Starting phenix.real_space_refine on Wed Feb 14 02:34:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpc_16149/02_2024/8bpc_16149_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpc_16149/02_2024/8bpc_16149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpc_16149/02_2024/8bpc_16149.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpc_16149/02_2024/8bpc_16149.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpc_16149/02_2024/8bpc_16149_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpc_16149/02_2024/8bpc_16149_neut_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 Ca 2 9.91 5 Zn 3 6.06 5 S 55 5.16 5 C 5342 2.51 5 N 1449 2.21 5 O 1582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A GLU 477": "OE1" <-> "OE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A GLU 562": "OE1" <-> "OE2" Residue "A GLU 595": "OE1" <-> "OE2" Residue "A GLU 605": "OE1" <-> "OE2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A GLU 811": "OE1" <-> "OE2" Residue "A GLU 813": "OE1" <-> "OE2" Residue "A GLU 879": "OE1" <-> "OE2" Residue "A GLU 937": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B GLU 287": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "B GLU 358": "OE1" <-> "OE2" Residue "C GLU 302": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8433 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4405 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 17, 'TRANS': 518} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2956 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 368, 2956 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 351} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 113} Chain breaks: 1 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 22 Unusual residues: {' CA': 2, ' ZN': 1, 'SHH': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7745 SG CYS C 289 37.812 59.778 45.110 1.00 57.24 S ATOM 7771 SG CYS C 292 35.245 58.180 42.684 1.00 45.08 S ATOM 7954 SG CYS C 315 38.906 57.170 42.432 1.00 59.56 S ATOM 7629 SG CYS C 274 38.038 47.655 47.545 1.00 38.25 S ATOM 7653 SG CYS C 277 37.502 44.027 48.618 1.00 48.40 S ATOM 7837 SG CYS C 300 41.011 45.328 48.053 1.00 41.17 S Time building chain proxies: 4.81, per 1000 atoms: 0.57 Number of scatterers: 8433 At special positions: 0 Unit cell: (121.92, 93.472, 110.744, 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) Zn 3 29.99 Ca 2 19.99 S 55 16.00 O 1582 8.00 N 1449 7.00 C 5342 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" ND1 HIS B 179 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" NE2 HIS C 318 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 292 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 315 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 289 " pdb=" ZN C 402 " pdb="ZN ZN C 402 " - pdb=" ND1 HIS C 297 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 300 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 277 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 274 " Number of angles added : 6 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1950 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 5 sheets defined 53.3% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 305 through 318 Processing helix chain 'A' and resid 322 through 335 Processing helix chain 'A' and resid 341 through 348 Processing helix chain 'A' and resid 356 through 366 Processing helix chain 'A' and resid 418 through 423 Processing helix chain 'A' and resid 442 through 444 No H-bonds generated for 'chain 'A' and resid 442 through 444' Processing helix chain 'A' and resid 447 through 485 removed outlier: 3.647A pdb=" N LEU A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG A 485 " --> pdb=" O LYS A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 removed outlier: 4.222A pdb=" N GLU A 492 " --> pdb=" O PRO A 488 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LYS A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 488 through 493' Processing helix chain 'A' and resid 507 through 529 removed outlier: 7.562A pdb=" N ASP A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LYS A 519 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) Proline residue: A 521 - end of helix Processing helix chain 'A' and resid 531 through 560 Proline residue: A 536 - end of helix Processing helix chain 'A' and resid 564 through 572 removed outlier: 5.035A pdb=" N LEU A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LYS A 570 " --> pdb=" O LYS A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 586 removed outlier: 4.095A pdb=" N GLN A 581 " --> pdb=" O VAL A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 609 removed outlier: 3.556A pdb=" N ILE A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 643 removed outlier: 3.851A pdb=" N ARG A 643 " --> pdb=" O TYR A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 660 Processing helix chain 'A' and resid 662 through 666 Processing helix chain 'A' and resid 747 through 785 Processing helix chain 'A' and resid 789 through 791 No H-bonds generated for 'chain 'A' and resid 789 through 791' Processing helix chain 'A' and resid 809 through 828 removed outlier: 5.040A pdb=" N TYR A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Proline residue: A 817 - end of helix Processing helix chain 'A' and resid 833 through 851 removed outlier: 8.070A pdb=" N ILE A 846 " --> pdb=" O GLU A 842 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N HIS A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA A 848 " --> pdb=" O PHE A 844 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TYR A 849 " --> pdb=" O THR A 845 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL A 850 " --> pdb=" O ILE A 846 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLY A 851 " --> pdb=" O HIS A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 870 Processing helix chain 'A' and resid 872 through 887 removed outlier: 3.594A pdb=" N ARG A 887 " --> pdb=" O ASN A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 914 removed outlier: 3.853A pdb=" N CYS A 898 " --> pdb=" O SER A 895 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA A 901 " --> pdb=" O CYS A 898 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ALA A 902 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 33 through 45 Processing helix chain 'B' and resid 62 through 65 No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 71 through 79 Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 86 through 94 removed outlier: 4.013A pdb=" N SER B 89 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LYS B 90 " --> pdb=" O GLU B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 126 removed outlier: 3.703A pdb=" N SER B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 166 removed outlier: 4.076A pdb=" N LYS B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 235 through 253 removed outlier: 3.618A pdb=" N LYS B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) Proline residue: B 244 - end of helix Processing helix chain 'B' and resid 279 through 292 removed outlier: 4.069A pdb=" N CYS B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL B 286 " --> pdb=" O HIS B 282 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE B 292 " --> pdb=" O VAL B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 320 Processing helix chain 'B' and resid 335 through 338 Processing helix chain 'B' and resid 357 through 373 removed outlier: 3.950A pdb=" N MET B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 27 Processing helix chain 'C' and resid 320 through 325 Processing helix chain 'C' and resid 331 through 341 removed outlier: 4.070A pdb=" N PHE C 341 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 359 Processing sheet with id= A, first strand: chain 'A' and resid 401 through 403 Processing sheet with id= B, first strand: chain 'A' and resid 620 through 624 removed outlier: 4.314A pdb=" N VAL A 739 " --> pdb=" O GLN A 927 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 13 through 15 removed outlier: 6.232A pdb=" N GLU B 53 " --> pdb=" O TYR B 14 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 132 through 135 removed outlier: 6.713A pdb=" N LEU B 296 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ASN B 135 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET B 298 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 286 through 288 386 hydrogen bonds defined for protein. 1062 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: 2.18 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2156 1.33 - 1.46: 1852 1.46 - 1.58: 4484 1.58 - 1.70: 0 1.70 - 1.83: 82 Bond restraints: 8574 Sorted by residual: bond pdb=" CA SER A 430 " pdb=" CB SER A 430 " ideal model delta sigma weight residual 1.529 1.485 0.044 1.34e-02 5.57e+03 1.08e+01 bond pdb=" N THR A 446 " pdb=" CA THR A 446 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.14e-02 7.69e+03 8.99e+00 bond pdb=" N TRP A 434 " pdb=" CA TRP A 434 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.16e-02 7.43e+03 8.80e+00 bond pdb=" N VAL A 429 " pdb=" CA VAL A 429 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.19e-02 7.06e+03 7.82e+00 bond pdb=" N LYS B 11 " pdb=" CA LYS B 11 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.21e-02 6.83e+03 7.44e+00 ... (remaining 8569 not shown) Histogram of bond angle deviations from ideal: 100.20 - 107.02: 247 107.02 - 113.83: 4633 113.83 - 120.65: 3776 120.65 - 127.46: 2825 127.46 - 134.28: 86 Bond angle restraints: 11567 Sorted by residual: angle pdb=" O PRO C 30 " pdb=" C PRO C 30 " pdb=" N PRO C 31 " ideal model delta sigma weight residual 121.31 117.73 3.58 4.60e-01 4.73e+00 6.06e+01 angle pdb=" C THR A 427 " pdb=" N TRP A 428 " pdb=" CA TRP A 428 " ideal model delta sigma weight residual 122.64 112.99 9.65 1.70e+00 3.46e-01 3.22e+01 angle pdb=" N PRO C 31 " pdb=" CA PRO C 31 " pdb=" CB PRO C 31 " ideal model delta sigma weight residual 102.35 105.94 -3.59 7.10e-01 1.98e+00 2.56e+01 angle pdb=" C VAL A 429 " pdb=" N SER A 430 " pdb=" CA SER A 430 " ideal model delta sigma weight residual 122.77 116.84 5.93 1.33e+00 5.65e-01 1.99e+01 angle pdb=" C GLU A 789 " pdb=" CA GLU A 789 " pdb=" CB GLU A 789 " ideal model delta sigma weight residual 116.63 111.48 5.15 1.16e+00 7.43e-01 1.97e+01 ... (remaining 11562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 4429 17.83 - 35.66: 528 35.66 - 53.49: 185 53.49 - 71.31: 30 71.31 - 89.14: 11 Dihedral angle restraints: 5183 sinusoidal: 2159 harmonic: 3024 Sorted by residual: dihedral pdb=" CA THR B 305 " pdb=" C THR B 305 " pdb=" N ILE B 306 " pdb=" CA ILE B 306 " ideal model delta harmonic sigma weight residual -180.00 -157.68 -22.32 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA GLU A 562 " pdb=" C GLU A 562 " pdb=" N GLN A 563 " pdb=" CA GLN A 563 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA TYR B 304 " pdb=" C TYR B 304 " pdb=" N THR B 305 " pdb=" CA THR B 305 " ideal model delta harmonic sigma weight residual 180.00 160.87 19.13 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5180 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1116 0.071 - 0.142: 110 0.142 - 0.213: 5 0.213 - 0.284: 1 0.284 - 0.355: 2 Chirality restraints: 1234 Sorted by residual: chirality pdb=" CB VAL B 12 " pdb=" CA VAL B 12 " pdb=" CG1 VAL B 12 " pdb=" CG2 VAL B 12 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CB VAL A 441 " pdb=" CA VAL A 441 " pdb=" CG1 VAL A 441 " pdb=" CG2 VAL A 441 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CB VAL A 429 " pdb=" CA VAL A 429 " pdb=" CG1 VAL A 429 " pdb=" CG2 VAL A 429 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1231 not shown) Planarity restraints: 1500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 SHH B 501 " 0.008 2.00e-02 2.50e+03 1.91e-02 6.40e+00 pdb=" C11 SHH B 501 " -0.012 2.00e-02 2.50e+03 pdb=" C12 SHH B 501 " -0.007 2.00e-02 2.50e+03 pdb=" C13 SHH B 501 " 0.001 2.00e-02 2.50e+03 pdb=" C14 SHH B 501 " -0.004 2.00e-02 2.50e+03 pdb=" C9 SHH B 501 " 0.040 2.00e-02 2.50e+03 pdb=" N2 SHH B 501 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 269 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO C 270 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 270 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 270 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C7 SHH B 501 " -0.015 2.00e-02 2.50e+03 1.57e-02 3.09e+00 pdb=" C8 SHH B 501 " 0.008 2.00e-02 2.50e+03 pdb=" C9 SHH B 501 " -0.019 2.00e-02 2.50e+03 pdb=" N2 SHH B 501 " 0.024 2.00e-02 2.50e+03 pdb=" O3 SHH B 501 " 0.001 2.00e-02 2.50e+03 ... (remaining 1497 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 12 2.23 - 2.89: 3269 2.89 - 3.56: 11997 3.56 - 4.23: 19747 4.23 - 4.90: 34127 Nonbonded interactions: 69152 Sorted by model distance: nonbonded pdb=" O HOH B 608 " pdb=" O HOH B 632 " model vdw 1.557 2.440 nonbonded pdb=" OH TYR B 16 " pdb=" O HOH B 601 " model vdw 1.648 2.440 nonbonded pdb=" OE2 GLU A 461 " pdb=" O HOH A1201 " model vdw 1.815 2.440 nonbonded pdb=" OD2 ASP B 265 " pdb="ZN ZN B 502 " model vdw 1.919 2.230 nonbonded pdb=" OD1 ASP B 177 " pdb="ZN ZN B 502 " model vdw 1.946 2.230 ... (remaining 69147 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 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: 0.710 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: 0.010 Extract box with map and model: 2.550 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 26.870 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 43.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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 0.065 8574 Z= 0.274 Angle : 0.686 10.650 11567 Z= 0.411 Chirality : 0.045 0.355 1234 Planarity : 0.004 0.047 1500 Dihedral : 17.594 89.143 3233 Min Nonbonded Distance : 1.557 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.18 % Allowed : 24.34 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.27), residues: 1016 helix: 1.13 (0.23), residues: 551 sheet: 0.60 (0.62), residues: 76 loop : -0.73 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 434 HIS 0.007 0.001 HIS A 867 PHE 0.012 0.001 PHE A 744 TYR 0.014 0.001 TYR B 304 ARG 0.004 0.000 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 189 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 LEU cc_start: 0.6042 (OUTLIER) cc_final: 0.5659 (mp) REVERT: A 395 LYS cc_start: 0.3960 (mttt) cc_final: 0.3599 (ttpt) REVERT: A 486 MET cc_start: 0.6555 (ptt) cc_final: 0.6302 (ptp) REVERT: C 21 MET cc_start: 0.8165 (tpp) cc_final: 0.7847 (tpt) outliers start: 29 outliers final: 5 residues processed: 210 average time/residue: 1.3278 time to fit residues: 294.7332 Evaluate side-chains 106 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 319 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 91 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 ASN ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 HIS A 773 GLN A 919 ASN B 22 ASN B 58 HIS B 96 ASN B 226 ASN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8574 Z= 0.194 Angle : 0.538 12.243 11567 Z= 0.281 Chirality : 0.040 0.204 1234 Planarity : 0.004 0.041 1500 Dihedral : 4.775 48.280 1148 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.28 % Allowed : 23.03 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.27), residues: 1016 helix: 1.38 (0.23), residues: 553 sheet: 0.81 (0.62), residues: 76 loop : -0.58 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 434 HIS 0.006 0.001 HIS A 867 PHE 0.011 0.001 PHE A 662 TYR 0.019 0.001 TYR B 304 ARG 0.003 0.000 ARG A 928 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 108 time to evaluate : 1.046 Fit side-chains REVERT: A 328 LEU cc_start: 0.5879 (OUTLIER) cc_final: 0.5353 (mp) REVERT: A 342 SER cc_start: 0.2521 (OUTLIER) cc_final: 0.2084 (m) REVERT: A 395 LYS cc_start: 0.4488 (mttt) cc_final: 0.3864 (ttmt) REVERT: A 486 MET cc_start: 0.6473 (ptt) cc_final: 0.6167 (ptp) REVERT: A 491 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7360 (mt0) REVERT: A 814 GLU cc_start: 0.7354 (pp20) cc_final: 0.6932 (tp30) REVERT: C 21 MET cc_start: 0.8261 (tpp) cc_final: 0.7954 (tpt) outliers start: 39 outliers final: 12 residues processed: 135 average time/residue: 1.2579 time to fit residues: 181.3078 Evaluate side-chains 94 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 369 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 76 optimal weight: 0.2980 chunk 62 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 90 optimal weight: 0.0570 overall best weight: 1.4704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN A 581 GLN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8574 Z= 0.278 Angle : 0.560 7.788 11567 Z= 0.293 Chirality : 0.042 0.176 1234 Planarity : 0.004 0.037 1500 Dihedral : 5.057 57.100 1146 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.15 % Allowed : 22.37 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.26), residues: 1016 helix: 1.24 (0.22), residues: 552 sheet: 0.87 (0.62), residues: 76 loop : -0.72 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 749 HIS 0.008 0.002 HIS C 318 PHE 0.014 0.002 PHE A 662 TYR 0.018 0.002 TYR B 304 ARG 0.005 0.001 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 90 time to evaluate : 1.043 Fit side-chains REVERT: A 342 SER cc_start: 0.2657 (OUTLIER) cc_final: 0.2378 (m) REVERT: A 347 LEU cc_start: 0.6545 (mt) cc_final: 0.6293 (tt) REVERT: A 486 MET cc_start: 0.6675 (ptt) cc_final: 0.6368 (ptp) REVERT: A 784 GLU cc_start: 0.5767 (pp20) cc_final: 0.5434 (mm-30) REVERT: A 813 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7119 (pp20) REVERT: A 814 GLU cc_start: 0.7623 (pp20) cc_final: 0.7283 (pp20) REVERT: C 21 MET cc_start: 0.8196 (tpp) cc_final: 0.7895 (tpt) REVERT: C 329 MET cc_start: 0.2763 (ttm) cc_final: 0.1041 (ppp) outliers start: 47 outliers final: 18 residues processed: 127 average time/residue: 1.2655 time to fit residues: 171.0515 Evaluate side-chains 98 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 78 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 740 TYR Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 306 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 87 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 ASN B 40 HIS B 93 GLN B 128 GLN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8574 Z= 0.236 Angle : 0.508 7.255 11567 Z= 0.266 Chirality : 0.040 0.150 1234 Planarity : 0.004 0.037 1500 Dihedral : 4.942 57.786 1146 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.28 % Allowed : 22.59 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.26), residues: 1016 helix: 1.33 (0.22), residues: 551 sheet: 0.98 (0.62), residues: 76 loop : -0.66 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 313 HIS 0.009 0.001 HIS C 318 PHE 0.012 0.001 PHE A 662 TYR 0.018 0.001 TYR B 304 ARG 0.010 0.000 ARG A 863 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 85 time to evaluate : 0.968 Fit side-chains REVERT: A 342 SER cc_start: 0.2640 (OUTLIER) cc_final: 0.2415 (m) REVERT: A 486 MET cc_start: 0.6835 (ptt) cc_final: 0.6504 (ptp) REVERT: A 780 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7425 (tp30) REVERT: A 784 GLU cc_start: 0.5921 (pp20) cc_final: 0.5662 (pp20) REVERT: A 813 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.7023 (pp20) REVERT: A 814 GLU cc_start: 0.7756 (pp20) cc_final: 0.7349 (pp20) REVERT: C 21 MET cc_start: 0.8179 (tpp) cc_final: 0.7901 (tpt) REVERT: C 272 LYS cc_start: 0.7988 (ptpp) cc_final: 0.7550 (mtpp) REVERT: C 329 MET cc_start: 0.2919 (ttm) cc_final: 0.1205 (ppp) outliers start: 39 outliers final: 21 residues processed: 117 average time/residue: 1.0523 time to fit residues: 132.6430 Evaluate side-chains 105 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 81 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain C residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 0.0040 chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 GLN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8574 Z= 0.149 Angle : 0.469 6.528 11567 Z= 0.246 Chirality : 0.038 0.149 1234 Planarity : 0.004 0.043 1500 Dihedral : 4.824 54.774 1146 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.74 % Allowed : 24.12 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.15 (0.27), residues: 1016 helix: 1.58 (0.23), residues: 547 sheet: 0.93 (0.63), residues: 76 loop : -0.40 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 313 HIS 0.004 0.001 HIS C 348 PHE 0.011 0.001 PHE A 662 TYR 0.016 0.001 TYR B 304 ARG 0.011 0.000 ARG A 928 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 83 time to evaluate : 0.993 Fit side-chains REVERT: A 328 LEU cc_start: 0.5885 (OUTLIER) cc_final: 0.5669 (mm) REVERT: A 347 LEU cc_start: 0.4550 (OUTLIER) cc_final: 0.4299 (mt) REVERT: A 486 MET cc_start: 0.6790 (ptt) cc_final: 0.6519 (ptp) REVERT: A 813 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.7055 (pp20) REVERT: A 814 GLU cc_start: 0.7603 (pp20) cc_final: 0.7239 (pp20) REVERT: B 127 ARG cc_start: 0.7689 (mtm-85) cc_final: 0.7429 (mtm-85) REVERT: C 272 LYS cc_start: 0.7822 (ptpp) cc_final: 0.7469 (mtpp) outliers start: 25 outliers final: 15 residues processed: 104 average time/residue: 1.1270 time to fit residues: 125.9466 Evaluate side-chains 99 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain C residue 350 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 1.9990 chunk 19 optimal weight: 0.0670 chunk 57 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 51 optimal weight: 0.3980 chunk 94 optimal weight: 3.9990 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN B 58 HIS B 128 GLN C 321 HIS ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8574 Z= 0.206 Angle : 0.490 7.173 11567 Z= 0.257 Chirality : 0.039 0.139 1234 Planarity : 0.004 0.034 1500 Dihedral : 4.912 57.089 1146 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.28 % Allowed : 22.70 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.09 (0.27), residues: 1016 helix: 1.56 (0.23), residues: 547 sheet: 0.79 (0.59), residues: 81 loop : -0.45 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 909 HIS 0.005 0.001 HIS B 58 PHE 0.009 0.001 PHE A 662 TYR 0.025 0.001 TYR A 740 ARG 0.003 0.000 ARG A 863 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 77 time to evaluate : 0.888 Fit side-chains REVERT: A 347 LEU cc_start: 0.4306 (OUTLIER) cc_final: 0.4017 (mt) REVERT: A 486 MET cc_start: 0.6734 (ptt) cc_final: 0.6390 (ptp) REVERT: A 813 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7097 (pp20) REVERT: A 814 GLU cc_start: 0.7653 (pp20) cc_final: 0.7313 (pp20) REVERT: B 127 ARG cc_start: 0.7705 (mtm-85) cc_final: 0.7424 (mtm-85) REVERT: C 272 LYS cc_start: 0.7923 (ptpp) cc_final: 0.7566 (mtpp) outliers start: 39 outliers final: 21 residues processed: 109 average time/residue: 1.0579 time to fit residues: 124.5191 Evaluate side-chains 97 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 74 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain C residue 350 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 656 HIS B 58 HIS B 128 GLN C 328 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8574 Z= 0.167 Angle : 0.476 6.733 11567 Z= 0.249 Chirality : 0.038 0.144 1234 Planarity : 0.003 0.033 1500 Dihedral : 4.489 58.045 1144 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.29 % Allowed : 24.56 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.12 (0.27), residues: 1016 helix: 1.59 (0.22), residues: 551 sheet: 0.76 (0.63), residues: 76 loop : -0.44 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 313 HIS 0.004 0.001 HIS B 58 PHE 0.011 0.001 PHE A 662 TYR 0.017 0.001 TYR B 304 ARG 0.004 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 77 time to evaluate : 0.880 Fit side-chains REVERT: A 347 LEU cc_start: 0.4215 (OUTLIER) cc_final: 0.3994 (mt) REVERT: A 486 MET cc_start: 0.6725 (ptt) cc_final: 0.6354 (ptp) REVERT: A 813 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7123 (pp20) REVERT: A 814 GLU cc_start: 0.7632 (pp20) cc_final: 0.7290 (pp20) REVERT: B 127 ARG cc_start: 0.7698 (mtm-85) cc_final: 0.7434 (mtm-85) REVERT: C 272 LYS cc_start: 0.7938 (ptpp) cc_final: 0.7606 (mtpp) outliers start: 30 outliers final: 18 residues processed: 101 average time/residue: 1.0395 time to fit residues: 113.6292 Evaluate side-chains 94 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 74 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain C residue 350 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 5.9990 chunk 19 optimal weight: 0.0070 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS B 58 HIS B 93 GLN B 128 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8574 Z= 0.139 Angle : 0.454 6.306 11567 Z= 0.238 Chirality : 0.038 0.138 1234 Planarity : 0.003 0.033 1500 Dihedral : 4.415 57.552 1144 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.29 % Allowed : 24.67 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.30 (0.27), residues: 1016 helix: 1.77 (0.23), residues: 545 sheet: 0.70 (0.63), residues: 76 loop : -0.35 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 909 HIS 0.004 0.001 HIS B 58 PHE 0.007 0.001 PHE A 662 TYR 0.029 0.001 TYR A 740 ARG 0.004 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 83 time to evaluate : 0.965 Fit side-chains REVERT: A 486 MET cc_start: 0.6653 (ptt) cc_final: 0.6248 (ptp) REVERT: A 813 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7125 (pp20) REVERT: A 814 GLU cc_start: 0.7596 (pp20) cc_final: 0.7271 (pp20) REVERT: B 127 ARG cc_start: 0.7692 (mtm-85) cc_final: 0.7430 (mtm-85) REVERT: C 272 LYS cc_start: 0.7933 (ptpp) cc_final: 0.7631 (mtpp) REVERT: C 288 GLN cc_start: 0.8215 (tp-100) cc_final: 0.7603 (tm130) outliers start: 30 outliers final: 20 residues processed: 108 average time/residue: 1.0803 time to fit residues: 125.6908 Evaluate side-chains 100 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 79 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain C residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 0.0270 chunk 71 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 HIS B 93 GLN B 128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8574 Z= 0.168 Angle : 0.472 6.545 11567 Z= 0.246 Chirality : 0.038 0.148 1234 Planarity : 0.003 0.031 1500 Dihedral : 4.455 57.359 1144 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.74 % Allowed : 25.44 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.29 (0.27), residues: 1016 helix: 1.77 (0.22), residues: 547 sheet: 0.78 (0.59), residues: 80 loop : -0.41 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 909 HIS 0.004 0.001 HIS B 58 PHE 0.011 0.001 PHE A 662 TYR 0.016 0.001 TYR B 304 ARG 0.003 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 81 time to evaluate : 1.028 Fit side-chains REVERT: A 486 MET cc_start: 0.6643 (ptt) cc_final: 0.6334 (ptp) REVERT: A 533 THR cc_start: 0.7828 (p) cc_final: 0.7617 (t) REVERT: A 813 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7136 (pp20) REVERT: A 814 GLU cc_start: 0.7616 (pp20) cc_final: 0.7288 (pp20) REVERT: C 272 LYS cc_start: 0.7971 (ptpp) cc_final: 0.7659 (mtpp) outliers start: 25 outliers final: 19 residues processed: 101 average time/residue: 1.0284 time to fit residues: 112.3104 Evaluate side-chains 99 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 79 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain C residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 HIS B 93 GLN B 128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8574 Z= 0.178 Angle : 0.476 6.550 11567 Z= 0.249 Chirality : 0.038 0.151 1234 Planarity : 0.003 0.030 1500 Dihedral : 4.494 57.343 1144 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.85 % Allowed : 25.33 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.33 (0.27), residues: 1016 helix: 1.81 (0.22), residues: 545 sheet: 0.76 (0.59), residues: 80 loop : -0.38 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 313 HIS 0.004 0.001 HIS B 58 PHE 0.011 0.001 PHE A 662 TYR 0.025 0.001 TYR A 740 ARG 0.004 0.000 ARG C 312 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 81 time to evaluate : 1.686 Fit side-chains REVERT: A 486 MET cc_start: 0.6658 (ptt) cc_final: 0.6338 (ptp) REVERT: A 813 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7169 (pp20) REVERT: A 814 GLU cc_start: 0.7641 (pp20) cc_final: 0.7316 (pp20) REVERT: B 85 MET cc_start: 0.7558 (mmm) cc_final: 0.7285 (mmm) REVERT: C 272 LYS cc_start: 0.7969 (ptpp) cc_final: 0.7652 (mtpp) REVERT: C 288 GLN cc_start: 0.8175 (tp-100) cc_final: 0.7481 (tm-30) outliers start: 26 outliers final: 21 residues processed: 103 average time/residue: 1.0491 time to fit residues: 116.7461 Evaluate side-chains 100 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 78 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain C residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 656 HIS B 58 HIS B 93 GLN B 128 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.167518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.129633 restraints weight = 10653.471| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.74 r_work: 0.3336 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.5295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8574 Z= 0.170 Angle : 0.481 7.521 11567 Z= 0.251 Chirality : 0.038 0.152 1234 Planarity : 0.003 0.029 1500 Dihedral : 4.462 57.277 1144 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.96 % Allowed : 25.22 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.36 (0.27), residues: 1016 helix: 1.85 (0.22), residues: 544 sheet: 0.76 (0.60), residues: 80 loop : -0.39 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 313 HIS 0.003 0.001 HIS C 348 PHE 0.008 0.001 PHE A 662 TYR 0.017 0.001 TYR B 304 ARG 0.003 0.000 ARG A 402 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3255.93 seconds wall clock time: 58 minutes 44.77 seconds (3524.77 seconds total)