0.7499 (m-80) REVERT: A 560 GLN cc_start: 0.8440 (tt0) cc_final: 0.8198 (tp40) REVERT: A 564 ILE cc_start: 0.9065 (tp) cc_final: 0.8792 (tp) REVERT: A 571 LYS cc_start: 0.8384 (mttt) cc_final: 0.8084 (mmtt) REVERT: A 627 TYR cc_start: 0.6574 (m-80) cc_final: 0.6188 (m-80) REVERT: A 636 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8405 (mm-30) REVERT: A 644 MET cc_start: 0.8952 (mmm) cc_final: 0.8632 (mmm) REVERT: A 652 ASN cc_start: 0.8436 (p0) cc_final: 0.8225 (p0) REVERT: A 653 TYR cc_start: 0.8593 (p90) cc_final: 0.8157 (p90) REVERT: A 688 LYS cc_start: 0.8388 (mtpt) cc_final: 0.7920 (tptt) REVERT: A 696 ILE cc_start: 0.8372 (tt) cc_final: 0.8140 (mm) REVERT: A 746 GLU cc_start: 0.6033 (tt0) cc_final: 0.5762 (tt0) REVERT: C 293 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7408 (mt-10) REVERT: C 358 HIS cc_start: 0.6436 (p90) cc_final: 0.5697 (t-90) REVERT: C 379 SER cc_start: 0.7895 (m) cc_final: 0.7459 (t) REVERT: C 393 ASN cc_start: 0.8166 (m-40) cc_final: 0.7661 (m-40) REVERT: C 420 ARG cc_start: 0.8148 (tpp80) cc_final: 0.7405 (tpp80) REVERT: C 427 ASP cc_start: 0.8642 (m-30) cc_final: 0.8438 (m-30) REVERT: C 432 ARG cc_start: 0.8005 (mtt90) cc_final: 0.7661 (mmt180) REVERT: C 438 PHE cc_start: 0.9149 (t80) cc_final: 0.8939 (t80) REVERT: C 560 GLN cc_start: 0.8164 (tt0) cc_final: 0.7401 (tp40) REVERT: C 564 ILE cc_start: 0.8688 (tt) cc_final: 0.8389 (tp) REVERT: C 571 LYS cc_start: 0.8305 (mtpp) cc_final: 0.8020 (mtpp) REVERT: C 627 TYR cc_start: 0.6501 (m-80) cc_final: 0.6052 (m-80) REVERT: C 653 TYR cc_start: 0.8668 (p90) cc_final: 0.8281 (p90) REVERT: C 697 TRP cc_start: 0.8273 (t60) cc_final: 0.8072 (t60) REVERT: C 743 ARG cc_start: 0.7853 (ttm110) cc_final: 0.7332 (ttm170) REVERT: D 308 MET cc_start: 0.7937 (mmm) cc_final: 0.7428 (mmm) REVERT: D 313 LEU cc_start: 0.8903 (mt) cc_final: 0.8485 (mt) REVERT: D 397 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7383 (tt0) REVERT: D 409 ARG cc_start: 0.7592 (ptt-90) cc_final: 0.7192 (ptp90) REVERT: D 420 ARG cc_start: 0.8259 (tpp80) cc_final: 0.7606 (tpp80) REVERT: D 432 ARG cc_start: 0.8018 (mtt90) cc_final: 0.7569 (mmt90) REVERT: D 465 LEU cc_start: 0.8125 (tp) cc_final: 0.7856 (tp) REVERT: D 560 GLN cc_start: 0.8139 (tt0) cc_final: 0.7833 (tp40) REVERT: D 561 GLN cc_start: 0.7337 (mt0) cc_final: 0.6956 (tt0) REVERT: D 571 LYS cc_start: 0.8665 (mttt) cc_final: 0.8331 (mmtt) REVERT: D 572 MET cc_start: 0.7074 (mtt) cc_final: 0.6164 (mtt) REVERT: D 684 GLU cc_start: 0.7389 (tm-30) cc_final: 0.7063 (tm-30) REVERT: D 696 ILE cc_start: 0.8389 (tt) cc_final: 0.8005 (mm) REVERT: B 288 LEU cc_start: 0.8987 (mt) cc_final: 0.8770 (mt) REVERT: B 308 MET cc_start: 0.8267 (mmm) cc_final: 0.7725 (mmm) REVERT: B 379 SER cc_start: 0.7763 (m) cc_final: 0.7403 (t) REVERT: B 420 ARG cc_start: 0.8518 (tpp80) cc_final: 0.8112 (tpp80) REVERT: B 432 ARG cc_start: 0.8027 (mtt90) cc_final: 0.7568 (mmt180) REVERT: B 471 ASP cc_start: 0.7609 (m-30) cc_final: 0.7396 (m-30) REVERT: B 472 TYR cc_start: 0.7482 (m-80) cc_final: 0.7280 (m-80) REVERT: B 589 PHE cc_start: 0.8624 (t80) cc_final: 0.8411 (t80) REVERT: B 627 TYR cc_start: 0.6630 (m-80) cc_final: 0.6182 (m-80) REVERT: B 644 MET cc_start: 0.8910 (mmm) cc_final: 0.8564 (mmm) REVERT: B 695 ASN cc_start: 0.7745 (m-40) cc_final: 0.7047 (t0) outliers start: 57 outliers final: 39 residues processed: 641 average time/residue: 0.2997 time to fit residues: 275.7900 Evaluate side-chains 600 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 561 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain D residue 695 ASN Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 133 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 160 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 158 optimal weight: 0.6980 chunk 54 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 GLN D 354 GLN D 687 ASN B 354 GLN B 378 HIS B 393 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15092 Z= 0.323 Angle : 0.592 9.226 20460 Z= 0.307 Chirality : 0.040 0.188 2304 Planarity : 0.004 0.039 2500 Dihedral : 7.501 59.983 2352 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.75 % Allowed : 15.62 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.20), residues: 1764 helix: 1.19 (0.15), residues: 1156 sheet: -2.59 (0.52), residues: 72 loop : -1.92 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 740 HIS 0.004 0.001 HIS D 410 PHE 0.026 0.002 PHE C 429 TYR 0.012 0.001 TYR C 463 ARG 0.006 0.001 ARG D 721 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 573 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.7954 (mmm) cc_final: 0.7699 (mmt) REVERT: A 313 LEU cc_start: 0.9013 (mt) cc_final: 0.8644 (mt) REVERT: A 326 GLU cc_start: 0.9008 (mp0) cc_final: 0.8758 (mp0) REVERT: A 356 GLU cc_start: 0.6643 (tt0) cc_final: 0.6342 (tt0) REVERT: A 379 SER cc_start: 0.7802 (m) cc_final: 0.7527 (t) REVERT: A 432 ARG cc_start: 0.8000 (mtt90) cc_final: 0.7669 (mmt90) REVERT: A 472 TYR cc_start: 0.7914 (m-80) cc_final: 0.7476 (m-80) REVERT: A 560 GLN cc_start: 0.8499 (tt0) cc_final: 0.8233 (tp40) REVERT: A 571 LYS cc_start: 0.8479 (mttt) cc_final: 0.8235 (mmtt) REVERT: A 572 MET cc_start: 0.7542 (ttm) cc_final: 0.6800 (ttm) REVERT: A 627 TYR cc_start: 0.6740 (m-80) cc_final: 0.6301 (m-80) REVERT: A 636 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8475 (mm-30) REVERT: A 653 TYR cc_start: 0.8578 (p90) cc_final: 0.8164 (p90) REVERT: A 673 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8073 (tp) REVERT: A 696 ILE cc_start: 0.8486 (tt) cc_final: 0.8265 (mm) REVERT: C 293 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7426 (mt-10) REVERT: C 379 SER cc_start: 0.7908 (m) cc_final: 0.7490 (t) REVERT: C 384 LEU cc_start: 0.8305 (mt) cc_final: 0.8094 (mt) REVERT: C 393 ASN cc_start: 0.8485 (m-40) cc_final: 0.8020 (m-40) REVERT: C 420 ARG cc_start: 0.8147 (tpp80) cc_final: 0.7460 (tpp80) REVERT: C 432 ARG cc_start: 0.8072 (mtt90) cc_final: 0.7691 (mmt180) REVERT: C 438 PHE cc_start: 0.9181 (t80) cc_final: 0.8934 (t80) REVERT: C 471 ASP cc_start: 0.7695 (m-30) cc_final: 0.7494 (t0) REVERT: C 560 GLN cc_start: 0.8227 (tt0) cc_final: 0.7892 (tt0) REVERT: C 571 LYS cc_start: 0.8364 (mtpp) cc_final: 0.8081 (mtpp) REVERT: C 627 TYR cc_start: 0.6773 (m-80) cc_final: 0.6289 (m-80) REVERT: C 653 TYR cc_start: 0.8586 (p90) cc_final: 0.8269 (p90) REVERT: C 743 ARG cc_start: 0.7768 (ttm110) cc_final: 0.7248 (ttm170) REVERT: D 308 MET cc_start: 0.7919 (mmm) cc_final: 0.7342 (mmm) REVERT: D 397 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7431 (tt0) REVERT: D 420 ARG cc_start: 0.8275 (tpp80) cc_final: 0.7680 (tpp80) REVERT: D 422 LEU cc_start: 0.8828 (mt) cc_final: 0.8542 (mt) REVERT: D 432 ARG cc_start: 0.8109 (mtt90) cc_final: 0.7629 (mmt90) REVERT: D 471 ASP cc_start: 0.8086 (t0) cc_final: 0.7463 (t0) REVERT: D 560 GLN cc_start: 0.8205 (tt0) cc_final: 0.7946 (tp40) REVERT: D 561 GLN cc_start: 0.7553 (mt0) cc_final: 0.6810 (tt0) REVERT: D 677 MET cc_start: 0.8402 (tpp) cc_final: 0.7957 (tpp) REVERT: D 684 GLU cc_start: 0.7367 (tm-30) cc_final: 0.6981 (tm-30) REVERT: D 698 LYS cc_start: 0.9088 (mmmt) cc_final: 0.8773 (mmtt) REVERT: B 288 LEU cc_start: 0.9086 (mt) cc_final: 0.8787 (mt) REVERT: B 293 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7512 (mt-10) REVERT: B 308 MET cc_start: 0.8314 (mmm) cc_final: 0.8095 (tpp) REVERT: B 324 LYS cc_start: 0.8077 (mttt) cc_final: 0.7876 (mmpt) REVERT: B 363 ARG cc_start: 0.7261 (ttt90) cc_final: 0.6668 (mtt90) REVERT: B 379 SER cc_start: 0.8044 (m) cc_final: 0.7693 (t) REVERT: B 397 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7628 (tt0) REVERT: B 420 ARG cc_start: 0.8512 (tpp80) cc_final: 0.8052 (tpp80) REVERT: B 432 ARG cc_start: 0.8056 (mtt90) cc_final: 0.7610 (mmt180) REVERT: B 472 TYR cc_start: 0.7461 (m-80) cc_final: 0.7182 (m-80) REVERT: B 560 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7420 (tp40) REVERT: B 627 TYR cc_start: 0.6846 (m-80) cc_final: 0.6316 (m-80) REVERT: B 695 ASN cc_start: 0.7656 (m-40) cc_final: 0.7079 (t0) REVERT: B 743 ARG cc_start: 0.8020 (ttm110) cc_final: 0.7345 (ttm170) outliers start: 60 outliers final: 42 residues processed: 596 average time/residue: 0.2707 time to fit residues: 232.7810 Evaluate side-chains 596 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 552 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 504 LYS Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 560 GLN Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 17 optimal weight: 0.0670 chunk 76 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 160 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN C 687 ASN D 354 GLN D 393 ASN B 393 ASN B 628 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15092 Z= 0.190 Angle : 0.544 8.091 20460 Z= 0.282 Chirality : 0.037 0.147 2304 Planarity : 0.003 0.024 2500 Dihedral : 7.388 59.740 2352 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.19 % Allowed : 17.12 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.13 (0.20), residues: 1764 helix: 1.24 (0.15), residues: 1144 sheet: -2.58 (0.51), residues: 72 loop : -2.04 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 697 HIS 0.003 0.001 HIS D 410 PHE 0.030 0.001 PHE D 429 TYR 0.011 0.001 TYR C 463 ARG 0.004 0.000 ARG D 721 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 596 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.7915 (mmm) cc_final: 0.7351 (mmm) REVERT: A 313 LEU cc_start: 0.8990 (mt) cc_final: 0.8628 (mt) REVERT: A 356 GLU cc_start: 0.6570 (tt0) cc_final: 0.6249 (tt0) REVERT: A 379 SER cc_start: 0.7833 (m) cc_final: 0.7559 (t) REVERT: A 397 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7350 (tt0) REVERT: A 432 ARG cc_start: 0.7997 (mtt90) cc_final: 0.7571 (mmt90) REVERT: A 472 TYR cc_start: 0.7918 (m-80) cc_final: 0.7493 (m-80) REVERT: A 560 GLN cc_start: 0.8508 (tt0) cc_final: 0.8283 (tp40) REVERT: A 564 ILE cc_start: 0.8951 (tp) cc_final: 0.8565 (tp) REVERT: A 571 LYS cc_start: 0.8447 (mttt) cc_final: 0.8195 (mmtt) REVERT: A 572 MET cc_start: 0.7523 (ttm) cc_final: 0.6795 (ttm) REVERT: A 627 TYR cc_start: 0.6744 (m-80) cc_final: 0.6280 (m-80) REVERT: A 636 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8432 (mm-30) REVERT: A 677 MET cc_start: 0.8246 (tpp) cc_final: 0.8042 (tpp) REVERT: A 696 ILE cc_start: 0.8449 (tt) cc_final: 0.8182 (mm) REVERT: C 293 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7374 (mt-10) REVERT: C 379 SER cc_start: 0.7909 (m) cc_final: 0.7533 (t) REVERT: C 420 ARG cc_start: 0.8162 (tpp80) cc_final: 0.7500 (tpp80) REVERT: C 432 ARG cc_start: 0.8005 (mtt90) cc_final: 0.7671 (mmt180) REVERT: C 438 PHE cc_start: 0.9161 (t80) cc_final: 0.8946 (t80) REVERT: C 471 ASP cc_start: 0.7697 (m-30) cc_final: 0.7436 (t0) REVERT: C 571 LYS cc_start: 0.8251 (mtpp) cc_final: 0.7976 (mtpp) REVERT: C 627 TYR cc_start: 0.6764 (m-80) cc_final: 0.6296 (m-80) REVERT: C 677 MET cc_start: 0.8118 (tpp) cc_final: 0.7795 (tpp) REVERT: C 743 ARG cc_start: 0.7792 (ttm110) cc_final: 0.7231 (ttm170) REVERT: D 308 MET cc_start: 0.7873 (mmm) cc_final: 0.7305 (mmm) REVERT: D 397 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7401 (tt0) REVERT: D 409 ARG cc_start: 0.7950 (ptm160) cc_final: 0.7527 (ttp-170) REVERT: D 420 ARG cc_start: 0.8230 (tpp80) cc_final: 0.7681 (tpp80) REVERT: D 432 ARG cc_start: 0.8107 (mtt90) cc_final: 0.7658 (mmt90) REVERT: D 471 ASP cc_start: 0.8094 (t0) cc_final: 0.7477 (t0) REVERT: D 561 GLN cc_start: 0.7494 (mt0) cc_final: 0.6818 (tt0) REVERT: D 684 GLU cc_start: 0.7303 (tm-30) cc_final: 0.6902 (tm-30) REVERT: D 698 LYS cc_start: 0.9043 (mmmt) cc_final: 0.8773 (mttp) REVERT: B 288 LEU cc_start: 0.9045 (mt) cc_final: 0.8758 (mt) REVERT: B 293 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7474 (mt-10) REVERT: B 308 MET cc_start: 0.8158 (mmm) cc_final: 0.7637 (mmm) REVERT: B 379 SER cc_start: 0.8090 (m) cc_final: 0.7773 (t) REVERT: B 397 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7495 (tt0) REVERT: B 420 ARG cc_start: 0.8480 (tpp80) cc_final: 0.8008 (tpp80) REVERT: B 432 ARG cc_start: 0.8027 (mtt90) cc_final: 0.7546 (mmt90) REVERT: B 472 TYR cc_start: 0.7555 (m-80) cc_final: 0.7257 (m-80) REVERT: B 627 TYR cc_start: 0.6862 (m-80) cc_final: 0.6280 (m-80) REVERT: B 695 ASN cc_start: 0.7615 (m-40) cc_final: 0.6972 (t0) REVERT: B 697 TRP cc_start: 0.8370 (t60) cc_final: 0.8115 (t60) REVERT: B 709 GLU cc_start: 0.8087 (tt0) cc_final: 0.7862 (tt0) outliers start: 67 outliers final: 46 residues processed: 622 average time/residue: 0.2678 time to fit residues: 240.2040 Evaluate side-chains 604 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 558 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 504 LYS Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 152 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN C 393 ASN D 354 GLN D 393 ASN B 354 GLN B 393 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15092 Z= 0.223 Angle : 0.548 7.989 20460 Z= 0.286 Chirality : 0.038 0.154 2304 Planarity : 0.003 0.024 2500 Dihedral : 7.313 59.629 2352 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.31 % Allowed : 19.12 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.09 (0.19), residues: 1764 helix: 1.21 (0.15), residues: 1144 sheet: -2.61 (0.52), residues: 72 loop : -2.05 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 740 HIS 0.002 0.001 HIS A 289 PHE 0.024 0.001 PHE D 304 TYR 0.011 0.001 TYR D 351 ARG 0.005 0.000 ARG D 721 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 568 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.7935 (mmm) cc_final: 0.7372 (mmm) REVERT: A 313 LEU cc_start: 0.8989 (mt) cc_final: 0.8629 (mt) REVERT: A 356 GLU cc_start: 0.6624 (tt0) cc_final: 0.6335 (tt0) REVERT: A 379 SER cc_start: 0.7818 (m) cc_final: 0.7547 (t) REVERT: A 397 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7364 (tt0) REVERT: A 432 ARG cc_start: 0.7987 (mtt90) cc_final: 0.7591 (mmt90) REVERT: A 472 TYR cc_start: 0.8009 (m-80) cc_final: 0.7575 (m-80) REVERT: A 560 GLN cc_start: 0.8519 (tt0) cc_final: 0.8290 (tp40) REVERT: A 571 LYS cc_start: 0.8427 (mttt) cc_final: 0.8196 (mmtt) REVERT: A 627 TYR cc_start: 0.6826 (m-80) cc_final: 0.6343 (m-80) REVERT: A 636 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8438 (mm-30) REVERT: A 695 ASN cc_start: 0.7483 (m-40) cc_final: 0.6902 (t0) REVERT: A 698 LYS cc_start: 0.9134 (mmmt) cc_final: 0.8868 (mmmt) REVERT: C 293 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7418 (mt-10) REVERT: C 356 GLU cc_start: 0.6703 (tt0) cc_final: 0.6497 (mm-30) REVERT: C 372 TRP cc_start: 0.6272 (m-10) cc_final: 0.6071 (m100) REVERT: C 379 SER cc_start: 0.7855 (m) cc_final: 0.7456 (t) REVERT: C 393 ASN cc_start: 0.8410 (m110) cc_final: 0.8000 (m-40) REVERT: C 420 ARG cc_start: 0.8231 (tpp80) cc_final: 0.7596 (tpp80) REVERT: C 432 ARG cc_start: 0.8037 (mtt90) cc_final: 0.7551 (mmt90) REVERT: C 438 PHE cc_start: 0.9166 (t80) cc_final: 0.8948 (t80) REVERT: C 471 ASP cc_start: 0.7759 (m-30) cc_final: 0.7546 (t0) REVERT: C 571 LYS cc_start: 0.8226 (mtpp) cc_final: 0.7989 (mtpp) REVERT: C 627 TYR cc_start: 0.6790 (m-80) cc_final: 0.6323 (m-80) REVERT: C 743 ARG cc_start: 0.7775 (ttm110) cc_final: 0.7204 (ttm170) REVERT: D 308 MET cc_start: 0.7878 (mmm) cc_final: 0.7313 (mmm) REVERT: D 397 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7404 (tt0) REVERT: D 409 ARG cc_start: 0.7901 (ptm160) cc_final: 0.7532 (ttp-170) REVERT: D 420 ARG cc_start: 0.8225 (tpp80) cc_final: 0.7695 (tpp80) REVERT: D 432 ARG cc_start: 0.8138 (mtt90) cc_final: 0.7720 (mmt180) REVERT: D 471 ASP cc_start: 0.8160 (t0) cc_final: 0.7526 (t0) REVERT: D 636 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8424 (tp30) REVERT: D 682 MET cc_start: 0.6149 (mtm) cc_final: 0.5366 (mtm) REVERT: D 684 GLU cc_start: 0.7255 (tm-30) cc_final: 0.6970 (tm-30) REVERT: D 698 LYS cc_start: 0.9069 (mmmt) cc_final: 0.8776 (mttp) REVERT: D 746 GLU cc_start: 0.5122 (tt0) cc_final: 0.4629 (tt0) REVERT: B 288 LEU cc_start: 0.9069 (mt) cc_final: 0.8795 (mt) REVERT: B 293 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7467 (mt-10) REVERT: B 308 MET cc_start: 0.8197 (mmm) cc_final: 0.7942 (mmt) REVERT: B 379 SER cc_start: 0.8063 (m) cc_final: 0.7714 (t) REVERT: B 397 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7467 (tt0) REVERT: B 420 ARG cc_start: 0.8490 (tpp80) cc_final: 0.8038 (tpp80) REVERT: B 432 ARG cc_start: 0.8049 (mtt90) cc_final: 0.7564 (mmt90) REVERT: B 471 ASP cc_start: 0.8151 (t0) cc_final: 0.7558 (t0) REVERT: B 472 TYR cc_start: 0.7557 (m-80) cc_final: 0.7268 (m-80) REVERT: B 627 TYR cc_start: 0.6900 (m-80) cc_final: 0.6316 (m-80) REVERT: B 644 MET cc_start: 0.8925 (mmm) cc_final: 0.7946 (mmm) REVERT: B 695 ASN cc_start: 0.7521 (m-40) cc_final: 0.6939 (t0) REVERT: B 697 TRP cc_start: 0.8570 (t60) cc_final: 0.8261 (t60) REVERT: B 709 GLU cc_start: 0.8075 (tt0) cc_final: 0.7821 (tt0) REVERT: B 743 ARG cc_start: 0.8076 (ttm110) cc_final: 0.7410 (ttm170) outliers start: 69 outliers final: 58 residues processed: 599 average time/residue: 0.2690 time to fit residues: 232.7324 Evaluate side-chains 601 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 543 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 504 LYS Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 656 LYS Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 99 optimal weight: 0.3980 chunk 41 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 141 optimal weight: 0.0050 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN A 561 GLN D 354 GLN B 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15092 Z= 0.205 Angle : 0.550 6.675 20460 Z= 0.286 Chirality : 0.038 0.204 2304 Planarity : 0.003 0.024 2500 Dihedral : 7.274 59.868 2352 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.25 % Allowed : 18.69 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.12 (0.20), residues: 1764 helix: 1.23 (0.15), residues: 1144 sheet: -2.56 (0.52), residues: 72 loop : -2.04 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 697 HIS 0.002 0.001 HIS A 289 PHE 0.024 0.001 PHE D 304 TYR 0.009 0.001 TYR C 463 ARG 0.004 0.000 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 567 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.7966 (mmm) cc_final: 0.7406 (mmm) REVERT: A 313 LEU cc_start: 0.8976 (mt) cc_final: 0.8623 (mt) REVERT: A 356 GLU cc_start: 0.6631 (tt0) cc_final: 0.6364 (tt0) REVERT: A 379 SER cc_start: 0.7812 (m) cc_final: 0.7532 (t) REVERT: A 397 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7370 (tt0) REVERT: A 432 ARG cc_start: 0.8004 (mtt90) cc_final: 0.7609 (mmt90) REVERT: A 472 TYR cc_start: 0.8084 (m-80) cc_final: 0.7578 (m-80) REVERT: A 560 GLN cc_start: 0.8555 (tt0) cc_final: 0.8322 (tp40) REVERT: A 571 LYS cc_start: 0.8405 (mttt) cc_final: 0.8137 (mmtt) REVERT: A 627 TYR cc_start: 0.6837 (m-80) cc_final: 0.6317 (m-80) REVERT: A 695 ASN cc_start: 0.7475 (m-40) cc_final: 0.6886 (t0) REVERT: A 696 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8152 (mm) REVERT: A 698 LYS cc_start: 0.9110 (mmmt) cc_final: 0.8865 (mmmt) REVERT: C 293 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7428 (mt-10) REVERT: C 356 GLU cc_start: 0.6674 (tt0) cc_final: 0.6472 (mm-30) REVERT: C 379 SER cc_start: 0.7831 (m) cc_final: 0.7426 (t) REVERT: C 393 ASN cc_start: 0.8253 (m110) cc_final: 0.7917 (m-40) REVERT: C 420 ARG cc_start: 0.8246 (tpp80) cc_final: 0.7630 (tpp80) REVERT: C 432 ARG cc_start: 0.8040 (mtt90) cc_final: 0.7550 (mmt90) REVERT: C 438 PHE cc_start: 0.9178 (t80) cc_final: 0.8969 (t80) REVERT: C 571 LYS cc_start: 0.8199 (mtpp) cc_final: 0.7954 (mtpp) REVERT: C 627 TYR cc_start: 0.6851 (m-80) cc_final: 0.6394 (m-80) REVERT: C 743 ARG cc_start: 0.7750 (ttm110) cc_final: 0.7221 (ttm170) REVERT: D 308 MET cc_start: 0.7885 (mmm) cc_final: 0.7599 (mmt) REVERT: D 356 GLU cc_start: 0.6949 (tt0) cc_final: 0.6715 (tp30) REVERT: D 397 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7291 (tt0) REVERT: D 409 ARG cc_start: 0.7883 (ptm160) cc_final: 0.7526 (ttp-170) REVERT: D 420 ARG cc_start: 0.8221 (tpp80) cc_final: 0.7682 (tpp80) REVERT: D 432 ARG cc_start: 0.8147 (mtt90) cc_final: 0.7723 (mmt180) REVERT: D 471 ASP cc_start: 0.8161 (t0) cc_final: 0.7544 (t0) REVERT: D 636 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8427 (tp30) REVERT: D 644 MET cc_start: 0.8988 (mmm) cc_final: 0.7944 (mmm) REVERT: D 684 GLU cc_start: 0.7269 (tm-30) cc_final: 0.7032 (tm-30) REVERT: D 698 LYS cc_start: 0.9053 (mmmt) cc_final: 0.8803 (mttp) REVERT: D 746 GLU cc_start: 0.5090 (tt0) cc_final: 0.4594 (tt0) REVERT: B 288 LEU cc_start: 0.9079 (mt) cc_final: 0.8788 (mt) REVERT: B 293 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7450 (mt-10) REVERT: B 308 MET cc_start: 0.8179 (mmm) cc_final: 0.7643 (mmm) REVERT: B 324 LYS cc_start: 0.7656 (mmpt) cc_final: 0.7172 (mtpt) REVERT: B 379 SER cc_start: 0.7812 (m) cc_final: 0.7439 (t) REVERT: B 397 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7470 (tt0) REVERT: B 420 ARG cc_start: 0.8459 (tpp80) cc_final: 0.8021 (tpp80) REVERT: B 432 ARG cc_start: 0.8071 (mtt90) cc_final: 0.7602 (mmt90) REVERT: B 471 ASP cc_start: 0.8168 (t0) cc_final: 0.7596 (t0) REVERT: B 472 TYR cc_start: 0.7539 (m-80) cc_final: 0.7239 (m-80) REVERT: B 627 TYR cc_start: 0.6921 (m-80) cc_final: 0.6334 (m-80) REVERT: B 673 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8225 (tt) REVERT: B 682 MET cc_start: 0.7356 (mtp) cc_final: 0.7061 (mtm) REVERT: B 695 ASN cc_start: 0.7503 (m-40) cc_final: 0.6874 (t0) REVERT: B 709 GLU cc_start: 0.8073 (tt0) cc_final: 0.7805 (tt0) REVERT: B 743 ARG cc_start: 0.8033 (ttm110) cc_final: 0.7369 (ttm170) outliers start: 68 outliers final: 52 residues processed: 595 average time/residue: 0.2644 time to fit residues: 227.5403 Evaluate side-chains 600 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 546 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 504 LYS Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 143 optimal weight: 0.0470 chunk 95 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS A 393 ASN D 354 GLN D 393 ASN B 354 GLN B 393 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 15092 Z= 0.203 Angle : 0.549 8.672 20460 Z= 0.286 Chirality : 0.038 0.254 2304 Planarity : 0.003 0.026 2500 Dihedral : 7.237 59.038 2352 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 4.12 % Allowed : 19.44 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.10 (0.20), residues: 1764 helix: 1.21 (0.15), residues: 1144 sheet: -2.44 (0.54), residues: 72 loop : -2.06 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 697 HIS 0.002 0.000 HIS A 289 PHE 0.024 0.001 PHE D 304 TYR 0.009 0.001 TYR C 463 ARG 0.005 0.000 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 569 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.7970 (mmm) cc_final: 0.7411 (mmm) REVERT: A 313 LEU cc_start: 0.8968 (mt) cc_final: 0.8635 (mt) REVERT: A 356 GLU cc_start: 0.6682 (tt0) cc_final: 0.6425 (tt0) REVERT: A 379 SER cc_start: 0.7727 (m) cc_final: 0.7446 (t) REVERT: A 397 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7371 (tt0) REVERT: A 432 ARG cc_start: 0.8011 (mtt90) cc_final: 0.7613 (mmt90) REVERT: A 465 LEU cc_start: 0.8206 (tp) cc_final: 0.7993 (tp) REVERT: A 472 TYR cc_start: 0.8128 (m-80) cc_final: 0.7618 (m-80) REVERT: A 561 GLN cc_start: 0.7328 (pt0) cc_final: 0.6674 (pm20) REVERT: A 571 LYS cc_start: 0.8348 (mttt) cc_final: 0.8121 (mmtt) REVERT: A 627 TYR cc_start: 0.6816 (m-80) cc_final: 0.6330 (m-80) REVERT: A 695 ASN cc_start: 0.7433 (m-40) cc_final: 0.6846 (t0) REVERT: A 696 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8170 (mm) REVERT: A 698 LYS cc_start: 0.9092 (mmmt) cc_final: 0.8861 (mmmt) REVERT: C 293 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7429 (mt-10) REVERT: C 356 GLU cc_start: 0.6667 (tt0) cc_final: 0.6465 (mm-30) REVERT: C 379 SER cc_start: 0.7768 (m) cc_final: 0.7404 (t) REVERT: C 393 ASN cc_start: 0.8268 (m110) cc_final: 0.7892 (m-40) REVERT: C 409 ARG cc_start: 0.8299 (ttp-170) cc_final: 0.8028 (ttp-170) REVERT: C 410 HIS cc_start: 0.7029 (OUTLIER) cc_final: 0.6806 (p90) REVERT: C 420 ARG cc_start: 0.8191 (tpp80) cc_final: 0.7525 (tpp80) REVERT: C 432 ARG cc_start: 0.8040 (mtt90) cc_final: 0.7544 (mmt90) REVERT: C 438 PHE cc_start: 0.9179 (t80) cc_final: 0.8978 (t80) REVERT: C 627 TYR cc_start: 0.6897 (m-80) cc_final: 0.6394 (m-80) REVERT: C 656 LYS cc_start: 0.8537 (tttt) cc_final: 0.8000 (ttpt) REVERT: C 743 ARG cc_start: 0.7773 (ttm110) cc_final: 0.7255 (ttm170) REVERT: D 308 MET cc_start: 0.7917 (mmm) cc_final: 0.7639 (mmt) REVERT: D 397 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7297 (tt0) REVERT: D 409 ARG cc_start: 0.7901 (ptm160) cc_final: 0.7609 (ttp-170) REVERT: D 420 ARG cc_start: 0.8215 (tpp80) cc_final: 0.7687 (tpp80) REVERT: D 432 ARG cc_start: 0.8113 (mtt90) cc_final: 0.7709 (mmt180) REVERT: D 471 ASP cc_start: 0.8156 (t0) cc_final: 0.7564 (t0) REVERT: D 636 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8438 (tp30) REVERT: D 644 MET cc_start: 0.8986 (mmm) cc_final: 0.7954 (mmm) REVERT: D 698 LYS cc_start: 0.9023 (mmmt) cc_final: 0.8817 (mttp) REVERT: D 746 GLU cc_start: 0.5127 (tt0) cc_final: 0.4636 (tt0) REVERT: B 293 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7378 (mt-10) REVERT: B 308 MET cc_start: 0.8165 (mmm) cc_final: 0.7908 (mmt) REVERT: B 324 LYS cc_start: 0.7722 (mmpt) cc_final: 0.7171 (mtpt) REVERT: B 379 SER cc_start: 0.7755 (m) cc_final: 0.7381 (t) REVERT: B 397 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7474 (tt0) REVERT: B 420 ARG cc_start: 0.8449 (tpp80) cc_final: 0.8031 (tpp80) REVERT: B 432 ARG cc_start: 0.8092 (mtt90) cc_final: 0.7665 (mmt180) REVERT: B 471 ASP cc_start: 0.8177 (t0) cc_final: 0.7614 (t0) REVERT: B 472 TYR cc_start: 0.7559 (m-80) cc_final: 0.7254 (m-80) REVERT: B 627 TYR cc_start: 0.6961 (m-80) cc_final: 0.6354 (m-80) REVERT: B 695 ASN cc_start: 0.7459 (m-40) cc_final: 0.6795 (t0) REVERT: B 743 ARG cc_start: 0.8029 (ttm110) cc_final: 0.7376 (ttm170) outliers start: 66 outliers final: 57 residues processed: 598 average time/residue: 0.2773 time to fit residues: 240.6045 Evaluate side-chains 607 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 548 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 504 LYS Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 656 LYS Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 133 optimal weight: 0.4980 chunk 154 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN A 393 ASN D 354 GLN D 393 ASN B 393 ASN B 423 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15092 Z= 0.209 Angle : 0.581 14.847 20460 Z= 0.300 Chirality : 0.039 0.284 2304 Planarity : 0.003 0.026 2500 Dihedral : 7.233 59.440 2352 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.56 % Allowed : 19.06 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.06 (0.20), residues: 1764 helix: 1.19 (0.15), residues: 1140 sheet: -2.37 (0.54), residues: 72 loop : -2.09 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 697 HIS 0.002 0.001 HIS A 289 PHE 0.026 0.001 PHE D 304 TYR 0.011 0.001 TYR D 351 ARG 0.006 0.000 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 558 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: A 308 MET cc_start: 0.7974 (mmm) cc_final: 0.7419 (mmm) REVERT: A 313 LEU cc_start: 0.8959 (mt) cc_final: 0.8620 (mt) REVERT: A 356 GLU cc_start: 0.6705 (tt0) cc_final: 0.6457 (tt0) REVERT: A 379 SER cc_start: 0.7756 (m) cc_final: 0.7486 (t) REVERT: A 432 ARG cc_start: 0.8011 (mtt90) cc_final: 0.7606 (mmt90) REVERT: A 472 TYR cc_start: 0.8116 (m-80) cc_final: 0.7572 (m-80) REVERT: A 491 ARG cc_start: 0.5958 (mmm-85) cc_final: 0.5586 (mmm-85) REVERT: A 568 MET cc_start: 0.7945 (mtp) cc_final: 0.7692 (mtt) REVERT: A 627 TYR cc_start: 0.6867 (m-80) cc_final: 0.6353 (m-80) REVERT: A 695 ASN cc_start: 0.7367 (m-40) cc_final: 0.6570 (t0) REVERT: A 696 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8076 (mm) REVERT: C 293 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7430 (mt-10) REVERT: C 356 GLU cc_start: 0.6629 (tt0) cc_final: 0.6425 (mm-30) REVERT: C 379 SER cc_start: 0.7757 (m) cc_final: 0.7392 (t) REVERT: C 393 ASN cc_start: 0.8266 (m110) cc_final: 0.7617 (m-40) REVERT: C 410 HIS cc_start: 0.6976 (OUTLIER) cc_final: 0.6752 (p90) REVERT: C 420 ARG cc_start: 0.8182 (tpp80) cc_final: 0.7518 (tpp80) REVERT: C 432 ARG cc_start: 0.8048 (mtt90) cc_final: 0.7541 (mmt90) REVERT: C 471 ASP cc_start: 0.8393 (t0) cc_final: 0.8170 (t0) REVERT: C 627 TYR cc_start: 0.6897 (m-80) cc_final: 0.6383 (m-80) REVERT: C 743 ARG cc_start: 0.7753 (ttm110) cc_final: 0.7251 (ttm170) REVERT: D 308 MET cc_start: 0.7938 (mmm) cc_final: 0.7400 (mmm) REVERT: D 409 ARG cc_start: 0.7923 (ptm160) cc_final: 0.7635 (ttp-170) REVERT: D 420 ARG cc_start: 0.8229 (tpp80) cc_final: 0.7669 (tpp80) REVERT: D 432 ARG cc_start: 0.8117 (mtt90) cc_final: 0.7725 (mmt180) REVERT: D 471 ASP cc_start: 0.8208 (t0) cc_final: 0.7597 (t0) REVERT: D 570 GLU cc_start: 0.8667 (tt0) cc_final: 0.8460 (tt0) REVERT: D 698 LYS cc_start: 0.9022 (mmmt) cc_final: 0.8815 (mttp) REVERT: D 746 GLU cc_start: 0.5166 (tt0) cc_final: 0.4673 (tt0) REVERT: B 288 LEU cc_start: 0.9063 (mt) cc_final: 0.8803 (mt) REVERT: B 293 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7334 (mt-10) REVERT: B 308 MET cc_start: 0.8164 (mmm) cc_final: 0.7648 (mmm) REVERT: B 379 SER cc_start: 0.7747 (m) cc_final: 0.7377 (t) REVERT: B 397 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7506 (tt0) REVERT: B 420 ARG cc_start: 0.8409 (tpp80) cc_final: 0.8058 (tpp80) REVERT: B 432 ARG cc_start: 0.8095 (mtt90) cc_final: 0.7671 (mmt180) REVERT: B 471 ASP cc_start: 0.8064 (t0) cc_final: 0.7554 (t0) REVERT: B 472 TYR cc_start: 0.7547 (m-80) cc_final: 0.7261 (m-80) REVERT: B 627 TYR cc_start: 0.6881 (m-80) cc_final: 0.6299 (m-80) REVERT: B 695 ASN cc_start: 0.7389 (m-40) cc_final: 0.6761 (t0) REVERT: B 743 ARG cc_start: 0.7964 (ttm110) cc_final: 0.7321 (ttm170) outliers start: 73 outliers final: 63 residues processed: 590 average time/residue: 0.2731 time to fit residues: 233.4030 Evaluate side-chains 598 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 532 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 504 LYS Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 656 LYS Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 142 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN D 354 GLN D 393 ASN B 393 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15092 Z= 0.228 Angle : 0.589 15.135 20460 Z= 0.305 Chirality : 0.040 0.308 2304 Planarity : 0.003 0.052 2500 Dihedral : 7.237 59.929 2352 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.00 % Allowed : 20.06 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.09 (0.20), residues: 1764 helix: 1.16 (0.15), residues: 1140 sheet: -1.71 (0.55), residues: 68 loop : -2.07 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 697 HIS 0.003 0.001 HIS A 289 PHE 0.027 0.001 PHE C 304 TYR 0.012 0.001 TYR D 351 ARG 0.010 0.000 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 548 time to evaluate : 1.795 Fit side-chains revert: symmetry clash REVERT: A 293 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: A 308 MET cc_start: 0.7957 (mmm) cc_final: 0.7441 (mmm) REVERT: A 313 LEU cc_start: 0.8956 (mt) cc_final: 0.8612 (mt) REVERT: A 353 LEU cc_start: 0.9214 (mt) cc_final: 0.9010 (mt) REVERT: A 379 SER cc_start: 0.7772 (m) cc_final: 0.7483 (t) REVERT: A 432 ARG cc_start: 0.8021 (mtt90) cc_final: 0.7607 (mmt90) REVERT: A 472 TYR cc_start: 0.8200 (m-80) cc_final: 0.7587 (m-80) REVERT: A 491 ARG cc_start: 0.5905 (mmm-85) cc_final: 0.5507 (mmm-85) REVERT: A 550 THR cc_start: 0.9047 (m) cc_final: 0.8743 (p) REVERT: A 571 LYS cc_start: 0.8195 (mttt) cc_final: 0.7931 (mmtt) REVERT: A 627 TYR cc_start: 0.6933 (m-80) cc_final: 0.6383 (m-80) REVERT: A 696 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8093 (mm) REVERT: C 293 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7419 (mt-10) REVERT: C 356 GLU cc_start: 0.6678 (tt0) cc_final: 0.6460 (mm-30) REVERT: C 379 SER cc_start: 0.7757 (m) cc_final: 0.7391 (t) REVERT: C 393 ASN cc_start: 0.8254 (m110) cc_final: 0.7632 (m-40) REVERT: C 410 HIS cc_start: 0.6951 (OUTLIER) cc_final: 0.6595 (p90) REVERT: C 420 ARG cc_start: 0.8162 (tpp80) cc_final: 0.7529 (tpp80) REVERT: C 432 ARG cc_start: 0.8054 (mtt90) cc_final: 0.7530 (mmt90) REVERT: C 471 ASP cc_start: 0.8403 (t0) cc_final: 0.8164 (t0) REVERT: C 562 MET cc_start: 0.8720 (mtm) cc_final: 0.8334 (mtm) REVERT: C 627 TYR cc_start: 0.6927 (m-80) cc_final: 0.6429 (m-80) REVERT: C 743 ARG cc_start: 0.7756 (ttm110) cc_final: 0.7248 (ttm170) REVERT: D 308 MET cc_start: 0.7946 (mmm) cc_final: 0.7412 (mmm) REVERT: D 409 ARG cc_start: 0.7923 (ptm160) cc_final: 0.7617 (ttp-170) REVERT: D 420 ARG cc_start: 0.8144 (tpp80) cc_final: 0.7521 (tpp80) REVERT: D 432 ARG cc_start: 0.8114 (mtt90) cc_final: 0.7721 (mmt180) REVERT: D 471 ASP cc_start: 0.8255 (t0) cc_final: 0.7626 (t0) REVERT: D 570 GLU cc_start: 0.8685 (tt0) cc_final: 0.8471 (tt0) REVERT: D 698 LYS cc_start: 0.9017 (mmmt) cc_final: 0.8815 (mttp) REVERT: D 746 GLU cc_start: 0.5168 (tt0) cc_final: 0.4653 (tt0) REVERT: B 293 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7338 (mt-10) REVERT: B 308 MET cc_start: 0.8152 (mmm) cc_final: 0.7900 (mmt) REVERT: B 379 SER cc_start: 0.7682 (m) cc_final: 0.7310 (t) REVERT: B 397 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7517 (tt0) REVERT: B 409 ARG cc_start: 0.7795 (ptt-90) cc_final: 0.7471 (ptt-90) REVERT: B 420 ARG cc_start: 0.8435 (tpp80) cc_final: 0.7989 (tpp80) REVERT: B 432 ARG cc_start: 0.8110 (mtt90) cc_final: 0.7674 (mmt180) REVERT: B 471 ASP cc_start: 0.8149 (t0) cc_final: 0.7578 (t0) REVERT: B 472 TYR cc_start: 0.7614 (m-80) cc_final: 0.7259 (m-80) REVERT: B 627 TYR cc_start: 0.6901 (m-80) cc_final: 0.6320 (m-80) REVERT: B 695 ASN cc_start: 0.7328 (m-40) cc_final: 0.6709 (t0) REVERT: B 743 ARG cc_start: 0.7962 (ttm110) cc_final: 0.7325 (ttm170) REVERT: B 746 GLU cc_start: 0.5788 (tt0) cc_final: 0.5185 (tt0) outliers start: 64 outliers final: 59 residues processed: 575 average time/residue: 0.2605 time to fit residues: 218.2279 Evaluate side-chains 595 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 533 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 504 LYS Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 656 LYS Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 2.9990 chunk 102 optimal weight: 0.0050 chunk 79 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 161 optimal weight: 0.6980 chunk 139 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 110 optimal weight: 0.0870 overall best weight: 0.4172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN A 560 GLN D 354 GLN D 393 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 15092 Z= 0.193 Angle : 0.594 8.745 20460 Z= 0.310 Chirality : 0.040 0.363 2304 Planarity : 0.003 0.038 2500 Dihedral : 7.194 59.322 2352 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.50 % Allowed : 21.06 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.20), residues: 1764 helix: 1.19 (0.15), residues: 1120 sheet: -1.55 (0.57), residues: 68 loop : -2.06 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 697 HIS 0.003 0.000 HIS A 289 PHE 0.030 0.001 PHE C 304 TYR 0.010 0.001 TYR D 351 ARG 0.008 0.000 ARG B 409 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 543 time to evaluate : 1.646 Fit side-chains REVERT: A 293 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7564 (mp0) REVERT: A 308 MET cc_start: 0.7945 (mmm) cc_final: 0.7525 (mmm) REVERT: A 313 LEU cc_start: 0.8927 (mt) cc_final: 0.8604 (mt) REVERT: A 379 SER cc_start: 0.7761 (m) cc_final: 0.7462 (t) REVERT: A 397 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7339 (tt0) REVERT: A 425 LYS cc_start: 0.8234 (tptt) cc_final: 0.7679 (tptt) REVERT: A 432 ARG cc_start: 0.8005 (mtt90) cc_final: 0.7591 (mmt90) REVERT: A 472 TYR cc_start: 0.8219 (m-80) cc_final: 0.7563 (m-80) REVERT: A 491 ARG cc_start: 0.5947 (mmm-85) cc_final: 0.5560 (mmm-85) REVERT: A 627 TYR cc_start: 0.6943 (m-80) cc_final: 0.6423 (m-80) REVERT: A 684 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7260 (tm-30) REVERT: A 696 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8045 (mm) REVERT: C 293 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7412 (mt-10) REVERT: C 356 GLU cc_start: 0.6781 (tt0) cc_final: 0.6541 (mm-30) REVERT: C 379 SER cc_start: 0.7740 (m) cc_final: 0.7379 (t) REVERT: C 393 ASN cc_start: 0.8213 (m110) cc_final: 0.7788 (m-40) REVERT: C 410 HIS cc_start: 0.6881 (OUTLIER) cc_final: 0.6485 (p90) REVERT: C 420 ARG cc_start: 0.8150 (tpp80) cc_final: 0.7499 (tpp80) REVERT: C 432 ARG cc_start: 0.8042 (mtt90) cc_final: 0.7524 (mmt90) REVERT: C 562 MET cc_start: 0.8737 (mtm) cc_final: 0.8189 (mmm) REVERT: C 577 LEU cc_start: 0.8585 (tp) cc_final: 0.8303 (tp) REVERT: C 627 TYR cc_start: 0.6931 (m-80) cc_final: 0.6426 (m-80) REVERT: C 743 ARG cc_start: 0.7773 (ttm110) cc_final: 0.7281 (ttm170) REVERT: D 308 MET cc_start: 0.7976 (mmm) cc_final: 0.7440 (mmm) REVERT: D 409 ARG cc_start: 0.7905 (ptm160) cc_final: 0.7634 (ttp-170) REVERT: D 420 ARG cc_start: 0.8077 (tpp80) cc_final: 0.7444 (tpp80) REVERT: D 432 ARG cc_start: 0.8100 (mtt90) cc_final: 0.7701 (mmt180) REVERT: D 471 ASP cc_start: 0.8250 (t0) cc_final: 0.7623 (t0) REVERT: D 570 GLU cc_start: 0.8652 (tt0) cc_final: 0.8444 (tt0) REVERT: D 698 LYS cc_start: 0.9016 (mmmt) cc_final: 0.8812 (mttp) REVERT: D 746 GLU cc_start: 0.5160 (tt0) cc_final: 0.4625 (tt0) REVERT: B 293 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7279 (mt-10) REVERT: B 308 MET cc_start: 0.8137 (mmm) cc_final: 0.7889 (mmt) REVERT: B 379 SER cc_start: 0.7667 (m) cc_final: 0.7291 (t) REVERT: B 409 ARG cc_start: 0.7755 (ptt-90) cc_final: 0.7465 (ptt-90) REVERT: B 420 ARG cc_start: 0.8413 (tpp80) cc_final: 0.7956 (tpp80) REVERT: B 432 ARG cc_start: 0.8090 (mtt90) cc_final: 0.7652 (mmt180) REVERT: B 471 ASP cc_start: 0.8186 (t0) cc_final: 0.7575 (t0) REVERT: B 472 TYR cc_start: 0.7631 (m-80) cc_final: 0.7292 (m-80) REVERT: B 627 TYR cc_start: 0.6920 (m-80) cc_final: 0.6362 (m-80) REVERT: B 684 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6927 (tm-30) REVERT: B 743 ARG cc_start: 0.7971 (ttm110) cc_final: 0.7341 (ttm170) REVERT: B 746 GLU cc_start: 0.5698 (tt0) cc_final: 0.5074 (tt0) outliers start: 56 outliers final: 50 residues processed: 568 average time/residue: 0.2619 time to fit residues: 217.3607 Evaluate side-chains 581 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 528 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 504 LYS Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 656 LYS Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 143 optimal weight: 0.0050 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 122 optimal weight: 2.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN A 494 GLN D 354 GLN D 393 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.162701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.118397 restraints weight = 20622.300| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.50 r_work: 0.3246 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 15092 Z= 0.203 Angle : 0.594 7.542 20460 Z= 0.310 Chirality : 0.040 0.350 2304 Planarity : 0.003 0.030 2500 Dihedral : 7.161 59.231 2352 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.69 % Allowed : 21.44 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.12 (0.20), residues: 1764 helix: 1.25 (0.15), residues: 1112 sheet: -1.36 (0.61), residues: 68 loop : -2.08 (0.23), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 697 HIS 0.003 0.000 HIS A 289 PHE 0.030 0.001 PHE C 304 TYR 0.013 0.001 TYR C 472 ARG 0.006 0.000 ARG B 409 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4600.43 seconds wall clock time: 83 minutes 3.04 seconds (4983.04 seconds total)