Starting phenix.real_space_refine (version: dev) on Tue Apr 5 16:45:25 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2n_23134/04_2022/7l2n_23134_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2n_23134/04_2022/7l2n_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_23134/04_2022/7l2n_23134.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2n_23134/04_2022/7l2n_23134.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2n_23134/04_2022/7l2n_23134_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2n_23134/04_2022/7l2n_23134_updated.pdb" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral 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-4553/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: {'PTRANS': 10, 'TRANS': 433, 'PCIS': 1} 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: {'PTRANS': 10, 'TRANS': 433, 'PCIS': 1} 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: {'PTRANS': 10, 'TRANS': 433, 'PCIS': 1} 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: {'PTRANS': 10, 'TRANS': 433, 'PCIS': 1} 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: 8.54, per 1000 atoms: 0.58 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: 6.22 Conformation dependent library (CDL) restraints added in 2.3 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: 1.28 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: 4.11 Time building geometry restraints manager: 6.61 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: 8267 16.19 - 32.37: 449 32.37 - 48.56: 76 48.56 - 64.74: 14 64.74 - 80.93: 6 Dihedral angle restraints: 8812 sinusoidal: 3548 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 8809 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 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. 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 6.500 Check model and map are aligned: 0.220 Convert atoms to be neutral: 0.120 Process input model: 39.480 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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 : 10.504 80.929 5428 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 % 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 *********************** 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 : 1.738 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 outliers start: 4 outliers final: 4 residues processed: 754 average time/residue: 0.2779 time to fit residues: 296.9816 Evaluate side-chains 556 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 552 time to evaluate : 1.784 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1260 time to fit residues: 3.3661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 53 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 C 354 GLN C 652 ASN D 354 GLN D 393 ASN B 354 GLN B 393 ASN ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 15092 Z= 0.257 Angle : 0.580 11.811 20460 Z= 0.302 Chirality : 0.039 0.162 2304 Planarity : 0.004 0.044 2500 Dihedral : 5.537 52.730 2000 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 3.50 % 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: 0.32 (0.20), residues: 1764 helix: 1.34 (0.15), residues: 1152 sheet: -2.47 (0.55), residues: 72 loop : -1.90 (0.24), residues: 540 *********************** 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 646 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 590 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 38 residues processed: 611 average time/residue: 0.2599 time to fit residues: 230.0948 Evaluate side-chains 577 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 539 time to evaluate : 1.783 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.1530 time to fit residues: 12.9458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 133 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 GLN B 354 GLN B 378 HIS B 393 ASN B 695 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 15092 Z= 0.280 Angle : 0.574 9.249 20460 Z= 0.300 Chirality : 0.039 0.184 2304 Planarity : 0.004 0.042 2500 Dihedral : 5.438 50.268 2000 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 2.12 % 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: 0.14 (0.20), residues: 1764 helix: 1.20 (0.15), residues: 1156 sheet: -2.51 (0.52), residues: 72 loop : -1.99 (0.24), residues: 536 *********************** 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 610 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 576 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 16 residues processed: 587 average time/residue: 0.2621 time to fit residues: 224.4839 Evaluate side-chains 557 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 541 time to evaluate : 1.866 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1810 time to fit residues: 7.4384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 76 optimal weight: 0.0970 chunk 107 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 141 optimal weight: 7.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 C 560 GLN C 561 GLN D 354 GLN D 393 ASN B 628 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3385 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= 0.185 Angle : 0.541 6.877 20460 Z= 0.282 Chirality : 0.037 0.173 2304 Planarity : 0.003 0.040 2500 Dihedral : 5.312 49.083 2000 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 2.75 % 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: 1.21 (0.15), residues: 1144 sheet: -2.40 (0.54), residues: 72 loop : -2.10 (0.23), residues: 548 *********************** 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 617 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 573 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 22 residues processed: 584 average time/residue: 0.2554 time to fit residues: 219.1643 Evaluate side-chains 560 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 538 time to evaluate : 1.731 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1325 time to fit residues: 7.7466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 145 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN A 423 GLN C 393 ASN C 560 GLN D 354 GLN B 393 ASN B 695 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3638 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= 0.199 Angle : 0.541 7.205 20460 Z= 0.284 Chirality : 0.038 0.177 2304 Planarity : 0.003 0.040 2500 Dihedral : 5.265 47.702 2000 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer Outliers : 2.38 % 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: 0.07 (0.19), residues: 1764 helix: 1.17 (0.15), residues: 1152 sheet: -2.43 (0.53), residues: 72 loop : -2.09 (0.23), residues: 540 *********************** 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 604 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 566 time to evaluate : 1.717 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 19 residues processed: 578 average time/residue: 0.2562 time to fit residues: 218.0987 Evaluate side-chains 551 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 532 time to evaluate : 1.749 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1931 time to fit residues: 8.2402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 141 optimal weight: 8.9990 chunk 78 optimal weight: 0.0770 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 89 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- 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: 0.7820 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 15092 Z= 0.232 Angle : 0.567 8.089 20460 Z= 0.296 Chirality : 0.039 0.204 2304 Planarity : 0.003 0.041 2500 Dihedral : 5.258 46.781 2000 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer Outliers : 1.81 % 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: -0.02 (0.19), residues: 1764 helix: 1.10 (0.15), residues: 1152 sheet: -2.46 (0.53), residues: 72 loop : -2.12 (0.23), residues: 540 *********************** 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 577 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 548 time to evaluate : 1.810 Fit side-chains outliers start: 29 outliers final: 21 residues processed: 553 average time/residue: 0.2531 time to fit residues: 207.0052 Evaluate side-chains 538 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 517 time to evaluate : 1.702 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1410 time to fit residues: 7.6361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 354 GLN B 393 ASN B 423 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 15092 Z= 0.221 Angle : 0.579 9.215 20460 Z= 0.303 Chirality : 0.040 0.288 2304 Planarity : 0.003 0.041 2500 Dihedral : 5.235 46.362 2000 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer Outliers : 1.06 % 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: 0.20 (0.19), residues: 1764 helix: 1.24 (0.15), residues: 1124 sheet: -2.35 (0.54), residues: 72 loop : -1.81 (0.23), residues: 568 *********************** 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 564 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 547 time to evaluate : 1.738 Fit side-chains outliers start: 17 outliers final: 12 residues processed: 549 average time/residue: 0.2533 time to fit residues: 205.3015 Evaluate side-chains 535 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 523 time to evaluate : 1.778 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2032 time to fit residues: 6.1139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 133 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 GLN B 393 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 15092 Z= 0.243 Angle : 0.594 7.612 20460 Z= 0.314 Chirality : 0.040 0.324 2304 Planarity : 0.004 0.051 2500 Dihedral : 5.266 45.976 2000 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer Outliers : 1.50 % 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: 1.03 (0.15), residues: 1152 sheet: -2.17 (0.57), residues: 72 loop : -2.08 (0.24), residues: 540 *********************** 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 556 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 532 time to evaluate : 1.702 Fit side-chains outliers start: 24 outliers final: 18 residues processed: 537 average time/residue: 0.2529 time to fit residues: 201.2077 Evaluate side-chains 527 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 509 time to evaluate : 1.706 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1911 time to fit residues: 7.9912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 48 optimal weight: 0.0070 chunk 142 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7790 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 15092 Z= 0.212 Angle : 0.598 7.631 20460 Z= 0.314 Chirality : 0.040 0.347 2304 Planarity : 0.003 0.048 2500 Dihedral : 5.204 44.888 2000 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer Outliers : 0.56 % 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: -0.06 (0.20), residues: 1764 helix: 1.09 (0.15), residues: 1132 sheet: -1.95 (0.59), residues: 72 loop : -2.16 (0.23), residues: 560 *********************** 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 544 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 535 time to evaluate : 1.799 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 536 average time/residue: 0.2511 time to fit residues: 200.4532 Evaluate side-chains 517 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 512 time to evaluate : 1.647 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1399 time to fit residues: 3.8933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 chunk 175 optimal weight: 4.9990 chunk 161 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN C 494 GLN D 354 GLN D 393 ASN B 393 ASN B 551 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 15092 Z= 0.253 Angle : 0.629 9.258 20460 Z= 0.329 Chirality : 0.042 0.347 2304 Planarity : 0.004 0.048 2500 Dihedral : 5.224 44.391 2000 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer Outliers : 0.75 % 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: -0.11 (0.20), residues: 1764 helix: 1.04 (0.15), residues: 1132 sheet: -1.86 (0.61), residues: 72 loop : -2.17 (0.24), residues: 560 ********************** 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 531 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 519 time to evaluate : 1.810 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 11 residues processed: 520 average time/residue: 0.2545 time to fit residues: 196.2950 Evaluate side-chains 511 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 500 time to evaluate : 1.799 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1742 time to fit residues: 5.6705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 143 optimal weight: 0.0070 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 122 optimal weight: 0.2980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 ASN 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 = 0.3929 r_free = 0.3929 target = 0.161573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.118293 restraints weight = 20680.630| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.50 r_work: 0.3371 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work: 0.3343 rms_B_bonded: 2.29 restraints_weight: 0.1250 r_work: 0.3329 rms_B_bonded: 2.36 restraints_weight: 0.0625 r_work: 0.3314 rms_B_bonded: 2.48 restraints_weight: 0.0312 r_work: 0.3298 rms_B_bonded: 2.62 restraints_weight: 0.0156 r_work: 0.3282 rms_B_bonded: 2.80 restraints_weight: 0.0078 r_work: 0.3264 rms_B_bonded: 3.02 restraints_weight: 0.0039 r_work: 0.3245 rms_B_bonded: 3.28 restraints_weight: 0.0020 r_work: 0.3224 rms_B_bonded: 3.58 restraints_weight: 0.0010 r_work: 0.3202 rms_B_bonded: 3.93 restraints_weight: 0.0005 r_work: 0.3179 rms_B_bonded: 4.34 restraints_weight: 0.0002 r_work: 0.3154 rms_B_bonded: 4.80 restraints_weight: 0.0001 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 15092 Z= 0.213 Angle : 0.625 9.351 20460 Z= 0.325 Chirality : 0.041 0.326 2304 Planarity : 0.004 0.047 2500 Dihedral : 5.215 43.700 2000 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer Outliers : 0.25 % 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: 1.00 (0.15), residues: 1140 sheet: -1.80 (0.62), residues: 72 loop : -2.13 (0.24), residues: 552 =============================================================================== Job complete usr+sys time: 4045.91 seconds wall clock time: 73 minutes 37.46 seconds (4417.46 seconds total)