Starting phenix.real_space_refine on Thu Jul 2 16:18:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lhv_23351/07_2026/7lhv_23351_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lhv_23351/07_2026/7lhv_23351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lhv_23351/07_2026/7lhv_23351_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lhv_23351/07_2026/7lhv_23351_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lhv_23351/07_2026/7lhv_23351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lhv_23351/07_2026/7lhv_23351.map" } resolution = 2.75 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 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= 0.162 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 32 5.16 5 C 5976 2.51 5 N 1452 2.21 5 O 1628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9094 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4465 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 575, 4454 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 549} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 575, 4454 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 549} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 4544 Chain: "B" Number of atoms: 4465 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 575, 4454 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 549} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 575, 4454 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 549} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 4544 Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Unusual residues: {'LBN': 1, 'S1P': 2, 'SO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Unusual residues: {'LBN': 1, 'S1P': 2, 'SO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N APHE A 391 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 391 " occ=0.50 residue: pdb=" N APHE B 391 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 391 " occ=0.50 Time building chain proxies: 2.95, per 1000 atoms: 0.32 Number of scatterers: 9094 At special positions: 0 Unit cell: (123.6, 104.03, 94.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 6 15.00 O 1628 8.00 N 1452 7.00 C 5976 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 - 3.00 Amino acid : True - 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: 0.48 Conformation dependent library (CDL) restraints added in 621.9 milliseconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 4 sheets defined 73.9% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 71 through 80 removed outlier: 3.758A pdb=" N ASP A 77 " --> pdb=" O VAL A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 87 Processing helix chain 'A' and resid 90 through 120 removed outlier: 4.191A pdb=" N LYS A 96 " --> pdb=" O SER A 92 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 124 through 142 removed outlier: 3.946A pdb=" N LEU A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Proline residue: A 134 - end of helix removed outlier: 3.592A pdb=" N ILE A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 Processing helix chain 'A' and resid 172 through 195 removed outlier: 3.620A pdb=" N GLU A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 201 Processing helix chain 'A' and resid 205 through 230 removed outlier: 4.616A pdb=" N LYS A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N TYR A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 250 removed outlier: 3.518A pdb=" N ILE A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 254 through 278 removed outlier: 3.857A pdb=" N PHE A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 301 Proline residue: A 289 - end of helix removed outlier: 3.690A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 328 No H-bonds generated for 'chain 'A' and resid 326 through 328' Processing helix chain 'A' and resid 329 through 347 Proline residue: A 335 - end of helix Processing helix chain 'A' and resid 347 through 359 Processing helix chain 'A' and resid 364 through 382 removed outlier: 3.674A pdb=" N LEU A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 400 removed outlier: 3.581A pdb=" N ALA A 395 " --> pdb=" O BPHE A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 422 removed outlier: 3.505A pdb=" N LEU A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 427 removed outlier: 4.006A pdb=" N LYS A 427 " --> pdb=" O THR A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 444 removed outlier: 3.601A pdb=" N LEU A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 458 removed outlier: 3.792A pdb=" N ALA A 451 " --> pdb=" O ASP A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 475 Processing helix chain 'A' and resid 476 through 497 Processing helix chain 'A' and resid 541 through 561 removed outlier: 4.299A pdb=" N TYR A 552 " --> pdb=" O ARG A 548 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 600 Processing helix chain 'A' and resid 610 through 620 Processing helix chain 'A' and resid 621 through 627 Processing helix chain 'A' and resid 628 through 631 Processing helix chain 'A' and resid 634 through 644 removed outlier: 3.812A pdb=" N ALA A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 80 removed outlier: 3.758A pdb=" N ASP B 77 " --> pdb=" O VAL B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 87 Processing helix chain 'B' and resid 90 through 120 removed outlier: 4.191A pdb=" N LYS B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 124 through 142 removed outlier: 3.946A pdb=" N LEU B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 133 " --> pdb=" O TYR B 129 " (cutoff:3.500A) Proline residue: B 134 - end of helix removed outlier: 3.592A pdb=" N ILE B 140 " --> pdb=" O PHE B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 Processing helix chain 'B' and resid 172 through 195 removed outlier: 3.620A pdb=" N GLU B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 201 Processing helix chain 'B' and resid 205 through 230 removed outlier: 4.616A pdb=" N LYS B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N TYR B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE B 228 " --> pdb=" O GLN B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 250 removed outlier: 3.518A pdb=" N ILE B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 254 through 278 removed outlier: 3.857A pdb=" N PHE B 258 " --> pdb=" O GLN B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 301 Proline residue: B 289 - end of helix removed outlier: 3.690A pdb=" N ILE B 293 " --> pdb=" O PRO B 289 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR B 298 " --> pdb=" O VAL B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 328 No H-bonds generated for 'chain 'B' and resid 326 through 328' Processing helix chain 'B' and resid 329 through 347 Proline residue: B 335 - end of helix Processing helix chain 'B' and resid 347 through 359 Processing helix chain 'B' and resid 364 through 382 removed outlier: 3.674A pdb=" N LEU B 369 " --> pdb=" O SER B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 400 removed outlier: 3.581A pdb=" N ALA B 395 " --> pdb=" O BPHE B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 422 removed outlier: 3.505A pdb=" N LEU B 409 " --> pdb=" O GLY B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 427 removed outlier: 4.006A pdb=" N LYS B 427 " --> pdb=" O THR B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 444 removed outlier: 3.601A pdb=" N LEU B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY B 444 " --> pdb=" O SER B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 458 removed outlier: 3.792A pdb=" N ALA B 451 " --> pdb=" O ASP B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 475 Processing helix chain 'B' and resid 476 through 497 Processing helix chain 'B' and resid 541 through 561 removed outlier: 4.299A pdb=" N TYR B 552 " --> pdb=" O ARG B 548 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU B 553 " --> pdb=" O LEU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 600 Processing helix chain 'B' and resid 610 through 620 Processing helix chain 'B' and resid 621 through 627 Processing helix chain 'B' and resid 628 through 631 Processing helix chain 'B' and resid 634 through 644 removed outlier: 3.812A pdb=" N ALA B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 150 Processing sheet with id=AA2, first strand: chain 'A' and resid 501 through 504 removed outlier: 4.693A pdb=" N ILE A 530 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY A 527 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ILE A 573 " --> pdb=" O GLY A 527 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL A 529 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N GLU A 575 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A 531 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 149 through 150 Processing sheet with id=AA4, first strand: chain 'B' and resid 501 through 504 removed outlier: 4.693A pdb=" N ILE B 530 " --> pdb=" O LEU B 504 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY B 527 " --> pdb=" O PHE B 571 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ILE B 573 " --> pdb=" O GLY B 527 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B 529 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N GLU B 575 " --> pdb=" O VAL B 529 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B 531 " --> pdb=" O GLU B 575 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1698 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: 1.04 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1392 1.31 - 1.43: 2426 1.43 - 1.56: 5418 1.56 - 1.68: 8 1.68 - 1.81: 50 Bond restraints: 9294 Sorted by residual: bond pdb=" O2 LBN B1004 " pdb=" P1 LBN B1004 " ideal model delta sigma weight residual 1.650 1.480 0.170 2.00e-02 2.50e+03 7.20e+01 bond pdb=" O2 LBN A1003 " pdb=" P1 LBN A1003 " ideal model delta sigma weight residual 1.650 1.480 0.170 2.00e-02 2.50e+03 7.20e+01 bond pdb=" O1 S1P A1001 " pdb=" P22 S1P A1001 " ideal model delta sigma weight residual 1.677 1.575 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" O1 S1P B1002 " pdb=" P22 S1P B1002 " ideal model delta sigma weight residual 1.677 1.575 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" O4 LBN B1004 " pdb=" P1 LBN B1004 " ideal model delta sigma weight residual 1.497 1.592 -0.095 2.00e-02 2.50e+03 2.27e+01 ... (remaining 9289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 12548 3.46 - 6.93: 66 6.93 - 10.39: 6 10.39 - 13.85: 2 13.85 - 17.31: 4 Bond angle restraints: 12626 Sorted by residual: angle pdb=" O1 LBN A1003 " pdb=" P1 LBN A1003 " pdb=" O2 LBN A1003 " ideal model delta sigma weight residual 93.45 110.76 -17.31 3.00e+00 1.11e-01 3.33e+01 angle pdb=" O1 LBN B1004 " pdb=" P1 LBN B1004 " pdb=" O2 LBN B1004 " ideal model delta sigma weight residual 93.45 110.76 -17.31 3.00e+00 1.11e-01 3.33e+01 angle pdb=" O3 LBN B1004 " pdb=" P1 LBN B1004 " pdb=" O4 LBN B1004 " ideal model delta sigma weight residual 119.36 104.85 14.51 3.00e+00 1.11e-01 2.34e+01 angle pdb=" O3 LBN A1003 " pdb=" P1 LBN A1003 " pdb=" O4 LBN A1003 " ideal model delta sigma weight residual 119.36 104.85 14.51 3.00e+00 1.11e-01 2.34e+01 angle pdb=" C2 S1P A1004 " pdb=" C1 S1P A1004 " pdb=" O1 S1P A1004 " ideal model delta sigma weight residual 113.77 101.80 11.97 3.00e+00 1.11e-01 1.59e+01 ... (remaining 12621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 5406 35.93 - 71.87: 76 71.87 - 107.80: 30 107.80 - 143.73: 4 143.73 - 179.67: 6 Dihedral angle restraints: 5522 sinusoidal: 2190 harmonic: 3332 Sorted by residual: dihedral pdb=" C39 LBN A1003 " pdb=" C40 LBN A1003 " pdb=" C41 LBN A1003 " pdb=" C42 LBN A1003 " ideal model delta sinusoidal sigma weight residual 178.66 -1.67 -179.67 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C39 LBN B1004 " pdb=" C40 LBN B1004 " pdb=" C41 LBN B1004 " pdb=" C42 LBN B1004 " ideal model delta sinusoidal sigma weight residual 178.66 -1.67 -179.67 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C10 S1P B1001 " pdb=" C11 S1P B1001 " pdb=" C12 S1P B1001 " pdb=" C13 S1P B1001 " ideal model delta sinusoidal sigma weight residual 179.74 6.15 173.59 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 5519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 876 0.030 - 0.059: 398 0.059 - 0.089: 148 0.089 - 0.118: 56 0.118 - 0.147: 10 Chirality restraints: 1488 Sorted by residual: chirality pdb=" CA THR A 423 " pdb=" N THR A 423 " pdb=" C THR A 423 " pdb=" CB THR A 423 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA THR B 423 " pdb=" N THR B 423 " pdb=" C THR B 423 " pdb=" CB THR B 423 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA GLU A 399 " pdb=" N GLU A 399 " pdb=" C GLU A 399 " pdb=" CB GLU A 399 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 1485 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C34 LBN A1003 " -0.030 2.00e-02 2.50e+03 1.72e-02 2.94e+00 pdb=" C35 LBN A1003 " 0.008 2.00e-02 2.50e+03 pdb=" O7 LBN A1003 " 0.009 2.00e-02 2.50e+03 pdb=" O8 LBN A1003 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C34 LBN B1004 " 0.030 2.00e-02 2.50e+03 1.72e-02 2.94e+00 pdb=" C35 LBN B1004 " -0.008 2.00e-02 2.50e+03 pdb=" O7 LBN B1004 " -0.009 2.00e-02 2.50e+03 pdb=" O8 LBN B1004 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 418 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C SER B 418 " -0.028 2.00e-02 2.50e+03 pdb=" O SER B 418 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU B 419 " 0.010 2.00e-02 2.50e+03 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2640 2.82 - 3.34: 8871 3.34 - 3.86: 15373 3.86 - 4.38: 17314 4.38 - 4.90: 30406 Nonbonded interactions: 74604 Sorted by model distance: nonbonded pdb=" O SER A 160 " pdb=" NH2 ARG A 235 " model vdw 2.299 3.120 nonbonded pdb=" O SER B 160 " pdb=" NH2 ARG B 235 " model vdw 2.299 3.120 nonbonded pdb=" N2 S1P B1001 " pdb=" O1 S1P B1001 " model vdw 2.302 2.496 nonbonded pdb=" N2 S1P A1004 " pdb=" O1 S1P A1004 " model vdw 2.302 2.496 nonbonded pdb=" N2 S1P B1001 " pdb=" O3 S1P B1001 " model vdw 2.303 2.496 ... (remaining 74599 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 70 through 390 or resid 392 through 644 or (resid 1001 and \ (name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C1 \ 5 or name C16 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 \ or name C8 or name C9 or name N2 or name O1 or name O23 or name O24 or name O25 \ or name O3 or name P22)))) selection = (chain 'B' and (resid 70 through 390 or resid 392 through 1001)) } 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=0.50 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: 0.400 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.790 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:5.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 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 : 0.006 0.170 9294 Z= 0.268 Angle : 0.688 17.314 12626 Z= 0.306 Chirality : 0.041 0.147 1488 Planarity : 0.004 0.033 1546 Dihedral : 17.062 179.668 3386 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.25), residues: 1152 helix: 1.40 (0.19), residues: 784 sheet: 3.34 (0.85), residues: 34 loop : -1.51 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 360 TYR 0.015 0.001 TYR B 385 PHE 0.011 0.001 PHE A 491 TRP 0.012 0.001 TRP A 91 HIS 0.003 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.27 ( 9294) covalent geometry : angle 0.68849 / 0.31 (12626) hydrogen bonds : bond 0.14872 / 10.08 ( 576) hydrogen bonds : angle 5.97725 / 4.32 ( 1698) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.259 Fit side-chains REVERT: A 364 ASP cc_start: 0.7148 (p0) cc_final: 0.6700 (p0) REVERT: A 557 ASP cc_start: 0.6185 (m-30) cc_final: 0.5710 (m-30) REVERT: B 70 MET cc_start: 0.4051 (ttm) cc_final: 0.3740 (ttp) REVERT: B 96 LYS cc_start: 0.7230 (ptmm) cc_final: 0.6945 (mmtm) REVERT: B 276 LYS cc_start: 0.8232 (ttmt) cc_final: 0.7897 (ptmm) outliers start: 0 outliers final: 1 residues processed: 147 average time/residue: 0.4302 time to fit residues: 67.9879 Evaluate side-chains 84 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 431 GLN B 570 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.174264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.129559 restraints weight = 22159.554| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 3.61 r_work: 0.3449 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3481 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3481 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9294 Z= 0.171 Angle : 0.639 11.885 12626 Z= 0.318 Chirality : 0.044 0.162 1488 Planarity : 0.004 0.040 1546 Dihedral : 17.129 175.180 1381 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.14 % Allowed : 8.88 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.26), residues: 1152 helix: 1.65 (0.19), residues: 806 sheet: 2.35 (0.96), residues: 38 loop : -1.04 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 90 TYR 0.016 0.002 TYR B 385 PHE 0.025 0.002 PHE A 95 TRP 0.012 0.001 TRP A 91 HIS 0.005 0.001 HIS B 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 9294) covalent geometry : angle 0.63903 / 0.32 (12626) hydrogen bonds : bond 0.04214 / 2.90 ( 576) hydrogen bonds : angle 4.25042 / 3.10 ( 1698) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.258 Fit side-chains REVERT: A 97 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7172 (mt) REVERT: A 364 ASP cc_start: 0.7638 (p0) cc_final: 0.7215 (p0) REVERT: A 475 PHE cc_start: 0.7716 (m-80) cc_final: 0.7472 (m-80) REVERT: A 557 ASP cc_start: 0.5054 (m-30) cc_final: 0.4625 (m-30) REVERT: B 276 LYS cc_start: 0.8152 (ttmt) cc_final: 0.7934 (ttmm) REVERT: B 364 ASP cc_start: 0.7681 (p0) cc_final: 0.7267 (p0) REVERT: B 428 TYR cc_start: 0.8104 (m-80) cc_final: 0.7578 (m-80) REVERT: B 495 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7890 (tm-30) outliers start: 11 outliers final: 5 residues processed: 112 average time/residue: 0.4549 time to fit residues: 54.7659 Evaluate side-chains 95 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain B residue 598 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 431 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.169244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.127106 restraints weight = 22921.175| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 3.40 r_work: 0.3380 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9294 Z= 0.149 Angle : 0.538 6.721 12626 Z= 0.276 Chirality : 0.042 0.149 1488 Planarity : 0.004 0.040 1546 Dihedral : 13.991 139.479 1381 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.55 % Allowed : 10.54 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.26), residues: 1152 helix: 1.88 (0.19), residues: 806 sheet: 2.35 (0.96), residues: 38 loop : -1.15 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 87 TYR 0.022 0.002 TYR A 126 PHE 0.018 0.001 PHE A 95 TRP 0.008 0.001 TRP A 91 HIS 0.003 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 9294) covalent geometry : angle 0.53764 / 0.28 (12626) hydrogen bonds : bond 0.04276 / 2.95 ( 576) hydrogen bonds : angle 4.09453 / 2.99 ( 1698) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 251 ASP cc_start: 0.7749 (t0) cc_final: 0.6988 (m-30) REVERT: A 267 ILE cc_start: 0.6580 (mm) cc_final: 0.6252 (mp) REVERT: A 334 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.7026 (mm) REVERT: A 364 ASP cc_start: 0.7462 (p0) cc_final: 0.7201 (p0) REVERT: A 557 ASP cc_start: 0.4532 (m-30) cc_final: 0.4204 (m-30) REVERT: A 569 ILE cc_start: 0.7260 (mm) cc_final: 0.7011 (mm) REVERT: B 172 GLU cc_start: 0.7450 (tp30) cc_final: 0.7097 (tp30) REVERT: B 223 SER cc_start: 0.7962 (OUTLIER) cc_final: 0.7717 (p) REVERT: B 276 LYS cc_start: 0.8095 (ttmt) cc_final: 0.7848 (ttmm) REVERT: B 495 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7790 (tm-30) outliers start: 15 outliers final: 4 residues processed: 110 average time/residue: 0.4433 time to fit residues: 52.6778 Evaluate side-chains 102 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain B residue 598 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 64 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.168511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.126614 restraints weight = 20889.480| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.24 r_work: 0.3374 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3427 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9294 Z= 0.160 Angle : 0.543 6.670 12626 Z= 0.278 Chirality : 0.042 0.149 1488 Planarity : 0.004 0.041 1546 Dihedral : 13.157 138.503 1378 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.83 % Allowed : 12.50 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.25), residues: 1152 helix: 1.81 (0.19), residues: 810 sheet: 2.98 (0.92), residues: 34 loop : -1.20 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 87 TYR 0.020 0.001 TYR A 126 PHE 0.009 0.001 PHE A 95 TRP 0.010 0.001 TRP B 85 HIS 0.003 0.001 HIS B 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.16 ( 9294) covalent geometry : angle 0.54343 / 0.28 (12626) hydrogen bonds : bond 0.03940 / 2.72 ( 576) hydrogen bonds : angle 4.04363 / 2.95 ( 1698) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 251 ASP cc_start: 0.7679 (t0) cc_final: 0.6991 (m-30) REVERT: A 557 ASP cc_start: 0.4595 (m-30) cc_final: 0.4278 (m-30) REVERT: A 569 ILE cc_start: 0.7469 (mm) cc_final: 0.7164 (mm) REVERT: B 172 GLU cc_start: 0.7659 (tp30) cc_final: 0.7435 (tp30) REVERT: B 276 LYS cc_start: 0.8099 (ttmt) cc_final: 0.7847 (ttmm) REVERT: B 364 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.6214 (p0) REVERT: B 495 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7787 (tm-30) outliers start: 8 outliers final: 4 residues processed: 100 average time/residue: 0.4408 time to fit residues: 47.4420 Evaluate side-chains 97 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain B residue 598 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.169917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.127748 restraints weight = 22143.064| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.35 r_work: 0.3384 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9294 Z= 0.132 Angle : 0.518 7.060 12626 Z= 0.264 Chirality : 0.041 0.142 1488 Planarity : 0.004 0.041 1546 Dihedral : 12.389 135.923 1378 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.83 % Allowed : 13.12 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.26), residues: 1152 helix: 1.90 (0.19), residues: 810 sheet: 2.76 (0.94), residues: 34 loop : -1.13 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 90 TYR 0.018 0.001 TYR A 126 PHE 0.008 0.001 PHE B 95 TRP 0.007 0.001 TRP A 465 HIS 0.003 0.000 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 ( 9294) covalent geometry : angle 0.51780 / 0.26 (12626) hydrogen bonds : bond 0.03663 / 2.53 ( 576) hydrogen bonds : angle 3.92910 / 2.86 ( 1698) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.7008 (mmp) cc_final: 0.6750 (mmm) REVERT: A 251 ASP cc_start: 0.7777 (t0) cc_final: 0.7130 (m-30) REVERT: A 260 MET cc_start: 0.6735 (ttm) cc_final: 0.6452 (ttm) REVERT: A 267 ILE cc_start: 0.6907 (mp) cc_final: 0.6628 (mp) REVERT: A 334 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.7081 (mm) REVERT: A 517 LYS cc_start: 0.7196 (mmmt) cc_final: 0.6566 (mppt) REVERT: A 557 ASP cc_start: 0.4705 (m-30) cc_final: 0.4317 (m-30) REVERT: A 569 ILE cc_start: 0.7489 (mm) cc_final: 0.7204 (mm) REVERT: B 172 GLU cc_start: 0.7783 (tp30) cc_final: 0.7483 (tp30) REVERT: B 276 LYS cc_start: 0.7981 (ttmt) cc_final: 0.7757 (ttmm) REVERT: B 364 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.6413 (p0) REVERT: B 495 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7948 (tm-30) outliers start: 8 outliers final: 3 residues processed: 103 average time/residue: 0.4202 time to fit residues: 46.7887 Evaluate side-chains 91 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 495 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.169597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.126605 restraints weight = 26134.759| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.63 r_work: 0.3363 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9294 Z= 0.132 Angle : 0.517 6.664 12626 Z= 0.264 Chirality : 0.040 0.143 1488 Planarity : 0.004 0.041 1546 Dihedral : 12.060 131.427 1378 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.14 % Allowed : 13.22 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.26), residues: 1152 helix: 1.92 (0.19), residues: 810 sheet: 2.56 (0.95), residues: 34 loop : -1.09 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 90 TYR 0.019 0.001 TYR A 126 PHE 0.007 0.001 PHE B 95 TRP 0.007 0.001 TRP B 85 HIS 0.002 0.000 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 ( 9294) covalent geometry : angle 0.51698 / 0.26 (12626) hydrogen bonds : bond 0.03580 / 2.48 ( 576) hydrogen bonds : angle 3.90517 / 2.84 ( 1698) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.6960 (mmp) cc_final: 0.6725 (mmm) REVERT: A 251 ASP cc_start: 0.7788 (t0) cc_final: 0.7130 (m-30) REVERT: A 267 ILE cc_start: 0.6819 (mp) cc_final: 0.6584 (mp) REVERT: A 517 LYS cc_start: 0.7155 (mmmt) cc_final: 0.6461 (mppt) REVERT: A 557 ASP cc_start: 0.4639 (m-30) cc_final: 0.4256 (m-30) REVERT: A 569 ILE cc_start: 0.7507 (mm) cc_final: 0.7273 (mm) REVERT: B 172 GLU cc_start: 0.7805 (tp30) cc_final: 0.7489 (tp30) REVERT: B 276 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7749 (ttmm) REVERT: B 364 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.6346 (p0) REVERT: B 495 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7925 (tm-30) outliers start: 11 outliers final: 5 residues processed: 98 average time/residue: 0.4043 time to fit residues: 42.8039 Evaluate side-chains 95 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 495 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 67 optimal weight: 0.9990 chunk 4 optimal weight: 0.0770 chunk 55 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 109 optimal weight: 0.2980 chunk 108 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.171424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.130261 restraints weight = 19968.382| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.12 r_work: 0.3409 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9294 Z= 0.117 Angle : 0.508 6.609 12626 Z= 0.259 Chirality : 0.040 0.141 1488 Planarity : 0.004 0.042 1546 Dihedral : 11.858 129.042 1378 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.62 % Allowed : 13.84 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.26), residues: 1152 helix: 2.01 (0.19), residues: 810 sheet: 1.57 (0.95), residues: 38 loop : -1.05 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 90 TYR 0.017 0.001 TYR B 385 PHE 0.007 0.001 PHE B 95 TRP 0.007 0.001 TRP B 465 HIS 0.001 0.000 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 9294) covalent geometry : angle 0.50812 / 0.26 (12626) hydrogen bonds : bond 0.03398 / 2.35 ( 576) hydrogen bonds : angle 3.86824 / 2.81 ( 1698) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.7004 (mmp) cc_final: 0.6766 (mmm) REVERT: A 251 ASP cc_start: 0.7757 (t0) cc_final: 0.7135 (m-30) REVERT: A 267 ILE cc_start: 0.6867 (mp) cc_final: 0.6636 (mp) REVERT: A 517 LYS cc_start: 0.7158 (mmmt) cc_final: 0.6440 (mppt) REVERT: A 557 ASP cc_start: 0.4700 (m-30) cc_final: 0.4374 (m-30) REVERT: B 172 GLU cc_start: 0.7827 (tp30) cc_final: 0.7496 (tp30) REVERT: B 276 LYS cc_start: 0.7898 (ttmt) cc_final: 0.7673 (ttmm) REVERT: B 364 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.6319 (p0) outliers start: 6 outliers final: 3 residues processed: 94 average time/residue: 0.4463 time to fit residues: 45.1552 Evaluate side-chains 90 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 364 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 82 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 106 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.170582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.129679 restraints weight = 17073.802| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.97 r_work: 0.3416 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9294 Z= 0.123 Angle : 0.511 6.640 12626 Z= 0.260 Chirality : 0.040 0.143 1488 Planarity : 0.004 0.043 1546 Dihedral : 11.538 122.845 1378 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.72 % Allowed : 13.84 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.26), residues: 1152 helix: 2.03 (0.19), residues: 810 sheet: 1.39 (0.95), residues: 38 loop : -1.06 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 90 TYR 0.018 0.001 TYR A 126 PHE 0.007 0.001 PHE B 95 TRP 0.007 0.001 TRP B 465 HIS 0.003 0.001 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.12 ( 9294) covalent geometry : angle 0.51058 / 0.26 (12626) hydrogen bonds : bond 0.03415 / 2.36 ( 576) hydrogen bonds : angle 3.85280 / 2.80 ( 1698) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.6867 (mmp) cc_final: 0.6584 (mmm) REVERT: A 251 ASP cc_start: 0.7731 (t0) cc_final: 0.7124 (m-30) REVERT: A 260 MET cc_start: 0.6684 (ttm) cc_final: 0.6423 (ttt) REVERT: A 267 ILE cc_start: 0.6763 (mp) cc_final: 0.6529 (mp) REVERT: A 517 LYS cc_start: 0.7050 (mmmt) cc_final: 0.6384 (mppt) REVERT: A 557 ASP cc_start: 0.4665 (m-30) cc_final: 0.4368 (m-30) REVERT: B 172 GLU cc_start: 0.7775 (tp30) cc_final: 0.7466 (tp30) REVERT: B 364 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.6172 (p0) outliers start: 7 outliers final: 4 residues processed: 91 average time/residue: 0.4423 time to fit residues: 43.4264 Evaluate side-chains 89 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 364 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 58 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 110 optimal weight: 0.4980 chunk 23 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.0670 chunk 59 optimal weight: 3.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.172138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.129676 restraints weight = 23745.364| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.48 r_work: 0.3404 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9294 Z= 0.112 Angle : 0.501 6.584 12626 Z= 0.253 Chirality : 0.039 0.142 1488 Planarity : 0.004 0.041 1546 Dihedral : 11.062 114.952 1378 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.52 % Allowed : 14.05 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.26), residues: 1152 helix: 2.11 (0.19), residues: 812 sheet: 1.20 (0.94), residues: 38 loop : -0.98 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 90 TYR 0.016 0.001 TYR B 385 PHE 0.006 0.001 PHE B 95 TRP 0.008 0.001 TRP A 465 HIS 0.001 0.000 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 9294) covalent geometry : angle 0.50113 / 0.25 (12626) hydrogen bonds : bond 0.03184 / 2.21 ( 576) hydrogen bonds : angle 3.80101 / 2.76 ( 1698) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.6941 (mmp) cc_final: 0.6654 (mmm) REVERT: A 225 ILE cc_start: 0.7894 (tp) cc_final: 0.7684 (tp) REVERT: A 251 ASP cc_start: 0.7733 (t0) cc_final: 0.7124 (m-30) REVERT: A 260 MET cc_start: 0.6732 (ttm) cc_final: 0.6445 (ttm) REVERT: A 267 ILE cc_start: 0.6755 (mp) cc_final: 0.6550 (mt) REVERT: A 517 LYS cc_start: 0.7059 (mmmt) cc_final: 0.6368 (mppt) REVERT: B 172 GLU cc_start: 0.7816 (tp30) cc_final: 0.7506 (tp30) REVERT: B 364 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.6133 (p0) outliers start: 5 outliers final: 4 residues processed: 85 average time/residue: 0.4583 time to fit residues: 41.9414 Evaluate side-chains 83 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 364 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 81 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 24 optimal weight: 0.0070 chunk 76 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 94 optimal weight: 0.0050 overall best weight: 0.5412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.172471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.129754 restraints weight = 24096.118| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 3.52 r_work: 0.3407 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9294 Z= 0.111 Angle : 0.499 6.589 12626 Z= 0.252 Chirality : 0.040 0.142 1488 Planarity : 0.004 0.040 1546 Dihedral : 10.671 115.441 1378 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.41 % Allowed : 13.95 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.26), residues: 1152 helix: 2.15 (0.19), residues: 812 sheet: 1.18 (0.94), residues: 38 loop : -0.95 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 87 TYR 0.016 0.001 TYR B 385 PHE 0.008 0.001 PHE A 95 TRP 0.008 0.001 TRP A 465 HIS 0.001 0.000 HIS B 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 9294) covalent geometry : angle 0.49899 / 0.25 (12626) hydrogen bonds : bond 0.03140 / 2.18 ( 576) hydrogen bonds : angle 3.78157 / 2.75 ( 1698) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.6939 (mmp) cc_final: 0.6647 (mmm) REVERT: A 225 ILE cc_start: 0.7928 (tp) cc_final: 0.7724 (tp) REVERT: A 251 ASP cc_start: 0.7717 (t0) cc_final: 0.7135 (m-30) REVERT: A 260 MET cc_start: 0.6787 (ttm) cc_final: 0.6519 (ttt) REVERT: A 267 ILE cc_start: 0.6771 (mp) cc_final: 0.6552 (mt) REVERT: B 172 GLU cc_start: 0.7781 (tp30) cc_final: 0.7487 (tp30) REVERT: B 364 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.6096 (p0) outliers start: 4 outliers final: 3 residues processed: 82 average time/residue: 0.4454 time to fit residues: 39.3919 Evaluate side-chains 83 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 364 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 63 optimal weight: 0.5980 chunk 56 optimal weight: 0.0570 chunk 105 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.172640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.132455 restraints weight = 16993.539| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.90 r_work: 0.3442 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9294 Z= 0.111 Angle : 0.499 6.603 12626 Z= 0.251 Chirality : 0.040 0.142 1488 Planarity : 0.004 0.040 1546 Dihedral : 10.369 115.351 1378 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.52 % Allowed : 13.95 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.26), residues: 1152 helix: 2.16 (0.19), residues: 812 sheet: 1.10 (0.95), residues: 38 loop : -0.93 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 90 TYR 0.016 0.001 TYR B 385 PHE 0.007 0.001 PHE A 83 TRP 0.007 0.001 TRP A 465 HIS 0.001 0.000 HIS B 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 9294) covalent geometry : angle 0.49859 / 0.25 (12626) hydrogen bonds : bond 0.03136 / 2.17 ( 576) hydrogen bonds : angle 3.77597 / 2.74 ( 1698) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2594.15 seconds wall clock time: 44 minutes 46.53 seconds (2686.53 seconds total)