Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 12 18:20:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stn_25434/10_2023/7stn_25434_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stn_25434/10_2023/7stn_25434.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stn_25434/10_2023/7stn_25434_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stn_25434/10_2023/7stn_25434_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stn_25434/10_2023/7stn_25434_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stn_25434/10_2023/7stn_25434.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stn_25434/10_2023/7stn_25434.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stn_25434/10_2023/7stn_25434_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stn_25434/10_2023/7stn_25434_trim_updated.pdb" } resolution = 3.19 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= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 56 5.16 5 C 8480 2.51 5 N 2062 2.21 5 O 2326 1.98 5 H 12256 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 991": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 991": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 25188 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 12400 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 24, 'TRANS': 765} Chain breaks: 3 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 12400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 12400 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 24, 'TRANS': 765} Chain breaks: 3 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 231 Unusual residues: {'3PE': 5, 'BGI': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 59 Chain: "B" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 157 Unusual residues: {'3PE': 3, 'BGI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Time building chain proxies: 10.57, per 1000 atoms: 0.42 Number of scatterers: 25188 At special positions: 0 Unit cell: (135, 76.68, 120.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 8 15.00 O 2326 8.00 N 2062 7.00 C 8480 6.00 H 12256 1.00 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: 20.14 Conformation dependent library (CDL) restraints added in 1.9 seconds 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 6 sheets defined 53.4% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.40 Creating SS restraints... Processing helix chain 'A' and resid 147 through 154 removed outlier: 3.663A pdb=" N ARG A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 255 through 259 Processing helix chain 'A' and resid 275 through 278 No H-bonds generated for 'chain 'A' and resid 275 through 278' Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 323 through 342 Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 371 through 379 Processing helix chain 'A' and resid 440 through 450 Processing helix chain 'A' and resid 452 through 456 Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 508 through 531 removed outlier: 4.747A pdb=" N LYS A 525 " --> pdb=" O ASN A 521 " (cutoff:3.500A) Proline residue: A 526 - end of helix Processing helix chain 'A' and resid 547 through 549 No H-bonds generated for 'chain 'A' and resid 547 through 549' Processing helix chain 'A' and resid 558 through 568 removed outlier: 4.002A pdb=" N GLY A 565 " --> pdb=" O LYS A 561 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU A 566 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 567 " --> pdb=" O PHE A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 589 Processing helix chain 'A' and resid 594 through 601 removed outlier: 5.444A pdb=" N TYR A 600 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 612 Processing helix chain 'A' and resid 637 through 660 removed outlier: 4.138A pdb=" N ARG A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP A 647 " --> pdb=" O GLN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 666 Processing helix chain 'A' and resid 672 through 693 Processing helix chain 'A' and resid 695 through 711 removed outlier: 3.600A pdb=" N LEU A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 744 Processing helix chain 'A' and resid 751 through 786 Processing helix chain 'A' and resid 792 through 797 Processing helix chain 'A' and resid 799 through 821 removed outlier: 4.092A pdb=" N ALA A 807 " --> pdb=" O ASP A 803 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 830 removed outlier: 4.166A pdb=" N THR A 830 " --> pdb=" O HIS A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 852 Proline residue: A 840 - end of helix removed outlier: 3.842A pdb=" N LEU A 846 " --> pdb=" O TYR A 842 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN A 847 " --> pdb=" O VAL A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 903 Processing helix chain 'A' and resid 919 through 945 Processing helix chain 'A' and resid 949 through 953 Processing helix chain 'A' and resid 958 through 1001 Processing helix chain 'B' and resid 147 through 154 removed outlier: 3.663A pdb=" N ARG B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 255 through 259 Processing helix chain 'B' and resid 275 through 278 No H-bonds generated for 'chain 'B' and resid 275 through 278' Processing helix chain 'B' and resid 300 through 302 No H-bonds generated for 'chain 'B' and resid 300 through 302' Processing helix chain 'B' and resid 323 through 342 Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 371 through 379 Processing helix chain 'B' and resid 440 through 450 Processing helix chain 'B' and resid 452 through 456 Processing helix chain 'B' and resid 474 through 484 Processing helix chain 'B' and resid 508 through 531 removed outlier: 4.747A pdb=" N LYS B 525 " --> pdb=" O ASN B 521 " (cutoff:3.500A) Proline residue: B 526 - end of helix Processing helix chain 'B' and resid 547 through 549 No H-bonds generated for 'chain 'B' and resid 547 through 549' Processing helix chain 'B' and resid 558 through 568 removed outlier: 4.002A pdb=" N GLY B 565 " --> pdb=" O LYS B 561 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU B 566 " --> pdb=" O TYR B 562 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE B 567 " --> pdb=" O PHE B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 589 Processing helix chain 'B' and resid 594 through 601 removed outlier: 5.444A pdb=" N TYR B 600 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 612 Processing helix chain 'B' and resid 637 through 660 removed outlier: 4.139A pdb=" N ARG B 646 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP B 647 " --> pdb=" O GLN B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 Processing helix chain 'B' and resid 672 through 693 Processing helix chain 'B' and resid 695 through 711 removed outlier: 3.600A pdb=" N LEU B 710 " --> pdb=" O LEU B 706 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 744 Processing helix chain 'B' and resid 751 through 786 Processing helix chain 'B' and resid 792 through 797 Processing helix chain 'B' and resid 799 through 821 removed outlier: 4.093A pdb=" N ALA B 807 " --> pdb=" O ASP B 803 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 830 removed outlier: 4.165A pdb=" N THR B 830 " --> pdb=" O HIS B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 852 Proline residue: B 840 - end of helix removed outlier: 3.842A pdb=" N LEU B 846 " --> pdb=" O TYR B 842 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN B 847 " --> pdb=" O VAL B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 903 Processing helix chain 'B' and resid 919 through 945 Processing helix chain 'B' and resid 949 through 953 Processing helix chain 'B' and resid 958 through 1001 Processing sheet with id= A, first strand: chain 'A' and resid 248 through 252 removed outlier: 7.964A pdb=" N PHE A 279 " --> pdb=" O THR A 405 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N THR A 405 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE A 357 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N LEU A 431 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL A 359 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N CYS A 433 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE A 361 " --> pdb=" O CYS A 433 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS A 435 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N SER A 363 " --> pdb=" O LYS A 435 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU A 312 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N CYS A 360 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 314 " --> pdb=" O CYS A 360 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL A 362 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE A 316 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL A 462 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N THR A 317 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU A 464 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N PHE A 541 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY A 493 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU A 620 " --> pdb=" O ALA A 489 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ALA A 491 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG A 622 " --> pdb=" O ALA A 491 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLY A 493 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N CYS A 624 " --> pdb=" O GLY A 493 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 494 through 497 Processing sheet with id= C, first strand: chain 'A' and resid 409 through 413 removed outlier: 7.188A pdb=" N LYS A 419 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 248 through 252 removed outlier: 7.964A pdb=" N PHE B 279 " --> pdb=" O THR B 405 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N THR B 405 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE B 357 " --> pdb=" O GLN B 429 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N LEU B 431 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL B 359 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N CYS B 433 " --> pdb=" O VAL B 359 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE B 361 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS B 435 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N SER B 363 " --> pdb=" O LYS B 435 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU B 312 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N CYS B 360 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE B 314 " --> pdb=" O CYS B 360 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL B 362 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE B 316 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL B 462 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N THR B 317 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU B 464 " --> pdb=" O THR B 317 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N PHE B 541 " --> pdb=" O GLY B 493 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY B 493 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU B 620 " --> pdb=" O ALA B 489 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ALA B 491 " --> pdb=" O LEU B 620 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG B 622 " --> pdb=" O ALA B 491 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY B 493 " --> pdb=" O ARG B 622 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N CYS B 624 " --> pdb=" O GLY B 493 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 494 through 497 Processing sheet with id= F, first strand: chain 'B' and resid 409 through 413 removed outlier: 7.187A pdb=" N LYS B 419 " --> pdb=" O SER B 411 " (cutoff:3.500A) 628 hydrogen bonds defined for protein. 1788 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: 9.49 Time building geometry restraints manager: 20.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12232 1.03 - 1.23: 46 1.23 - 1.42: 5654 1.42 - 1.61: 7460 1.61 - 1.81: 106 Bond restraints: 25498 Sorted by residual: bond pdb=" C20 BGI A1202 " pdb=" O21 BGI A1202 " ideal model delta sigma weight residual 1.659 1.278 0.381 2.00e-02 2.50e+03 3.63e+02 bond pdb=" C20 BGI B1202 " pdb=" O21 BGI B1202 " ideal model delta sigma weight residual 1.659 1.279 0.380 2.00e-02 2.50e+03 3.62e+02 bond pdb=" C19 BGI B1202 " pdb=" C20 BGI B1202 " ideal model delta sigma weight residual 1.342 1.654 -0.312 2.00e-02 2.50e+03 2.43e+02 bond pdb=" C19 BGI A1202 " pdb=" C20 BGI A1202 " ideal model delta sigma weight residual 1.342 1.653 -0.311 2.00e-02 2.50e+03 2.42e+02 bond pdb=" C17 BGI B1202 " pdb=" O21 BGI B1202 " ideal model delta sigma weight residual 1.299 1.521 -0.222 2.00e-02 2.50e+03 1.23e+02 ... (remaining 25493 not shown) Histogram of bond angle deviations from ideal: 100.39 - 107.11: 392 107.11 - 113.83: 29184 113.83 - 120.54: 9336 120.54 - 127.26: 6611 127.26 - 133.98: 129 Bond angle restraints: 45652 Sorted by residual: angle pdb=" O12 3PE A1203 " pdb=" P 3PE A1203 " pdb=" O14 3PE A1203 " ideal model delta sigma weight residual 123.79 109.39 14.40 3.00e+00 1.11e-01 2.30e+01 angle pdb=" O12 3PE B1203 " pdb=" P 3PE B1203 " pdb=" O14 3PE B1203 " ideal model delta sigma weight residual 123.79 109.42 14.37 3.00e+00 1.11e-01 2.30e+01 angle pdb=" O12 3PE A1206 " pdb=" P 3PE A1206 " pdb=" O14 3PE A1206 " ideal model delta sigma weight residual 123.79 109.44 14.35 3.00e+00 1.11e-01 2.29e+01 angle pdb=" O12 3PE A1204 " pdb=" P 3PE A1204 " pdb=" O14 3PE A1204 " ideal model delta sigma weight residual 123.79 109.47 14.32 3.00e+00 1.11e-01 2.28e+01 angle pdb=" O12 3PE B1204 " pdb=" P 3PE B1204 " pdb=" O14 3PE B1204 " ideal model delta sigma weight residual 123.79 109.48 14.31 3.00e+00 1.11e-01 2.28e+01 ... (remaining 45647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 10022 17.84 - 35.69: 332 35.69 - 53.53: 64 53.53 - 71.38: 4 71.38 - 89.22: 4 Dihedral angle restraints: 10426 sinusoidal: 4664 harmonic: 5762 Sorted by residual: dihedral pdb=" N TYR B 699 " pdb=" CA TYR B 699 " pdb=" CB TYR B 699 " pdb=" CG TYR B 699 " ideal model delta sinusoidal sigma weight residual -60.00 -114.31 54.31 3 1.50e+01 4.44e-03 9.27e+00 dihedral pdb=" N TYR A 699 " pdb=" CA TYR A 699 " pdb=" CB TYR A 699 " pdb=" CG TYR A 699 " ideal model delta sinusoidal sigma weight residual -60.00 -114.28 54.28 3 1.50e+01 4.44e-03 9.27e+00 dihedral pdb=" CB ARG A 645 " pdb=" CG ARG A 645 " pdb=" CD ARG A 645 " pdb=" NE ARG A 645 " ideal model delta sinusoidal sigma weight residual 60.00 111.47 -51.47 3 1.50e+01 4.44e-03 9.02e+00 ... (remaining 10423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1939 0.110 - 0.220: 31 0.220 - 0.331: 1 0.331 - 0.441: 1 0.441 - 0.551: 2 Chirality restraints: 1974 Sorted by residual: chirality pdb=" C19 BGI A1202 " pdb=" C18 BGI A1202 " pdb=" C20 BGI A1202 " pdb=" O30 BGI A1202 " both_signs ideal model delta sigma weight residual False 2.42 2.97 -0.55 2.00e-01 2.50e+01 7.59e+00 chirality pdb=" C19 BGI B1202 " pdb=" C18 BGI B1202 " pdb=" C20 BGI B1202 " pdb=" O30 BGI B1202 " both_signs ideal model delta sigma weight residual False 2.42 2.97 -0.55 2.00e-01 2.50e+01 7.52e+00 chirality pdb=" C18 BGI B1202 " pdb=" C17 BGI B1202 " pdb=" C19 BGI B1202 " pdb=" O31 BGI B1202 " both_signs ideal model delta sigma weight residual False 2.59 2.92 -0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 1971 not shown) Planarity restraints: 3738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 945 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.71e+00 pdb=" N GLU B 946 " -0.033 2.00e-02 2.50e+03 pdb=" CA GLU B 946 " 0.009 2.00e-02 2.50e+03 pdb=" H GLU B 946 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 945 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" N GLU A 946 " -0.033 2.00e-02 2.50e+03 pdb=" CA GLU A 946 " 0.009 2.00e-02 2.50e+03 pdb=" H GLU A 946 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 943 " 0.009 2.00e-02 2.50e+03 1.73e-02 3.01e+00 pdb=" N VAL A 944 " -0.030 2.00e-02 2.50e+03 pdb=" CA VAL A 944 " 0.008 2.00e-02 2.50e+03 pdb=" H VAL A 944 " 0.013 2.00e-02 2.50e+03 ... (remaining 3735 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1100 2.21 - 2.80: 50951 2.80 - 3.40: 67250 3.40 - 4.00: 87591 4.00 - 4.60: 139745 Nonbonded interactions: 346637 Sorted by model distance: nonbonded pdb=" OE1 GLU A 341 " pdb=" HG SER A 353 " model vdw 1.608 1.850 nonbonded pdb=" OE1 GLU B 341 " pdb=" HG SER B 353 " model vdw 1.608 1.850 nonbonded pdb=" O GLY B 453 " pdb=" H ASP B 457 " model vdw 1.650 1.850 nonbonded pdb=" O GLY A 453 " pdb=" H ASP A 457 " model vdw 1.651 1.850 nonbonded pdb=" O VAL B 665 " pdb=" HG SER B 668 " model vdw 1.670 1.850 ... (remaining 346632 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 135 through 1002 or resid 1201 through 1204)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 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: 0.310 Extract box with map and model: 3.410 Check model and map are aligned: 0.440 Set scattering table: 0.290 Process input model: 77.220 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.100 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 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 : 0.008 0.381 13242 Z= 0.495 Angle : 0.751 14.398 17896 Z= 0.316 Chirality : 0.043 0.551 1974 Planarity : 0.002 0.030 2214 Dihedral : 9.951 89.221 4734 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.15 % Allowed : 1.67 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.22), residues: 1564 helix: 3.01 (0.17), residues: 828 sheet: 1.12 (0.45), residues: 140 loop : -0.60 (0.25), residues: 596 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 1.921 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 142 average time/residue: 0.6486 time to fit residues: 128.7101 Evaluate side-chains 63 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 2.118 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 66 optimal weight: 30.0000 chunk 40 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN A 797 GLN B 582 GLN B 598 ASN B 797 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13242 Z= 0.348 Angle : 0.521 5.520 17896 Z= 0.277 Chirality : 0.040 0.152 1974 Planarity : 0.003 0.034 2214 Dihedral : 8.224 81.331 1918 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.91 % Allowed : 4.47 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.21), residues: 1564 helix: 2.53 (0.17), residues: 846 sheet: 0.95 (0.45), residues: 140 loop : -0.72 (0.24), residues: 578 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 1.980 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 11 residues processed: 72 average time/residue: 0.6330 time to fit residues: 65.0891 Evaluate side-chains 67 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 1.837 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4606 time to fit residues: 9.8651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 13242 Z= 0.167 Angle : 0.405 4.926 17896 Z= 0.217 Chirality : 0.037 0.145 1974 Planarity : 0.003 0.029 2214 Dihedral : 7.857 79.584 1918 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.15 % Allowed : 5.00 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.21), residues: 1564 helix: 2.82 (0.18), residues: 834 sheet: 1.03 (0.45), residues: 140 loop : -0.61 (0.24), residues: 590 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 60 average time/residue: 0.5454 time to fit residues: 50.1420 Evaluate side-chains 56 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 2.054 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2807 time to fit residues: 3.7493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 74 optimal weight: 0.0060 chunk 15 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 chunk 96 optimal weight: 0.0570 chunk 144 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13242 Z= 0.231 Angle : 0.424 5.026 17896 Z= 0.230 Chirality : 0.038 0.152 1974 Planarity : 0.003 0.026 2214 Dihedral : 7.894 82.762 1918 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.23 % Allowed : 5.23 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.21), residues: 1564 helix: 2.75 (0.18), residues: 830 sheet: 0.98 (0.44), residues: 140 loop : -0.64 (0.24), residues: 594 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 57 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 2.067 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 57 average time/residue: 0.5937 time to fit residues: 51.2214 Evaluate side-chains 58 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 1.991 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.9991 time to fit residues: 6.2322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13242 Z= 0.335 Angle : 0.486 5.319 17896 Z= 0.265 Chirality : 0.039 0.157 1974 Planarity : 0.003 0.028 2214 Dihedral : 8.616 89.985 1918 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.23 % Allowed : 5.98 % Favored : 93.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.21), residues: 1564 helix: 2.46 (0.17), residues: 828 sheet: 0.85 (0.46), residues: 130 loop : -0.66 (0.24), residues: 606 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 2.177 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 62 average time/residue: 0.5188 time to fit residues: 50.3889 Evaluate side-chains 56 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 2.050 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.3167 time to fit residues: 4.0854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 0.6980 chunk 137 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 37 optimal weight: 0.3980 chunk 152 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13242 Z= 0.177 Angle : 0.415 4.978 17896 Z= 0.223 Chirality : 0.037 0.132 1974 Planarity : 0.003 0.025 2214 Dihedral : 8.213 87.735 1918 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.21), residues: 1564 helix: 2.58 (0.18), residues: 842 sheet: 0.90 (0.46), residues: 130 loop : -0.68 (0.24), residues: 592 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 55 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.934 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.5211 time to fit residues: 44.9994 Evaluate side-chains 55 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 2.080 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 152 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 92 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13242 Z= 0.289 Angle : 0.456 5.204 17896 Z= 0.247 Chirality : 0.038 0.128 1974 Planarity : 0.003 0.029 2214 Dihedral : 8.412 85.289 1918 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.21), residues: 1564 helix: 2.56 (0.18), residues: 830 sheet: 0.74 (0.45), residues: 130 loop : -0.65 (0.24), residues: 604 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 55 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 2.180 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.5579 time to fit residues: 47.4503 Evaluate side-chains 53 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.994 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 13242 Z= 0.229 Angle : 0.434 6.143 17896 Z= 0.233 Chirality : 0.038 0.126 1974 Planarity : 0.003 0.045 2214 Dihedral : 8.211 80.304 1918 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.21), residues: 1564 helix: 2.63 (0.18), residues: 830 sheet: 0.75 (0.46), residues: 130 loop : -0.66 (0.24), residues: 604 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 53 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.943 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.4696 time to fit residues: 40.6903 Evaluate side-chains 52 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.995 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 20.0000 chunk 133 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13242 Z= 0.276 Angle : 0.458 7.020 17896 Z= 0.246 Chirality : 0.038 0.126 1974 Planarity : 0.003 0.036 2214 Dihedral : 8.244 72.856 1918 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.21), residues: 1564 helix: 2.54 (0.18), residues: 830 sheet: 0.68 (0.46), residues: 130 loop : -0.68 (0.24), residues: 604 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 53 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 2.201 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.4761 time to fit residues: 41.7500 Evaluate side-chains 53 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 2.163 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13242 Z= 0.178 Angle : 0.418 6.161 17896 Z= 0.223 Chirality : 0.037 0.123 1974 Planarity : 0.003 0.026 2214 Dihedral : 7.829 59.752 1918 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.08 % Allowed : 7.05 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.21), residues: 1564 helix: 2.74 (0.18), residues: 826 sheet: 0.77 (0.47), residues: 130 loop : -0.65 (0.24), residues: 608 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 53 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 2.137 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 53 average time/residue: 0.4524 time to fit residues: 42.0494 Evaluate side-chains 52 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 3.090 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.122465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.084931 restraints weight = 53194.819| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.43 r_work: 0.2959 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13242 Z= 0.236 Angle : 0.438 5.902 17896 Z= 0.235 Chirality : 0.038 0.126 1974 Planarity : 0.003 0.027 2214 Dihedral : 7.640 58.951 1918 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.21), residues: 1564 helix: 2.69 (0.18), residues: 826 sheet: 0.73 (0.46), residues: 130 loop : -0.66 (0.24), residues: 608 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4228.92 seconds wall clock time: 76 minutes 18.06 seconds (4578.06 seconds total)