Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 14:07:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sto_25435/04_2023/7sto_25435_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sto_25435/04_2023/7sto_25435.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sto_25435/04_2023/7sto_25435_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sto_25435/04_2023/7sto_25435_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sto_25435/04_2023/7sto_25435_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sto_25435/04_2023/7sto_25435.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sto_25435/04_2023/7sto_25435.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sto_25435/04_2023/7sto_25435_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sto_25435/04_2023/7sto_25435_trim_updated.pdb" } resolution = 3.15 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= 0.002 sd= 0.009 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 8478 2.51 5 N 2064 2.21 5 O 2336 1.98 5 H 12268 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-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 25210 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 12410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 12410 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 24, 'TRANS': 765} Chain breaks: 3 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 56 Chain: "A" Number of atoms: 12410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 12410 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 24, 'TRANS': 765} Chain breaks: 3 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 158 Unusual residues: {'3PE': 3, 'BJ9': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "A" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 232 Unusual residues: {'3PE': 5, 'BJ9': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 59 Time building chain proxies: 11.36, per 1000 atoms: 0.45 Number of scatterers: 25210 At special positions: 0 Unit cell: (93.96, 126.36, 119.88, 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 2336 8.00 N 2064 7.00 C 8478 6.00 H 12268 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: 21.61 Conformation dependent library (CDL) restraints added in 2.2 seconds 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 6 sheets defined 53.3% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'B' and resid 147 through 154 removed outlier: 3.571A pdb=" N ARG B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 255 through 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: 3.730A 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: 4.791A 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: 4.044A pdb=" N GLY B 565 " --> pdb=" O LYS B 561 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLU B 566 " --> pdb=" O TYR B 562 " (cutoff:3.500A) removed outlier: 3.768A 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: 4.071A pdb=" N ARG B 646 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP B 647 " --> pdb=" O GLN B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 665 removed outlier: 3.519A 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: 3.581A pdb=" N LEU B 710 " --> pdb=" O LEU B 706 " (cutoff:3.500A) removed outlier: 3.793A 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 removed outlier: 3.862A pdb=" N SER B 786 " --> pdb=" O ASP B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 797 Processing helix chain 'B' and resid 799 through 821 removed outlier: 3.948A pdb=" N ALA B 807 " --> pdb=" O ASP B 803 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 830 removed outlier: 4.114A 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: 3.821A pdb=" N LEU B 846 " --> pdb=" O TYR B 842 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN B 847 " --> pdb=" O VAL B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 903 Processing helix chain 'B' and resid 919 through 945 Processing helix chain 'B' and resid 950 through 953 Processing helix chain 'B' and resid 958 through 1001 Processing helix chain 'A' and resid 147 through 154 removed outlier: 3.571A pdb=" N ARG A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 255 through 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: 3.730A 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: 4.791A 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: 4.043A pdb=" N GLY A 565 " --> pdb=" O LYS A 561 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLU A 566 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 3.768A 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: 4.071A pdb=" N ARG A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP A 647 " --> pdb=" O GLN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 665 removed outlier: 3.519A 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: 3.581A pdb=" N LEU A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) removed outlier: 3.793A 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 removed outlier: 3.862A pdb=" N SER A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 797 Processing helix chain 'A' and resid 799 through 821 removed outlier: 3.948A pdb=" N ALA A 807 " --> pdb=" O ASP A 803 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 830 removed outlier: 4.113A 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: 3.821A pdb=" N LEU A 846 " --> pdb=" O TYR A 842 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN A 847 " --> pdb=" O VAL A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 903 Processing helix chain 'A' and resid 919 through 945 Processing helix chain 'A' and resid 950 through 953 Processing helix chain 'A' and resid 958 through 1001 Processing sheet with id= A, first strand: chain 'B' and resid 248 through 252 removed outlier: 7.885A pdb=" N PHE B 279 " --> pdb=" O THR B 405 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N THR B 405 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLN B 429 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU B 312 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N CYS B 360 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE B 314 " --> pdb=" O CYS B 360 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL B 362 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE B 316 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL B 462 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N THR B 317 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU B 464 " --> pdb=" O THR B 317 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU B 620 " --> pdb=" O ALA B 489 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA B 491 " --> pdb=" O LEU B 620 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG B 622 " --> pdb=" O ALA B 491 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 494 through 497 Processing sheet with id= C, first strand: chain 'B' and resid 409 through 413 removed outlier: 7.174A pdb=" N LYS B 419 " --> pdb=" O SER B 411 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 248 through 252 removed outlier: 7.885A pdb=" N PHE A 279 " --> pdb=" O THR A 405 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N THR A 405 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLN A 429 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU A 312 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N CYS A 360 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE A 314 " --> pdb=" O CYS A 360 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL A 362 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE A 316 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL A 462 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N THR A 317 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU A 464 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU A 620 " --> pdb=" O ALA A 489 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA A 491 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG A 622 " --> pdb=" O ALA A 491 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 494 through 497 Processing sheet with id= F, first strand: chain 'A' and resid 409 through 413 removed outlier: 7.173A pdb=" N LYS A 419 " --> pdb=" O SER A 411 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1812 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: 9.38 Time building geometry restraints manager: 21.65 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: 12244 1.03 - 1.22: 48 1.22 - 1.42: 5650 1.42 - 1.61: 7472 1.61 - 1.81: 104 Bond restraints: 25518 Sorted by residual: bond pdb=" C11 BJ9 B1204 " pdb=" C12 BJ9 B1204 " ideal model delta sigma weight residual 1.348 1.537 -0.189 2.00e-02 2.50e+03 8.90e+01 bond pdb=" C11 BJ9 A1205 " pdb=" C12 BJ9 A1205 " ideal model delta sigma weight residual 1.348 1.536 -0.188 2.00e-02 2.50e+03 8.86e+01 bond pdb=" C12 BJ9 B1204 " pdb=" O13 BJ9 B1204 " ideal model delta sigma weight residual 1.604 1.440 0.164 2.00e-02 2.50e+03 6.71e+01 bond pdb=" C12 BJ9 A1205 " pdb=" O13 BJ9 A1205 " ideal model delta sigma weight residual 1.604 1.441 0.163 2.00e-02 2.50e+03 6.68e+01 bond pdb=" C11 BJ9 A1205 " pdb=" O32 BJ9 A1205 " ideal model delta sigma weight residual 1.486 1.329 0.157 2.00e-02 2.50e+03 6.15e+01 ... (remaining 25513 not shown) Histogram of bond angle deviations from ideal: 100.27 - 107.03: 383 107.03 - 113.79: 29200 113.79 - 120.55: 9450 120.55 - 127.30: 6525 127.30 - 134.06: 130 Bond angle restraints: 45688 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 120.24 114.36 5.88 1.11e+00 8.12e-01 2.81e+01 angle pdb=" CA THR A 947 " pdb=" C THR A 947 " pdb=" O THR A 947 " ideal model delta sigma weight residual 120.24 114.39 5.85 1.11e+00 8.12e-01 2.78e+01 angle pdb=" O12 3PE B1202 " pdb=" P 3PE B1202 " pdb=" O14 3PE B1202 " ideal model delta sigma weight residual 123.79 109.61 14.18 3.00e+00 1.11e-01 2.23e+01 angle pdb=" O12 3PE A1202 " pdb=" P 3PE A1202 " pdb=" O14 3PE A1202 " ideal model delta sigma weight residual 123.79 109.66 14.13 3.00e+00 1.11e-01 2.22e+01 angle pdb=" O12 3PE A1204 " pdb=" P 3PE A1204 " pdb=" O14 3PE A1204 " ideal model delta sigma weight residual 123.79 109.71 14.08 3.00e+00 1.11e-01 2.20e+01 ... (remaining 45683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 10023 17.82 - 35.64: 337 35.64 - 53.46: 64 53.46 - 71.28: 12 71.28 - 89.10: 4 Dihedral angle restraints: 10440 sinusoidal: 4678 harmonic: 5762 Sorted by residual: 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 -111.35 51.35 3 1.50e+01 4.44e-03 9.00e+00 dihedral pdb=" N TYR B 699 " pdb=" CA TYR B 699 " pdb=" CB TYR B 699 " pdb=" CG TYR B 699 " ideal model delta sinusoidal sigma weight residual -60.00 -111.35 51.35 3 1.50e+01 4.44e-03 9.00e+00 dihedral pdb=" CA ARG B 999 " pdb=" CB ARG B 999 " pdb=" CG ARG B 999 " pdb=" CD ARG B 999 " ideal model delta sinusoidal sigma weight residual 180.00 129.94 50.06 3 1.50e+01 4.44e-03 8.85e+00 ... (remaining 10437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1598 0.048 - 0.096: 286 0.096 - 0.144: 84 0.144 - 0.191: 2 0.191 - 0.239: 4 Chirality restraints: 1974 Sorted by residual: chirality pdb=" CA ILE B 790 " pdb=" N ILE B 790 " pdb=" C ILE B 790 " pdb=" CB ILE B 790 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ILE A 790 " pdb=" N ILE A 790 " pdb=" C ILE A 790 " pdb=" CB ILE A 790 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C10 BJ9 B1204 " pdb=" C09 BJ9 B1204 " pdb=" C11 BJ9 B1204 " pdb=" O33 BJ9 B1204 " both_signs ideal model delta sigma weight residual False -2.55 -2.78 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1971 not shown) Planarity restraints: 3742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 785 " -0.014 2.00e-02 2.50e+03 2.63e-02 6.93e+00 pdb=" N SER A 786 " 0.045 2.00e-02 2.50e+03 pdb=" CA SER A 786 " -0.012 2.00e-02 2.50e+03 pdb=" H SER A 786 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 785 " 0.014 2.00e-02 2.50e+03 2.62e-02 6.88e+00 pdb=" N SER B 786 " -0.045 2.00e-02 2.50e+03 pdb=" CA SER B 786 " 0.012 2.00e-02 2.50e+03 pdb=" H SER B 786 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 788 " 0.011 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" N ARG B 789 " -0.034 2.00e-02 2.50e+03 pdb=" CA ARG B 789 " 0.009 2.00e-02 2.50e+03 pdb=" H ARG B 789 " 0.014 2.00e-02 2.50e+03 ... (remaining 3739 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 1620 2.23 - 2.82: 53339 2.82 - 3.41: 65246 3.41 - 4.01: 87712 4.01 - 4.60: 139131 Nonbonded interactions: 347048 Sorted by model distance: nonbonded pdb=" O GLY A 453 " pdb=" H ASP A 457 " model vdw 1.631 1.850 nonbonded pdb=" O GLY B 453 " pdb=" H ASP B 457 " model vdw 1.632 1.850 nonbonded pdb=" O TRP A 666 " pdb=" HZ3 LYS A 675 " model vdw 1.685 1.850 nonbonded pdb=" O TRP B 666 " pdb=" HZ3 LYS B 675 " model vdw 1.686 1.850 nonbonded pdb=" O GLU B 256 " pdb=" HG SER B 259 " model vdw 1.689 1.850 ... (remaining 347043 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 135 through 1002 or resid 1201 through 1203)) selection = (chain 'B' and (resid 135 through 1002 or resid 1201 through 1203)) } 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: 0.610 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: 0.390 Extract box with map and model: 4.750 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 79.420 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 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 : 0.007 0.189 13250 Z= 0.438 Angle : 0.818 14.180 17906 Z= 0.376 Chirality : 0.041 0.239 1974 Planarity : 0.003 0.023 2218 Dihedral : 10.395 89.104 4746 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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: 1.91 (0.21), residues: 1564 helix: 2.70 (0.18), residues: 816 sheet: 0.98 (0.46), residues: 140 loop : -0.73 (0.24), residues: 608 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 2.167 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 132 average time/residue: 0.5814 time to fit residues: 110.9044 Evaluate side-chains 69 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 2.239 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN A 244 ASN A 891 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 13250 Z= 0.154 Angle : 0.422 4.637 17906 Z= 0.218 Chirality : 0.037 0.154 1974 Planarity : 0.002 0.037 2218 Dihedral : 7.696 89.200 1924 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 0.30 % 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: 1.98 (0.22), residues: 1564 helix: 2.73 (0.18), residues: 832 sheet: 0.95 (0.46), residues: 140 loop : -0.73 (0.24), residues: 592 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 1.954 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 73 average time/residue: 0.4874 time to fit residues: 56.4599 Evaluate side-chains 65 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 2.072 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2536 time to fit residues: 3.5888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 0.0970 chunk 44 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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: 0.8143 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 13250 Z= 0.228 Angle : 0.445 5.366 17906 Z= 0.234 Chirality : 0.038 0.155 1974 Planarity : 0.003 0.030 2218 Dihedral : 8.249 85.800 1924 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 0.30 % 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: 1.85 (0.21), residues: 1564 helix: 2.59 (0.18), residues: 832 sheet: 0.96 (0.44), residues: 140 loop : -0.76 (0.24), residues: 592 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 2.300 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 66 average time/residue: 0.4555 time to fit residues: 49.5005 Evaluate side-chains 63 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 2.122 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2931 time to fit residues: 4.5977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 3.9990 chunk 108 optimal weight: 0.0670 chunk 74 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.5924 ------------------------------------------------------------------------------- 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: 0.8183 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 13250 Z= 0.227 Angle : 0.435 4.731 17906 Z= 0.231 Chirality : 0.038 0.149 1974 Planarity : 0.003 0.025 2218 Dihedral : 8.194 82.754 1924 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.88 % Favored : 96.99 % Rotamer Outliers : 0.38 % 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: 1.77 (0.21), residues: 1564 helix: 2.53 (0.18), residues: 832 sheet: 0.92 (0.43), residues: 140 loop : -0.81 (0.24), residues: 592 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 64 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 2.138 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 64 average time/residue: 0.4687 time to fit residues: 51.5677 Evaluate side-chains 57 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 2.303 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2458 time to fit residues: 3.9877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN B 797 GLN A 244 ASN A 797 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 13250 Z= 0.258 Angle : 0.436 4.642 17906 Z= 0.233 Chirality : 0.038 0.151 1974 Planarity : 0.003 0.024 2218 Dihedral : 8.281 81.080 1924 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.88 % Favored : 96.99 % 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: 1.75 (0.21), residues: 1564 helix: 2.51 (0.18), residues: 830 sheet: 0.87 (0.43), residues: 140 loop : -0.77 (0.24), residues: 594 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 2.275 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 61 average time/residue: 0.4386 time to fit residues: 44.4743 Evaluate side-chains 60 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 2.205 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2310 time to fit residues: 3.2593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 0.9980 chunk 137 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 303 HIS A 303 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 13250 Z= 0.274 Angle : 0.443 4.672 17906 Z= 0.237 Chirality : 0.038 0.151 1974 Planarity : 0.003 0.024 2218 Dihedral : 8.420 80.114 1924 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.07 % Favored : 96.80 % 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: 1.71 (0.21), residues: 1564 helix: 2.50 (0.18), residues: 818 sheet: 0.75 (0.44), residues: 144 loop : -0.74 (0.23), residues: 602 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 1.954 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 57 average time/residue: 0.4657 time to fit residues: 44.4201 Evaluate side-chains 55 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 2.303 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 9.9990 chunk 17 optimal weight: 0.4980 chunk 87 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 152 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 13250 Z= 0.226 Angle : 0.422 4.669 17906 Z= 0.225 Chirality : 0.038 0.147 1974 Planarity : 0.002 0.027 2218 Dihedral : 8.274 78.115 1924 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.32 % Favored : 96.55 % 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: 1.79 (0.21), residues: 1564 helix: 2.56 (0.18), residues: 818 sheet: 0.74 (0.45), residues: 144 loop : -0.69 (0.23), residues: 602 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 58 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 2.262 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 56 average time/residue: 0.4578 time to fit residues: 43.2476 Evaluate side-chains 55 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 2.216 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 13250 Z= 0.207 Angle : 0.416 5.021 17906 Z= 0.221 Chirality : 0.037 0.146 1974 Planarity : 0.002 0.026 2218 Dihedral : 8.236 77.290 1924 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.32 % Favored : 96.55 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.21), residues: 1564 helix: 2.61 (0.18), residues: 818 sheet: 0.74 (0.45), residues: 144 loop : -0.69 (0.23), residues: 602 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 57 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 2.317 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 57 average time/residue: 0.4326 time to fit residues: 41.5026 Evaluate side-chains 56 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 2.087 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2798 time to fit residues: 3.1448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 20.0000 chunk 133 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 150 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.8178 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 13250 Z= 0.119 Angle : 0.381 4.822 17906 Z= 0.201 Chirality : 0.037 0.140 1974 Planarity : 0.002 0.027 2218 Dihedral : 7.750 74.704 1924 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.88 % Favored : 96.99 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.22), residues: 1564 helix: 2.76 (0.18), residues: 822 sheet: 0.81 (0.45), residues: 144 loop : -0.65 (0.24), residues: 598 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 57 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 2.065 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.4563 time to fit residues: 43.7027 Evaluate side-chains 55 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 2.362 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 144 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN A 244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 13250 Z= 0.290 Angle : 0.443 4.645 17906 Z= 0.236 Chirality : 0.038 0.151 1974 Planarity : 0.003 0.025 2218 Dihedral : 8.399 77.829 1924 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.64 % Favored : 96.23 % Rotamer Outliers : 0.08 % 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: 1.81 (0.21), residues: 1564 helix: 2.61 (0.18), residues: 818 sheet: 0.62 (0.45), residues: 146 loop : -0.69 (0.23), residues: 600 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 2.161 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 60 average time/residue: 0.4333 time to fit residues: 43.7312 Evaluate side-chains 56 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 2.046 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2738 time to fit residues: 3.1470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.096823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.070603 restraints weight = 59763.331| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.97 r_work: 0.2768 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 13250 Z= 0.196 Angle : 0.409 4.560 17906 Z= 0.217 Chirality : 0.037 0.143 1974 Planarity : 0.002 0.026 2218 Dihedral : 8.281 76.708 1924 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.20 % Favored : 96.68 % Rotamer Outliers : 0.23 % 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: 1.88 (0.21), residues: 1564 helix: 2.67 (0.18), residues: 818 sheet: 0.72 (0.45), residues: 144 loop : -0.67 (0.23), residues: 602 =============================================================================== Job complete usr+sys time: 4105.40 seconds wall clock time: 74 minutes 17.13 seconds (4457.13 seconds total)