Starting phenix.real_space_refine (version: dev) on Sat Feb 25 17:54:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stl_25432/02_2023/7stl_25432_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stl_25432/02_2023/7stl_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_25432/02_2023/7stl_25432.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stl_25432/02_2023/7stl_25432.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stl_25432/02_2023/7stl_25432_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stl_25432/02_2023/7stl_25432_trim_updated.pdb" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 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-4877/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: 11.68, 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: 21.64 Conformation dependent library (CDL) restraints added in 2.0 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: 1.99 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: 9.57 Time building geometry restraints manager: 22.18 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: 10200 17.80 - 35.61: 362 35.61 - 53.41: 68 53.41 - 71.21: 12 71.21 - 89.02: 4 Dihedral angle restraints: 10646 sinusoidal: 4806 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=" 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 -111.24 51.24 3 1.50e+01 4.44e-03 8.99e+00 ... (remaining 10643 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 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. 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: 0.420 Extract box with map and model: 4.190 Check model and map are aligned: 0.370 Process input model: 79.390 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.230 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:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 : 10.313 89.015 4854 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 % 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 *********************** 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 : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 187 average time/residue: 2.2874 time to fit residues: 474.9835 Evaluate side-chains 108 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.017 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6107 ------------------------------------------------------------------------------- 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: 10.0000 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: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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: 0.8340 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 13414 Z= 0.310 Angle : 0.498 4.513 18120 Z= 0.258 Chirality : 0.039 0.148 1990 Planarity : 0.003 0.023 2250 Dihedral : 7.773 56.553 1946 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 0.96 % 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: 1.67 (0.21), residues: 1588 helix: 2.38 (0.18), residues: 838 sheet: 0.81 (0.44), residues: 144 loop : -0.68 (0.24), residues: 606 *********************** 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 140 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 137 average time/residue: 1.9566 time to fit residues: 304.4017 Evaluate side-chains 112 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 2.329 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 3.9292 time to fit residues: 6.9032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN B 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 13414 Z= 0.223 Angle : 0.434 5.350 18120 Z= 0.228 Chirality : 0.038 0.146 1990 Planarity : 0.002 0.019 2250 Dihedral : 7.288 53.480 1946 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.27 % Favored : 97.61 % Rotamer Outliers : 1.03 % 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: 1.68 (0.21), residues: 1588 helix: 2.40 (0.18), residues: 836 sheet: 0.89 (0.44), residues: 144 loop : -0.70 (0.23), residues: 608 *********************** 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 128 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 122 average time/residue: 1.8873 time to fit residues: 263.7567 Evaluate side-chains 116 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 2.096 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.3081 time to fit residues: 3.7612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 138 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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: 0.8396 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 13414 Z= 0.335 Angle : 0.486 6.685 18120 Z= 0.257 Chirality : 0.040 0.193 1990 Planarity : 0.003 0.030 2250 Dihedral : 8.245 56.258 1946 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.53 % Favored : 96.35 % Rotamer Outliers : 1.33 % 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: 1.44 (0.21), residues: 1588 helix: 2.22 (0.18), residues: 822 sheet: 0.65 (0.43), residues: 150 loop : -0.73 (0.22), residues: 616 *********************** 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 121 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 121 average time/residue: 1.9336 time to fit residues: 267.0714 Evaluate side-chains 102 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 1.843 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 2.3693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 115 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 951 ASN B 951 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 13414 Z= 0.314 Angle : 0.471 5.358 18120 Z= 0.250 Chirality : 0.039 0.152 1990 Planarity : 0.003 0.028 2250 Dihedral : 8.556 59.342 1946 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.64 % Favored : 97.23 % Rotamer Outliers : 1.03 % 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: 1.42 (0.21), residues: 1588 helix: 2.18 (0.18), residues: 822 sheet: 0.76 (0.43), residues: 148 loop : -0.74 (0.22), residues: 618 *********************** 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 111 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 108 average time/residue: 2.0079 time to fit residues: 246.1916 Evaluate side-chains 101 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 2.025 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.2654 time to fit residues: 3.5705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 0.0170 chunk 38 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN B 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2503 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= 0.168 Angle : 0.416 5.099 18120 Z= 0.219 Chirality : 0.037 0.145 1990 Planarity : 0.002 0.025 2250 Dihedral : 8.077 59.935 1946 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.09 % Favored : 96.79 % Rotamer Outliers : 1.18 % 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: 1.67 (0.21), residues: 1588 helix: 2.42 (0.18), residues: 822 sheet: 0.82 (0.43), residues: 148 loop : -0.66 (0.23), residues: 618 *********************** 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 113 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 111 average time/residue: 2.0242 time to fit residues: 255.2612 Evaluate side-chains 100 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 2.224 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 1.8589 time to fit residues: 4.9148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 154 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN B 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 13414 Z= 0.271 Angle : 0.446 5.279 18120 Z= 0.235 Chirality : 0.038 0.148 1990 Planarity : 0.003 0.025 2250 Dihedral : 8.445 57.557 1946 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.34 % Favored : 96.54 % Rotamer Outliers : 0.96 % 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: 1.57 (0.21), residues: 1588 helix: 2.31 (0.18), residues: 822 sheet: 0.78 (0.43), residues: 148 loop : -0.66 (0.23), residues: 618 *********************** 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 107 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 102 average time/residue: 2.1110 time to fit residues: 244.6046 Evaluate side-chains 98 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 2.115 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.3063 time to fit residues: 3.8130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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: 0.8414 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 13414 Z= 0.316 Angle : 0.470 5.163 18120 Z= 0.248 Chirality : 0.039 0.148 1990 Planarity : 0.003 0.029 2250 Dihedral : 8.826 57.017 1946 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.90 % Favored : 95.97 % Rotamer Outliers : 0.66 % 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: 1.47 (0.21), residues: 1588 helix: 2.18 (0.18), residues: 822 sheet: 0.82 (0.43), residues: 148 loop : -0.67 (0.23), residues: 618 *********************** 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 99 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 98 average time/residue: 2.0903 time to fit residues: 232.2336 Evaluate side-chains 93 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 1.997 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 2.7087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 134 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.8385 moved from start: 0.2770 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= 0.147 Angle : 0.414 4.690 18120 Z= 0.218 Chirality : 0.037 0.129 1990 Planarity : 0.002 0.026 2250 Dihedral : 8.308 58.779 1946 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.77 % Favored : 97.10 % Rotamer Outliers : 0.52 % 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: 0.87 (0.43), residues: 148 loop : -0.60 (0.23), residues: 618 *********************** 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 101 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 100 average time/residue: 2.0594 time to fit residues: 233.1708 Evaluate side-chains 96 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 2.106 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 2.8333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.0770 chunk 92 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.9344 ------------------------------------------------------------------------------- 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: 0.8374 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 13414 Z= 0.148 Angle : 0.405 4.566 18120 Z= 0.212 Chirality : 0.037 0.128 1990 Planarity : 0.002 0.028 2250 Dihedral : 7.735 59.695 1946 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.27 % Favored : 96.60 % Rotamer Outliers : 0.59 % 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: 1.80 (0.21), residues: 1588 helix: 2.50 (0.18), residues: 824 sheet: 0.86 (0.43), residues: 148 loop : -0.57 (0.23), residues: 616 ********************** 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 106 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 106 average time/residue: 1.9601 time to fit residues: 237.7062 Evaluate side-chains 98 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 2.268 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 2.7372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 111 optimal weight: 0.4980 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.137234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.093721 restraints weight = 44123.178| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.45 r_work: 0.2861 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 13414 Z= 0.242 Angle : 0.440 4.786 18120 Z= 0.231 Chirality : 0.038 0.131 1990 Planarity : 0.003 0.027 2250 Dihedral : 8.137 59.371 1946 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.53 % Favored : 96.35 % Rotamer Outliers : 0.59 % 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: 2.38 (0.18), residues: 824 sheet: 0.82 (0.42), residues: 148 loop : -0.64 (0.23), residues: 616 =============================================================================== Job complete usr+sys time: 6350.96 seconds wall clock time: 113 minutes 28.07 seconds (6808.07 seconds total)