Starting phenix.real_space_refine on Wed Mar 20 02:12:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stl_25432/03_2024/7stl_25432_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stl_25432/03_2024/7stl_25432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stl_25432/03_2024/7stl_25432.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stl_25432/03_2024/7stl_25432.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stl_25432/03_2024/7stl_25432_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stl_25432/03_2024/7stl_25432_trim_updated.pdb" } resolution = 2.95 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= 0.005 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 8586 2.51 5 N 2094 2.21 5 O 2356 1.98 5 H 12568 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25668 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 800, 12675 Classifications: {'peptide': 800} Link IDs: {'PTRANS': 25, 'TRANS': 774} Chain breaks: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 3, 'GLU:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 53 Chain: "B" Number of atoms: 12675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 800, 12675 Classifications: {'peptide': 800} Link IDs: {'PTRANS': 25, 'TRANS': 774} Chain breaks: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 3, 'GLU:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 53 Chain: "A" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 159 Unusual residues: {'3PE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "B" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 159 Unusual residues: {'3PE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Time building chain proxies: 11.69, per 1000 atoms: 0.46 Number of scatterers: 25668 At special positions: 0 Unit cell: (132.84, 78.84, 123.12, 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 2356 8.00 N 2094 7.00 C 8586 6.00 H 12568 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: 20.82 Conformation dependent library (CDL) restraints added in 2.6 seconds 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3016 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 6 sheets defined 53.2% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.46 Creating SS restraints... Processing helix chain 'A' and resid 143 through 154 removed outlier: 3.954A pdb=" N ASN A 146 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ASP A 147 " --> pdb=" O GLU A 144 " (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 260 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 380 Processing helix chain 'A' and resid 440 through 450 removed outlier: 3.798A pdb=" N SER A 444 " --> pdb=" O LYS A 440 " (cutoff:3.500A) 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: 4.793A 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: 4.054A pdb=" N GLY A 565 " --> pdb=" O LYS A 561 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU A 566 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 3.829A 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 597 No H-bonds generated for 'chain 'A' and resid 594 through 597' Processing helix chain 'A' and resid 599 through 601 No H-bonds generated for 'chain 'A' and resid 599 through 601' Processing helix chain 'A' and resid 603 through 612 Processing helix chain 'A' and resid 637 through 660 removed outlier: 4.094A pdb=" N ARG A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP A 647 " --> pdb=" O GLN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 665 removed outlier: 3.560A pdb=" N VAL A 665 " --> pdb=" O PHE A 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 662 through 665' Processing helix chain 'A' and resid 672 through 693 Processing helix chain 'A' and resid 695 through 711 removed outlier: 3.577A pdb=" N LEU A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) removed outlier: 3.778A 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: 3.940A pdb=" N ALA A 807 " --> pdb=" O ASP A 803 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 830 removed outlier: 4.160A 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: 3.501A pdb=" N VAL A 843 " --> pdb=" O SER A 839 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 846 " --> pdb=" O TYR A 842 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN A 847 " --> pdb=" O VAL A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 904 Processing helix chain 'A' and resid 919 through 945 Processing helix chain 'A' and resid 950 through 953 Processing helix chain 'A' and resid 958 through 1001 Processing helix chain 'B' and resid 143 through 154 removed outlier: 3.954A pdb=" N ASN B 146 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ASP B 147 " --> pdb=" O GLU B 144 " (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 260 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 380 Processing helix chain 'B' and resid 440 through 450 removed outlier: 3.798A pdb=" N SER B 444 " --> pdb=" O LYS B 440 " (cutoff:3.500A) 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: 4.793A 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: 4.053A pdb=" N GLY B 565 " --> pdb=" O LYS B 561 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU B 566 " --> pdb=" O TYR B 562 " (cutoff:3.500A) removed outlier: 3.829A 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 597 No H-bonds generated for 'chain 'B' and resid 594 through 597' Processing helix chain 'B' and resid 599 through 601 No H-bonds generated for 'chain 'B' and resid 599 through 601' Processing helix chain 'B' and resid 603 through 612 Processing helix chain 'B' and resid 637 through 660 removed outlier: 4.094A pdb=" N ARG B 646 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP B 647 " --> pdb=" O GLN B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 665 removed outlier: 3.560A pdb=" N VAL B 665 " --> pdb=" O PHE B 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 662 through 665' Processing helix chain 'B' and resid 672 through 693 Processing helix chain 'B' and resid 695 through 711 removed outlier: 3.576A pdb=" N LEU B 710 " --> pdb=" O LEU B 706 " (cutoff:3.500A) removed outlier: 3.779A 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: 3.941A pdb=" N ALA B 807 " --> pdb=" O ASP B 803 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 830 removed outlier: 4.160A 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: 3.502A pdb=" N VAL B 843 " --> pdb=" O SER B 839 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 846 " --> pdb=" O TYR B 842 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN B 847 " --> pdb=" O VAL B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 904 Processing helix chain 'B' and resid 919 through 945 Processing helix chain 'B' and resid 950 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: 7.781A pdb=" N PHE A 279 " --> pdb=" O THR A 405 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N THR A 405 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN A 429 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 312 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N CYS A 360 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE A 314 " --> pdb=" O CYS A 360 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL A 362 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE A 316 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL A 462 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N THR A 317 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU A 464 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE A 541 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY A 493 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU A 620 " --> pdb=" O ALA A 489 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA A 491 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ARG A 622 " --> pdb=" O ALA A 491 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLY A 493 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 6.809A 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: 7.201A 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: 7.781A pdb=" N PHE B 279 " --> pdb=" O THR B 405 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N THR B 405 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN B 429 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU B 312 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N CYS B 360 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE B 314 " --> pdb=" O CYS B 360 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL B 362 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE B 316 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL B 462 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N THR B 317 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU B 464 " --> pdb=" O THR B 317 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE B 541 " --> pdb=" O GLY B 493 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY B 493 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU B 620 " --> pdb=" O ALA B 489 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA B 491 " --> pdb=" O LEU B 620 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ARG B 622 " --> pdb=" O ALA B 491 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY B 493 " --> pdb=" O ARG B 622 " (cutoff:3.500A) removed outlier: 6.809A 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: 7.201A pdb=" N LYS B 419 " --> pdb=" O SER B 411 " (cutoff:3.500A) 640 hydrogen bonds defined for protein. 1800 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: 9.43 Time building geometry restraints manager: 21.62 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: 12544 1.03 - 1.22: 40 1.22 - 1.42: 5732 1.42 - 1.61: 7562 1.61 - 1.81: 104 Bond restraints: 25982 Sorted by residual: bond pdb=" C21 3PE A1204 " pdb=" O21 3PE A1204 " ideal model delta sigma weight residual 1.316 1.404 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C21 3PE B1204 " pdb=" O21 3PE B1204 " ideal model delta sigma weight residual 1.316 1.404 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C21 3PE B1201 " pdb=" O21 3PE B1201 " ideal model delta sigma weight residual 1.316 1.400 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C21 3PE A1201 " pdb=" O21 3PE A1201 " ideal model delta sigma weight residual 1.316 1.400 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" C21 3PE B1202 " pdb=" O21 3PE B1202 " ideal model delta sigma weight residual 1.316 1.400 -0.084 2.00e-02 2.50e+03 1.75e+01 ... (remaining 25977 not shown) Histogram of bond angle deviations from ideal: 100.23 - 106.99: 367 106.99 - 113.75: 29829 113.75 - 120.51: 9446 120.51 - 127.27: 6808 127.27 - 134.03: 136 Bond angle restraints: 46586 Sorted by residual: angle pdb=" CA THR B 947 " pdb=" C THR B 947 " pdb=" O THR B 947 " ideal model delta sigma weight residual 120.24 114.61 5.63 1.11e+00 8.12e-01 2.57e+01 angle pdb=" CA THR A 947 " pdb=" C THR A 947 " pdb=" O THR A 947 " ideal model delta sigma weight residual 120.24 114.67 5.57 1.11e+00 8.12e-01 2.52e+01 angle pdb=" O12 3PE A1202 " pdb=" P 3PE A1202 " pdb=" O14 3PE A1202 " ideal model delta sigma weight residual 123.79 109.41 14.38 3.00e+00 1.11e-01 2.30e+01 angle pdb=" O12 3PE B1202 " pdb=" P 3PE B1202 " pdb=" O14 3PE B1202 " ideal model delta sigma weight residual 123.79 109.43 14.36 3.00e+00 1.11e-01 2.29e+01 angle pdb=" O12 3PE A1203 " pdb=" P 3PE A1203 " pdb=" O14 3PE A1203 " ideal model delta sigma weight residual 123.79 109.61 14.18 3.00e+00 1.11e-01 2.23e+01 ... (remaining 46581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 11726 17.80 - 35.61: 482 35.61 - 53.41: 175 53.41 - 71.21: 57 71.21 - 89.02: 12 Dihedral angle restraints: 12452 sinusoidal: 6612 harmonic: 5840 Sorted by residual: dihedral pdb=" CA ASN A 443 " pdb=" CB ASN A 443 " pdb=" CG ASN A 443 " pdb=" OD1 ASN A 443 " ideal model delta sinusoidal sigma weight residual 120.00 -167.71 -72.29 2 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA ASN B 443 " pdb=" CB ASN B 443 " pdb=" CG ASN B 443 " pdb=" OD1 ASN B 443 " ideal model delta sinusoidal sigma weight residual 120.00 -167.71 -72.29 2 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" O21 3PE B1202 " pdb=" C2 3PE B1202 " pdb=" C3 3PE B1202 " pdb=" O31 3PE B1202 " ideal model delta sinusoidal sigma weight residual 60.47 -23.69 84.16 1 3.00e+01 1.11e-03 9.58e+00 ... (remaining 12449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1364 0.030 - 0.060: 388 0.060 - 0.090: 144 0.090 - 0.119: 73 0.119 - 0.149: 21 Chirality restraints: 1990 Sorted by residual: chirality pdb=" C2 3PE B1204 " pdb=" C1 3PE B1204 " pdb=" C3 3PE B1204 " pdb=" O21 3PE B1204 " both_signs ideal model delta sigma weight residual False -2.53 -2.38 -0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" C2 3PE A1204 " pdb=" C1 3PE A1204 " pdb=" C3 3PE A1204 " pdb=" O21 3PE A1204 " both_signs ideal model delta sigma weight residual False -2.53 -2.38 -0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA ILE B 306 " pdb=" N ILE B 306 " pdb=" C ILE B 306 " pdb=" CB ILE B 306 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 1987 not shown) Planarity restraints: 3794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 945 " 0.011 2.00e-02 2.50e+03 1.98e-02 3.91e+00 pdb=" N GLU A 946 " -0.034 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 B 945 " 0.011 2.00e-02 2.50e+03 1.94e-02 3.75e+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 943 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+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 3791 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 1716 2.22 - 2.82: 54392 2.82 - 3.41: 67275 3.41 - 4.01: 89729 4.01 - 4.60: 142327 Nonbonded interactions: 355439 Sorted by model distance: nonbonded pdb=" O GLY A 593 " pdb=" HG SER A 597 " model vdw 1.629 1.850 nonbonded pdb=" O GLY B 593 " pdb=" HG SER B 597 " model vdw 1.630 1.850 nonbonded pdb=" OE1 GLU B 341 " pdb=" HG SER B 353 " model vdw 1.640 1.850 nonbonded pdb=" OE1 GLU A 341 " pdb=" HG SER A 353 " model vdw 1.641 1.850 nonbonded pdb=" O GLY A 453 " pdb=" H ASP A 457 " model vdw 1.677 1.850 ... (remaining 355434 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' } 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: 0.490 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: 0.400 Extract box with map and model: 3.580 Check model and map are aligned: 0.400 Set scattering table: 0.270 Process input model: 82.180 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 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 : 0.004 0.088 13414 Z= 0.255 Angle : 0.752 14.381 18120 Z= 0.321 Chirality : 0.039 0.149 1990 Planarity : 0.002 0.022 2250 Dihedral : 11.528 89.015 4950 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.15 % Allowed : 1.62 % Favored : 98.23 % 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: 1588 helix: 2.60 (0.18), residues: 828 sheet: 0.96 (0.45), residues: 144 loop : -0.74 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 933 HIS 0.003 0.001 HIS B 679 PHE 0.012 0.001 PHE A 984 TYR 0.009 0.001 TYR A 731 ARG 0.004 0.001 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 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 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 LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 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 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 LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 185 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.6569 (mt0) cc_final: 0.6071 (mm110) REVERT: A 440 LYS cc_start: 0.8906 (mttt) cc_final: 0.8620 (mttp) REVERT: B 149 GLN cc_start: 0.6654 (mt0) cc_final: 0.6132 (mm110) REVERT: B 440 LYS cc_start: 0.8902 (mttt) cc_final: 0.8619 (mttp) REVERT: B 480 LYS cc_start: 0.8348 (tttp) cc_final: 0.8136 (tptp) outliers start: 2 outliers final: 0 residues processed: 187 average time/residue: 2.1985 time to fit residues: 456.9743 Evaluate side-chains 111 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN B 429 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13414 Z= 0.278 Angle : 0.488 5.070 18120 Z= 0.251 Chirality : 0.039 0.150 1990 Planarity : 0.003 0.025 2250 Dihedral : 10.439 97.841 2042 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.03 % Allowed : 7.22 % Favored : 91.75 % 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: 1.71 (0.21), residues: 1588 helix: 2.41 (0.18), residues: 838 sheet: 0.82 (0.44), residues: 144 loop : -0.66 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 933 HIS 0.005 0.001 HIS B 679 PHE 0.015 0.001 PHE A 984 TYR 0.009 0.001 TYR B 731 ARG 0.005 0.001 ARG A 644 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 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 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 LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 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 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 LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.6926 (mt0) cc_final: 0.6188 (mm110) REVERT: A 604 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7408 (p0) REVERT: B 149 GLN cc_start: 0.6931 (mt0) cc_final: 0.6184 (mm110) REVERT: B 391 ARG cc_start: 0.8208 (mtp85) cc_final: 0.8007 (mtp85) REVERT: B 480 LYS cc_start: 0.8365 (tttp) cc_final: 0.8143 (tptp) outliers start: 14 outliers final: 9 residues processed: 135 average time/residue: 1.7614 time to fit residues: 272.3161 Evaluate side-chains 116 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 502 ARG Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 502 ARG Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain B residue 779 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 0.0770 chunk 45 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- 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: 0.8140 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13414 Z= 0.162 Angle : 0.411 4.916 18120 Z= 0.216 Chirality : 0.037 0.143 1990 Planarity : 0.002 0.023 2250 Dihedral : 9.777 92.818 2042 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.88 % Allowed : 8.76 % Favored : 90.35 % 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: 1588 helix: 2.55 (0.18), residues: 836 sheet: 0.92 (0.44), residues: 144 loop : -0.62 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 976 HIS 0.003 0.001 HIS A 679 PHE 0.011 0.001 PHE A 984 TYR 0.007 0.001 TYR B 731 ARG 0.002 0.000 ARG B 446 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 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 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 LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 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 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 LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.6890 (mt0) cc_final: 0.6124 (mm110) REVERT: A 502 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.6722 (mtm180) REVERT: A 604 ASP cc_start: 0.7714 (m-30) cc_final: 0.7456 (p0) REVERT: B 149 GLN cc_start: 0.6950 (mt0) cc_final: 0.6178 (mm110) REVERT: B 480 LYS cc_start: 0.8348 (tttp) cc_final: 0.8140 (tptp) REVERT: B 502 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.6735 (mtm180) REVERT: B 604 ASP cc_start: 0.7720 (m-30) cc_final: 0.7470 (p0) REVERT: B 775 MET cc_start: 0.7870 (mtm) cc_final: 0.7601 (mtp) outliers start: 12 outliers final: 8 residues processed: 125 average time/residue: 1.9582 time to fit residues: 277.7497 Evaluate side-chains 121 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 502 ARG Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 502 ARG Chi-restraints excluded: chain B residue 632 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 ASN B 598 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13414 Z= 0.408 Angle : 0.509 4.601 18120 Z= 0.271 Chirality : 0.041 0.169 1990 Planarity : 0.004 0.035 2250 Dihedral : 10.762 89.987 2042 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.84 % Favored : 96.03 % Rotamer: Outliers : 1.33 % Allowed : 8.47 % Favored : 90.21 % 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: 1.39 (0.21), residues: 1588 helix: 2.18 (0.18), residues: 824 sheet: 0.58 (0.42), residues: 150 loop : -0.76 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 693 HIS 0.005 0.001 HIS B 679 PHE 0.023 0.002 PHE B 984 TYR 0.011 0.002 TYR B 511 ARG 0.004 0.001 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 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 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 LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 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 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 LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.6931 (mt0) cc_final: 0.6200 (mm110) REVERT: A 604 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7484 (p0) REVERT: A 775 MET cc_start: 0.8154 (mtm) cc_final: 0.7773 (mtp) REVERT: B 149 GLN cc_start: 0.6898 (mt0) cc_final: 0.6172 (mm110) REVERT: B 604 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7477 (p0) REVERT: B 775 MET cc_start: 0.7995 (mtm) cc_final: 0.7694 (mtp) outliers start: 18 outliers final: 6 residues processed: 125 average time/residue: 1.9301 time to fit residues: 273.6619 Evaluate side-chains 103 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain B residue 632 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 131 optimal weight: 0.3980 chunk 106 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 951 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13414 Z= 0.201 Angle : 0.427 4.179 18120 Z= 0.227 Chirality : 0.038 0.147 1990 Planarity : 0.003 0.026 2250 Dihedral : 10.347 88.857 2042 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.39 % Favored : 97.48 % Rotamer: Outliers : 0.88 % Allowed : 9.28 % Favored : 89.84 % 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: 1.54 (0.21), residues: 1588 helix: 2.32 (0.18), residues: 824 sheet: 0.79 (0.43), residues: 148 loop : -0.76 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 976 HIS 0.004 0.001 HIS A 679 PHE 0.013 0.001 PHE A 984 TYR 0.007 0.001 TYR A 731 ARG 0.003 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 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 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 LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 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 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 LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.6925 (mt0) cc_final: 0.6203 (mm110) REVERT: A 775 MET cc_start: 0.8176 (mtm) cc_final: 0.7775 (mtp) REVERT: B 149 GLN cc_start: 0.6925 (mt0) cc_final: 0.6201 (mm110) REVERT: B 775 MET cc_start: 0.8047 (mtm) cc_final: 0.7781 (mtp) outliers start: 12 outliers final: 7 residues processed: 110 average time/residue: 1.9440 time to fit residues: 243.6765 Evaluate side-chains 100 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 779 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 0.0670 chunk 38 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- 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: 0.8206 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13414 Z= 0.238 Angle : 0.430 4.304 18120 Z= 0.228 Chirality : 0.038 0.146 1990 Planarity : 0.003 0.027 2250 Dihedral : 10.351 86.537 2042 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.53 % Favored : 96.35 % Rotamer: Outliers : 0.88 % Allowed : 9.35 % Favored : 89.76 % 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: 1.63 (0.21), residues: 1588 helix: 2.37 (0.18), residues: 820 sheet: 0.80 (0.43), residues: 148 loop : -0.65 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 976 HIS 0.004 0.001 HIS A 679 PHE 0.014 0.001 PHE B 984 TYR 0.009 0.001 TYR B 511 ARG 0.003 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 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 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 LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 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 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 LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.6997 (mt0) cc_final: 0.6333 (mm110) REVERT: A 775 MET cc_start: 0.8178 (mtm) cc_final: 0.7735 (mtp) REVERT: B 149 GLN cc_start: 0.6917 (mt0) cc_final: 0.6249 (mm110) REVERT: B 775 MET cc_start: 0.8067 (mtm) cc_final: 0.7758 (mtp) outliers start: 12 outliers final: 11 residues processed: 109 average time/residue: 1.9550 time to fit residues: 241.9721 Evaluate side-chains 107 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 779 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 86 optimal weight: 0.0030 chunk 154 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- 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: 0.8200 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13414 Z= 0.204 Angle : 0.416 4.198 18120 Z= 0.221 Chirality : 0.037 0.145 1990 Planarity : 0.003 0.029 2250 Dihedral : 10.289 84.418 2042 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.71 % Favored : 97.17 % Rotamer: Outliers : 0.81 % Allowed : 9.28 % Favored : 89.91 % 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: 1.69 (0.21), residues: 1588 helix: 2.40 (0.18), residues: 822 sheet: 0.83 (0.43), residues: 148 loop : -0.61 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 976 HIS 0.004 0.001 HIS B 679 PHE 0.013 0.001 PHE A 984 TYR 0.008 0.001 TYR B 511 ARG 0.003 0.000 ARG B 446 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 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 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 LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 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 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 LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.7003 (mt0) cc_final: 0.6350 (mm110) REVERT: A 775 MET cc_start: 0.8200 (mtm) cc_final: 0.7828 (mtp) REVERT: B 149 GLN cc_start: 0.7009 (mt0) cc_final: 0.6336 (mm110) REVERT: B 775 MET cc_start: 0.8054 (mtm) cc_final: 0.7721 (mtp) outliers start: 11 outliers final: 11 residues processed: 109 average time/residue: 1.9768 time to fit residues: 244.7907 Evaluate side-chains 106 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 779 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 13414 Z= 0.370 Angle : 0.492 4.496 18120 Z= 0.262 Chirality : 0.040 0.151 1990 Planarity : 0.003 0.035 2250 Dihedral : 11.248 82.011 2042 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.09 % Favored : 95.78 % Rotamer: Outliers : 1.03 % Allowed : 9.20 % Favored : 89.76 % 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: 1.39 (0.21), residues: 1588 helix: 2.12 (0.18), residues: 818 sheet: 0.66 (0.42), residues: 146 loop : -0.64 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 693 HIS 0.006 0.001 HIS A 679 PHE 0.021 0.002 PHE B 984 TYR 0.012 0.002 TYR B 511 ARG 0.004 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 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 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 LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 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 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 LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.7074 (mt0) cc_final: 0.6501 (mm110) REVERT: A 775 MET cc_start: 0.8204 (mtm) cc_final: 0.7828 (mtp) REVERT: B 149 GLN cc_start: 0.7067 (mt0) cc_final: 0.6496 (mm110) REVERT: B 775 MET cc_start: 0.8100 (mtm) cc_final: 0.7659 (mtp) outliers start: 14 outliers final: 14 residues processed: 106 average time/residue: 2.1015 time to fit residues: 255.7726 Evaluate side-chains 105 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 779 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 2.9990 chunk 147 optimal weight: 0.0270 chunk 134 optimal weight: 0.5980 chunk 143 optimal weight: 0.9990 chunk 86 optimal weight: 0.2980 chunk 62 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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: 0.8180 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13414 Z= 0.120 Angle : 0.403 4.194 18120 Z= 0.213 Chirality : 0.037 0.130 1990 Planarity : 0.003 0.029 2250 Dihedral : 10.272 81.705 2042 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.20 % Favored : 97.67 % Rotamer: Outliers : 0.59 % Allowed : 9.79 % Favored : 89.62 % 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: 1.72 (0.21), residues: 1588 helix: 2.45 (0.18), residues: 822 sheet: 0.83 (0.44), residues: 148 loop : -0.62 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 976 HIS 0.002 0.000 HIS B 679 PHE 0.009 0.001 PHE B 984 TYR 0.008 0.001 TYR A 476 ARG 0.002 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 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 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 LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 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 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 LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.7050 (mt0) cc_final: 0.6475 (mm110) REVERT: A 775 MET cc_start: 0.8184 (mtm) cc_final: 0.7806 (mtp) REVERT: B 149 GLN cc_start: 0.7015 (mt0) cc_final: 0.6342 (mm110) REVERT: B 775 MET cc_start: 0.8035 (mtm) cc_final: 0.7675 (mtp) outliers start: 8 outliers final: 8 residues processed: 107 average time/residue: 1.9794 time to fit residues: 240.7536 Evaluate side-chains 102 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 496 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 126 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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: 0.8217 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13414 Z= 0.265 Angle : 0.449 4.538 18120 Z= 0.236 Chirality : 0.038 0.131 1990 Planarity : 0.003 0.027 2250 Dihedral : 10.501 76.672 2042 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.53 % Favored : 96.35 % Rotamer: Outliers : 0.59 % Allowed : 10.01 % Favored : 89.40 % 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: 1.65 (0.21), residues: 1588 helix: 2.39 (0.18), residues: 820 sheet: 0.80 (0.43), residues: 148 loop : -0.62 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 933 HIS 0.004 0.001 HIS A 679 PHE 0.013 0.001 PHE A 984 TYR 0.010 0.001 TYR B 511 ARG 0.003 0.000 ARG B 446 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 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 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 LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 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 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 LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.7086 (mt0) cc_final: 0.6369 (mm110) REVERT: A 775 MET cc_start: 0.8211 (mtm) cc_final: 0.7827 (mtp) REVERT: B 149 GLN cc_start: 0.7047 (mt0) cc_final: 0.6365 (mm110) REVERT: B 775 MET cc_start: 0.8071 (mtm) cc_final: 0.7763 (mtp) outliers start: 8 outliers final: 8 residues processed: 99 average time/residue: 2.0084 time to fit residues: 224.4967 Evaluate side-chains 101 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 496 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 117 optimal weight: 0.0050 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.133188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.089328 restraints weight = 43477.309| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.15 r_work: 0.2883 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13414 Z= 0.165 Angle : 0.414 4.146 18120 Z= 0.218 Chirality : 0.037 0.127 1990 Planarity : 0.003 0.028 2250 Dihedral : 10.126 79.571 2042 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.46 % Favored : 96.41 % Rotamer: Outliers : 0.59 % Allowed : 9.79 % Favored : 89.62 % 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: 1.76 (0.21), residues: 1588 helix: 2.48 (0.18), residues: 820 sheet: 0.84 (0.43), residues: 148 loop : -0.58 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 976 HIS 0.003 0.001 HIS B 679 PHE 0.011 0.001 PHE A 984 TYR 0.007 0.001 TYR A 731 ARG 0.002 0.000 ARG A 446 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6575.46 seconds wall clock time: 116 minutes 5.00 seconds (6965.00 seconds total)