Starting phenix.real_space_refine on Fri Aug 7 12:20:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ger_51305/08_2026/9ger_51305.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ger_51305/08_2026/9ger_51305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ger_51305/08_2026/9ger_51305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ger_51305/08_2026/9ger_51305.map" model { file = "/net/cci-nas-00/data/ceres_data/9ger_51305/08_2026/9ger_51305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ger_51305/08_2026/9ger_51305.cif" } resolution = 3.58 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= 0.278 sd= 1.209 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: 8 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 2 7.16 5 P 290 5.49 5 S 76 5.16 5 Cl 1 4.86 5 C 12507 2.51 5 N 3918 2.21 5 O 4521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21316 Number of models: 1 Model: "" Number of chains: 20 Chain: "K" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 837 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 10, 'TRANS': 93} Chain: "L" Number of atoms: 3732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3732 Classifications: {'peptide': 466} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 429} Chain: "M" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 837 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 10, 'TRANS': 93} Chain: "N" Number of atoms: 3732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3732 Classifications: {'peptide': 466} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 429} Chain: "A" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "O" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "P" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {' CL': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.12, per 1000 atoms: 0.24 Number of scatterers: 21316 At special positions: 0 Unit cell: (113.56, 128.52, 173.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 2 26.01 Ca 1 19.99 Cl 1 17.00 S 76 16.00 P 290 15.00 O 4521 8.00 N 3918 7.00 C 12507 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS K 1 " - pdb=" SG CYS K 14 " distance=2.03 Simple disulfide: pdb=" SG CYS L 115 " - pdb=" SG CYS L 125 " distance=2.03 Simple disulfide: pdb=" SG CYS L 119 " - pdb=" SG CYS L 143 " distance=2.03 Simple disulfide: pdb=" SG CYS L 221 " - pdb=" SG CYS L 232 " distance=2.03 Simple disulfide: pdb=" SG CYS L 538 " - pdb=" SG CYS L 564 " distance=2.03 Simple disulfide: pdb=" SG CYS M 1 " - pdb=" SG CYS M 14 " distance=2.03 Simple disulfide: pdb=" SG CYS N 115 " - pdb=" SG CYS N 125 " distance=2.03 Simple disulfide: pdb=" SG CYS N 119 " - pdb=" SG CYS N 143 " distance=2.03 Simple disulfide: pdb=" SG CYS N 221 " - pdb=" SG CYS N 232 " distance=2.03 Simple disulfide: pdb=" SG CYS N 440 " - pdb=" SG CYS N 497 " distance=2.03 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=5, symmetry=0 Links applied ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA P 3 " - " MAN P 5 " BETA1-4 " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " BETA1-6 " NAG O 1 " - " FUC O 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG P 1 " - " FUC P 6 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 795.5 milliseconds 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3550 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 10 sheets defined 53.8% alpha, 1.8% beta 139 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 3.23 Creating SS restraints... Processing helix chain 'K' and resid 60 through 69 Processing helix chain 'K' and resid 72 through 76 removed outlier: 3.860A pdb=" N GLN K 75 " --> pdb=" O PRO K 72 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU K 76 " --> pdb=" O THR K 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 72 through 76' Processing helix chain 'K' and resid 84 through 98 removed outlier: 4.326A pdb=" N GLN K 88 " --> pdb=" O LEU K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 173 through 178 removed outlier: 3.744A pdb=" N TYR L 177 " --> pdb=" O ALA L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 186 Processing helix chain 'L' and resid 219 through 224 removed outlier: 3.525A pdb=" N LEU L 222 " --> pdb=" O ASP L 219 " (cutoff:3.500A) Processing helix chain 'L' and resid 239 through 242 removed outlier: 3.886A pdb=" N GLU L 242 " --> pdb=" O ARG L 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 239 through 242' Processing helix chain 'L' and resid 243 through 268 removed outlier: 3.545A pdb=" N THR L 247 " --> pdb=" O MET L 243 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN L 268 " --> pdb=" O LEU L 264 " (cutoff:3.500A) Processing helix chain 'L' and resid 272 through 297 Processing helix chain 'L' and resid 298 through 300 No H-bonds generated for 'chain 'L' and resid 298 through 300' Processing helix chain 'L' and resid 302 through 310 Processing helix chain 'L' and resid 325 through 332 Processing helix chain 'L' and resid 333 through 339 removed outlier: 3.690A pdb=" N HIS L 336 " --> pdb=" O ARG L 333 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE L 339 " --> pdb=" O HIS L 336 " (cutoff:3.500A) Processing helix chain 'L' and resid 362 through 365 removed outlier: 3.811A pdb=" N PHE L 365 " --> pdb=" O SER L 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 362 through 365' Processing helix chain 'L' and resid 368 through 373 removed outlier: 3.547A pdb=" N VAL L 372 " --> pdb=" O SER L 368 " (cutoff:3.500A) Processing helix chain 'L' and resid 377 through 386 removed outlier: 3.520A pdb=" N LEU L 381 " --> pdb=" O ILE L 377 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA L 386 " --> pdb=" O ARG L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 405 Processing helix chain 'L' and resid 416 through 429 removed outlier: 3.555A pdb=" N GLY L 429 " --> pdb=" O SER L 425 " (cutoff:3.500A) Processing helix chain 'L' and resid 432 through 440 Processing helix chain 'L' and resid 447 through 456 Processing helix chain 'L' and resid 458 through 468 Processing helix chain 'L' and resid 470 through 474 Processing helix chain 'L' and resid 475 through 483 removed outlier: 3.638A pdb=" N GLU L 483 " --> pdb=" O GLY L 479 " (cutoff:3.500A) Processing helix chain 'L' and resid 494 through 508 Processing helix chain 'L' and resid 521 through 528 Processing helix chain 'L' and resid 532 through 541 removed outlier: 3.519A pdb=" N THR L 541 " --> pdb=" O ILE L 537 " (cutoff:3.500A) Processing helix chain 'L' and resid 572 through 576 Processing helix chain 'M' and resid 60 through 68 Processing helix chain 'M' and resid 72 through 76 removed outlier: 4.014A pdb=" N GLN M 75 " --> pdb=" O PRO M 72 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU M 76 " --> pdb=" O THR M 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 72 through 76' Processing helix chain 'M' and resid 84 through 98 removed outlier: 3.548A pdb=" N ASP M 98 " --> pdb=" O ASP M 94 " (cutoff:3.500A) Processing helix chain 'N' and resid 180 through 187 Processing helix chain 'N' and resid 243 through 268 removed outlier: 3.720A pdb=" N THR N 247 " --> pdb=" O MET N 243 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN N 268 " --> pdb=" O LEU N 264 " (cutoff:3.500A) Processing helix chain 'N' and resid 272 through 297 Processing helix chain 'N' and resid 298 through 300 No H-bonds generated for 'chain 'N' and resid 298 through 300' Processing helix chain 'N' and resid 302 through 310 Processing helix chain 'N' and resid 327 through 333 removed outlier: 3.643A pdb=" N ALA N 331 " --> pdb=" O VAL N 327 " (cutoff:3.500A) Processing helix chain 'N' and resid 334 through 338 removed outlier: 3.896A pdb=" N LEU N 338 " --> pdb=" O GLY N 335 " (cutoff:3.500A) Processing helix chain 'N' and resid 368 through 374 removed outlier: 3.658A pdb=" N VAL N 372 " --> pdb=" O SER N 368 " (cutoff:3.500A) Processing helix chain 'N' and resid 377 through 386 removed outlier: 3.727A pdb=" N ALA N 386 " --> pdb=" O ARG N 382 " (cutoff:3.500A) Processing helix chain 'N' and resid 400 through 405 removed outlier: 3.670A pdb=" N ARG N 405 " --> pdb=" O GLU N 401 " (cutoff:3.500A) Processing helix chain 'N' and resid 416 through 429 Processing helix chain 'N' and resid 432 through 441 removed outlier: 3.535A pdb=" N TRP N 436 " --> pdb=" O GLY N 432 " (cutoff:3.500A) Processing helix chain 'N' and resid 447 through 456 Processing helix chain 'N' and resid 457 through 469 removed outlier: 3.861A pdb=" N GLN N 467 " --> pdb=" O LYS N 463 " (cutoff:3.500A) Processing helix chain 'N' and resid 470 through 474 Processing helix chain 'N' and resid 475 through 483 removed outlier: 3.616A pdb=" N GLU N 483 " --> pdb=" O GLY N 479 " (cutoff:3.500A) Processing helix chain 'N' and resid 492 through 508 removed outlier: 3.747A pdb=" N THR N 501 " --> pdb=" O CYS N 497 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN N 502 " --> pdb=" O ILE N 498 " (cutoff:3.500A) Processing helix chain 'N' and resid 521 through 529 Processing helix chain 'N' and resid 535 through 541 removed outlier: 3.639A pdb=" N ASP N 539 " --> pdb=" O ARG N 535 " (cutoff:3.500A) Processing helix chain 'N' and resid 572 through 576 Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.655A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 87 through 114 removed outlier: 3.574A pdb=" N ALA A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.811A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.824A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 39 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.819A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.939A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.559A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 71 removed outlier: 4.300A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.514A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 36 through 46 removed outlier: 3.756A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.633A pdb=" N VAL D 63 " --> pdb=" O MET D 59 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASN D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL D 66 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.559A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 121 removed outlier: 4.111A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 87 through 114 removed outlier: 4.041A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.597A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.719A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 removed outlier: 4.474A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.244A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.653A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.587A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 16 through 21' Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 45 through 71 removed outlier: 4.638A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.801A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.519A pdb=" N MET H 56 " --> pdb=" O SER H 52 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.539A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.925A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 78 through 83 removed outlier: 6.933A pdb=" N ARG K 82 " --> pdb=" O ALA L 389 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 342 through 343 Processing sheet with id=AA3, first strand: chain 'L' and resid 545 through 546 Processing sheet with id=AA4, first strand: chain 'M' and resid 78 through 83 removed outlier: 4.110A pdb=" N ALA N 389 " --> pdb=" O ASP M 79 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 188 through 189 removed outlier: 4.457A pdb=" N LEU N 196 " --> pdb=" O ASN N 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 342 through 344 Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.564A pdb=" N THR G 101 " --> pdb=" O THR B 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.210A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.345A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.558A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 619 hydrogen bonds defined for protein. 1803 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 355 hydrogen bonds 706 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 4.08 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 8597 1.39 - 1.56: 13045 1.56 - 1.74: 579 1.74 - 1.91: 122 1.91 - 2.08: 8 Bond restraints: 22351 Sorted by residual: bond pdb=" C3' DT I -67 " pdb=" C2' DT I -67 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DA J -67 " pdb=" C2' DA J -67 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DG I -19 " pdb=" C2' DG I -19 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DG I 23 " pdb=" C2' DG I 23 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DA I -1 " pdb=" C2' DA I -1 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.81e+00 ... (remaining 22346 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 31026 2.35 - 4.70: 464 4.70 - 7.06: 37 7.06 - 9.41: 4 9.41 - 11.76: 2 Bond angle restraints: 31533 Sorted by residual: angle pdb=" N3 DT I -67 " pdb=" C4 DT I -67 " pdb=" O4 DT I -67 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT I 33 " pdb=" C4 DT I 33 " pdb=" O4 DT I 33 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT J 1 " pdb=" C4 DT J 1 " pdb=" O4 DT J 1 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT I -24 " pdb=" C4 DT I -24 " pdb=" O4 DT I -24 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT I 67 " pdb=" C4 DT I 67 " pdb=" O4 DT I 67 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 ... (remaining 31528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.36: 10999 31.36 - 62.72: 1923 62.72 - 94.09: 53 94.09 - 125.45: 0 125.45 - 156.81: 3 Dihedral angle restraints: 12978 sinusoidal: 7491 harmonic: 5487 Sorted by residual: dihedral pdb=" CB CYS N 115 " pdb=" SG CYS N 115 " pdb=" SG CYS N 125 " pdb=" CB CYS N 125 " ideal model delta sinusoidal sigma weight residual 93.00 -179.51 -87.49 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CB CYS L 115 " pdb=" SG CYS L 115 " pdb=" SG CYS L 125 " pdb=" CB CYS L 125 " ideal model delta sinusoidal sigma weight residual -86.00 -170.85 84.85 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CB CYS M 1 " pdb=" SG CYS M 1 " pdb=" SG CYS M 14 " pdb=" CB CYS M 14 " ideal model delta sinusoidal sigma weight residual -86.00 -119.90 33.90 1 1.00e+01 1.00e-02 1.63e+01 ... (remaining 12975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2805 0.049 - 0.099: 639 0.099 - 0.148: 85 0.148 - 0.197: 5 0.197 - 0.247: 1 Chirality restraints: 3535 Sorted by residual: chirality pdb=" CA GLN N 193 " pdb=" N GLN N 193 " pdb=" C GLN N 193 " pdb=" CB GLN N 193 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB ILE N 290 " pdb=" CA ILE N 290 " pdb=" CG1 ILE N 290 " pdb=" CG2 ILE N 290 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.09 -0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 3532 not shown) Planarity restraints: 3036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR K 77 " 0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO K 78 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO K 78 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO K 78 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN N 193 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.79e+00 pdb=" C GLN N 193 " -0.029 2.00e-02 2.50e+03 pdb=" O GLN N 193 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU N 194 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR N 293 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.74e+00 pdb=" C TYR N 293 " -0.029 2.00e-02 2.50e+03 pdb=" O TYR N 293 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG N 294 " 0.010 2.00e-02 2.50e+03 ... (remaining 3033 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 281 2.65 - 3.21: 17426 3.21 - 3.77: 32707 3.77 - 4.34: 41135 4.34 - 4.90: 64201 Nonbonded interactions: 155750 Sorted by model distance: nonbonded pdb=" O2 DT I -72 " pdb=" O6 DG J 71 " model vdw 2.083 3.040 nonbonded pdb=" OD1 ASN L 549 " pdb=" N ASN L 550 " model vdw 2.171 3.120 nonbonded pdb=" NH2 ARG N 349 " pdb=" OH TYR N 557 " model vdw 2.194 3.120 nonbonded pdb=" C2 DT I -72 " pdb=" O6 DG J 71 " model vdw 2.217 3.260 nonbonded pdb=" OG SER N 521 " pdb=" OE1 GLN N 523 " model vdw 2.248 3.040 ... (remaining 155745 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 117) selection = (chain 'G' and resid 13 through 117) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'K' and resid 1 through 104) selection = (chain 'M' and resid 1 through 104) } ncs_group { reference = (chain 'L' and resid 113 through 602) selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 6.860 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: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.900 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 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:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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 : 0.005 0.096 22376 Z= 0.389 Angle : 0.688 11.759 31583 Z= 0.526 Chirality : 0.041 0.247 3535 Planarity : 0.004 0.052 3036 Dihedral : 24.130 156.812 9398 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.81 % Favored : 96.14 % Rotamer: Outliers : 3.14 % Allowed : 29.34 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.50 (0.20), residues: 1865 helix: 2.36 (0.19), residues: 860 sheet: -2.06 (1.18), residues: 20 loop : -1.60 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 349 TYR 0.026 0.001 TYR D 80 PHE 0.019 0.001 PHE K 71 TRP 0.027 0.001 TRP N 271 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.39 (22351) covalent geometry : angle 0.68585 / 0.53 (31533) SS BOND : bond 0.00212 / 0.14 ( 10) SS BOND : angle 1.01909 / 0.49 ( 20) hydrogen bonds : bond 0.13113 / 8.45 ( 974) hydrogen bonds : angle 4.35973 / 3.10 ( 2509) Misc. bond : bond 0.04927 / 3.20 ( 5) link_ALPHA1-3 : bond 0.01009 / 0.52 ( 2) link_ALPHA1-3 : angle 1.75744 / 0.89 ( 6) link_ALPHA1-6 : bond 0.01180 / 0.62 ( 2) link_ALPHA1-6 : angle 1.42084 / 0.79 ( 6) link_BETA1-4 : bond 0.00380 / 0.19 ( 4) link_BETA1-4 : angle 1.74275 / 1.35 ( 12) link_BETA1-6 : bond 0.00342 / 0.17 ( 2) link_BETA1-6 : angle 1.27797 / 0.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 245 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 122 GLN cc_start: 0.7875 (pp30) cc_final: 0.7344 (pp30) REVERT: L 134 ASP cc_start: 0.7696 (t0) cc_final: 0.7289 (t70) REVERT: L 142 ASP cc_start: 0.6929 (t0) cc_final: 0.6662 (m-30) REVERT: L 293 TYR cc_start: 0.6061 (OUTLIER) cc_final: 0.4134 (t80) REVERT: L 349 ARG cc_start: 0.7669 (ttp80) cc_final: 0.7430 (ttp80) REVERT: L 395 ASN cc_start: 0.7610 (OUTLIER) cc_final: 0.6999 (p0) REVERT: L 507 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7337 (ttm170) REVERT: L 540 ASN cc_start: 0.7305 (m110) cc_final: 0.6801 (m110) REVERT: L 561 PHE cc_start: 0.7265 (m-80) cc_final: 0.6965 (m-80) REVERT: N 175 MET cc_start: 0.7439 (pmm) cc_final: 0.6984 (pmm) REVERT: N 353 MET cc_start: 0.5447 (tpp) cc_final: 0.5118 (tpp) REVERT: B 27 GLN cc_start: 0.8463 (mm-40) cc_final: 0.7687 (tm-30) REVERT: C 15 LYS cc_start: 0.9084 (mtpt) cc_final: 0.8624 (mtmm) REVERT: D 102 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7280 (tm-30) REVERT: G 110 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8445 (p0) outliers start: 51 outliers final: 42 residues processed: 283 average time/residue: 0.1780 time to fit residues: 73.7612 Evaluate side-chains 284 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 238 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 88 GLN Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain L residue 293 TYR Chi-restraints excluded: chain L residue 297 LEU Chi-restraints excluded: chain L residue 312 THR Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 448 VAL Chi-restraints excluded: chain L residue 458 LEU Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 507 ARG Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 86 PHE Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 221 CYS Chi-restraints excluded: chain N residue 232 CYS Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 304 THR Chi-restraints excluded: chain N residue 332 PHE Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 378 ASP Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 448 VAL Chi-restraints excluded: chain N residue 453 THR Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 30.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 133 ASN N 428 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.103988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.080419 restraints weight = 47840.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.082389 restraints weight = 25224.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.083267 restraints weight = 16989.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.083525 restraints weight = 13694.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.083645 restraints weight = 13852.184| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.132 22376 Z= 0.215 Angle : 0.683 14.004 31583 Z= 0.368 Chirality : 0.044 0.233 3535 Planarity : 0.005 0.040 3036 Dihedral : 25.523 154.037 5685 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.09 % Favored : 94.85 % Rotamer: Outliers : 5.41 % Allowed : 28.23 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.33 (0.20), residues: 1865 helix: 2.23 (0.18), residues: 865 sheet: -2.00 (1.19), residues: 20 loop : -1.73 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 99 TYR 0.018 0.002 TYR D 80 PHE 0.017 0.002 PHE M 71 TRP 0.017 0.002 TRP N 271 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.21 (22351) covalent geometry : angle 0.68066 / 0.37 (31533) SS BOND : bond 0.00236 / 0.15 ( 10) SS BOND : angle 1.13167 / 0.66 ( 20) hydrogen bonds : bond 0.07577 / 4.95 ( 974) hydrogen bonds : angle 3.59679 / 2.57 ( 2509) Misc. bond : bond 0.06528 / 3.60 ( 5) link_ALPHA1-3 : bond 0.01001 / 0.51 ( 2) link_ALPHA1-3 : angle 2.30289 / 1.14 ( 6) link_ALPHA1-6 : bond 0.01165 / 0.61 ( 2) link_ALPHA1-6 : angle 1.24593 / 0.70 ( 6) link_BETA1-4 : bond 0.00552 / 0.27 ( 4) link_BETA1-4 : angle 2.14911 / 1.70 ( 12) link_BETA1-6 : bond 0.00300 / 0.15 ( 2) link_BETA1-6 : angle 1.57911 / 0.82 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 240 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 122 GLN cc_start: 0.7953 (pp30) cc_final: 0.7375 (pp30) REVERT: L 134 ASP cc_start: 0.7597 (t0) cc_final: 0.7204 (t70) REVERT: L 293 TYR cc_start: 0.6284 (OUTLIER) cc_final: 0.4429 (t80) REVERT: L 540 ASN cc_start: 0.7602 (m110) cc_final: 0.7022 (m110) REVERT: L 561 PHE cc_start: 0.7331 (m-80) cc_final: 0.6899 (m-80) REVERT: M 85 MET cc_start: 0.7891 (tpp) cc_final: 0.7603 (tpt) REVERT: N 175 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7102 (pmm) REVERT: N 271 TRP cc_start: 0.8346 (OUTLIER) cc_final: 0.8090 (m-10) REVERT: N 353 MET cc_start: 0.5851 (tpp) cc_final: 0.5482 (mpp) REVERT: N 412 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6853 (ptp-170) REVERT: N 488 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8323 (mtpt) REVERT: B 27 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7696 (tm-30) REVERT: C 15 LYS cc_start: 0.8941 (mtpt) cc_final: 0.8559 (mtmm) REVERT: C 90 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7582 (t0) REVERT: D 102 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7365 (tm-30) REVERT: G 33 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8654 (mp) REVERT: G 110 ASN cc_start: 0.8744 (t0) cc_final: 0.8349 (p0) outliers start: 88 outliers final: 58 residues processed: 315 average time/residue: 0.1582 time to fit residues: 73.6650 Evaluate side-chains 300 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 235 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 125 CYS Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 264 LEU Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain L residue 293 TYR Chi-restraints excluded: chain L residue 297 LEU Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 312 THR Chi-restraints excluded: chain L residue 327 VAL Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 364 VAL Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 448 VAL Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 458 LEU Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain L residue 481 VAL Chi-restraints excluded: chain L residue 485 LEU Chi-restraints excluded: chain L residue 491 VAL Chi-restraints excluded: chain L residue 547 SER Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 221 CYS Chi-restraints excluded: chain N residue 232 CYS Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 271 TRP Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 378 ASP Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 412 ARG Chi-restraints excluded: chain N residue 448 VAL Chi-restraints excluded: chain N residue 454 VAL Chi-restraints excluded: chain N residue 481 VAL Chi-restraints excluded: chain N residue 488 LYS Chi-restraints excluded: chain N residue 519 VAL Chi-restraints excluded: chain N residue 543 ILE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 22 optimal weight: 8.9990 chunk 102 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 196 optimal weight: 21.9990 chunk 59 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 330 ASN N 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.104620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.080956 restraints weight = 47744.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.082869 restraints weight = 26842.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.084094 restraints weight = 18616.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.084840 restraints weight = 14947.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.085285 restraints weight = 13168.293| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 22376 Z= 0.155 Angle : 0.612 12.661 31583 Z= 0.336 Chirality : 0.041 0.239 3535 Planarity : 0.004 0.042 3036 Dihedral : 25.440 153.878 5648 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.97 % Favored : 95.98 % Rotamer: Outliers : 5.23 % Allowed : 28.04 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.46 (0.20), residues: 1865 helix: 2.36 (0.18), residues: 876 sheet: -2.03 (1.19), residues: 20 loop : -1.72 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 185 TYR 0.023 0.001 TYR D 80 PHE 0.013 0.001 PHE K 71 TRP 0.019 0.001 TRP N 271 HIS 0.003 0.001 HIS N 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (22351) covalent geometry : angle 0.60912 / 0.34 (31533) SS BOND : bond 0.00226 / 0.16 ( 10) SS BOND : angle 0.91108 / 0.55 ( 20) hydrogen bonds : bond 0.06513 / 4.22 ( 974) hydrogen bonds : angle 3.33178 / 2.40 ( 2509) Misc. bond : bond 0.07823 / 5.02 ( 5) link_ALPHA1-3 : bond 0.00919 / 0.48 ( 2) link_ALPHA1-3 : angle 2.31105 / 1.15 ( 6) link_ALPHA1-6 : bond 0.01127 / 0.59 ( 2) link_ALPHA1-6 : angle 1.35496 / 0.75 ( 6) link_BETA1-4 : bond 0.00411 / 0.20 ( 4) link_BETA1-4 : angle 1.87069 / 1.45 ( 12) link_BETA1-6 : bond 0.00291 / 0.14 ( 2) link_BETA1-6 : angle 1.39987 / 0.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 245 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 122 GLN cc_start: 0.7958 (pp30) cc_final: 0.7457 (pp30) REVERT: L 134 ASP cc_start: 0.7528 (t0) cc_final: 0.7226 (t70) REVERT: L 540 ASN cc_start: 0.7485 (m110) cc_final: 0.6963 (m110) REVERT: L 549 ASN cc_start: 0.7357 (p0) cc_final: 0.7147 (p0) REVERT: L 561 PHE cc_start: 0.7219 (m-80) cc_final: 0.6844 (m-80) REVERT: M 85 MET cc_start: 0.7684 (tpp) cc_final: 0.7393 (tpt) REVERT: N 175 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.7069 (pmm) REVERT: N 271 TRP cc_start: 0.8352 (OUTLIER) cc_final: 0.7660 (m-10) REVERT: N 412 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6773 (ptp-170) REVERT: N 577 GLU cc_start: 0.7874 (tp30) cc_final: 0.7540 (tt0) REVERT: B 27 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7583 (tm-30) REVERT: C 15 LYS cc_start: 0.8805 (mtpt) cc_final: 0.8520 (mtmm) REVERT: G 110 ASN cc_start: 0.8590 (t0) cc_final: 0.8354 (p0) outliers start: 85 outliers final: 61 residues processed: 313 average time/residue: 0.1625 time to fit residues: 75.2933 Evaluate side-chains 302 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 238 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 125 CYS Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 196 LEU Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain L residue 297 LEU Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 312 THR Chi-restraints excluded: chain L residue 319 SER Chi-restraints excluded: chain L residue 327 VAL Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 364 VAL Chi-restraints excluded: chain L residue 373 LEU Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 448 VAL Chi-restraints excluded: chain L residue 458 LEU Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain L residue 485 LEU Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 86 PHE Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 221 CYS Chi-restraints excluded: chain N residue 232 CYS Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 271 TRP Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 304 THR Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 412 ARG Chi-restraints excluded: chain N residue 425 SER Chi-restraints excluded: chain N residue 448 VAL Chi-restraints excluded: chain N residue 481 VAL Chi-restraints excluded: chain N residue 519 VAL Chi-restraints excluded: chain N residue 543 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 39 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 101 optimal weight: 0.0570 chunk 14 optimal weight: 0.6980 chunk 161 optimal weight: 0.2980 chunk 123 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 330 ASN N 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.106873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.082981 restraints weight = 47571.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.085049 restraints weight = 25567.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.086376 restraints weight = 17293.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.087201 restraints weight = 13650.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.087696 restraints weight = 11890.890| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 22376 Z= 0.131 Angle : 0.578 11.191 31583 Z= 0.319 Chirality : 0.039 0.237 3535 Planarity : 0.004 0.041 3036 Dihedral : 25.433 153.078 5642 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.34 % Favored : 95.60 % Rotamer: Outliers : 4.31 % Allowed : 29.03 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.55 (0.20), residues: 1865 helix: 2.32 (0.18), residues: 899 sheet: -1.96 (1.21), residues: 20 loop : -1.66 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 349 TYR 0.015 0.001 TYR F 88 PHE 0.015 0.001 PHE K 71 TRP 0.025 0.001 TRP N 271 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.13 (22351) covalent geometry : angle 0.57596 / 0.32 (31533) SS BOND : bond 0.00211 / 0.14 ( 10) SS BOND : angle 0.79863 / 0.48 ( 20) hydrogen bonds : bond 0.05537 / 3.58 ( 974) hydrogen bonds : angle 3.12883 / 2.26 ( 2509) Misc. bond : bond 0.07126 / 4.65 ( 5) link_ALPHA1-3 : bond 0.00993 / 0.51 ( 2) link_ALPHA1-3 : angle 2.12931 / 1.07 ( 6) link_ALPHA1-6 : bond 0.01080 / 0.56 ( 2) link_ALPHA1-6 : angle 1.37198 / 0.76 ( 6) link_BETA1-4 : bond 0.00359 / 0.18 ( 4) link_BETA1-4 : angle 1.84406 / 1.44 ( 12) link_BETA1-6 : bond 0.00332 / 0.16 ( 2) link_BETA1-6 : angle 1.30299 / 0.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 240 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 122 GLN cc_start: 0.7930 (pp30) cc_final: 0.7414 (pp30) REVERT: L 134 ASP cc_start: 0.7606 (t0) cc_final: 0.7272 (t70) REVERT: L 349 ARG cc_start: 0.7536 (ttp80) cc_final: 0.7273 (ttp80) REVERT: L 540 ASN cc_start: 0.7421 (m110) cc_final: 0.6909 (m110) REVERT: L 561 PHE cc_start: 0.7181 (m-80) cc_final: 0.6803 (m-80) REVERT: N 175 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7035 (pmm) REVERT: N 271 TRP cc_start: 0.8248 (OUTLIER) cc_final: 0.7972 (m-10) REVERT: N 412 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.6799 (ptp-170) REVERT: B 27 GLN cc_start: 0.8205 (mm-40) cc_final: 0.7539 (tm-30) REVERT: B 92 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8171 (ttp80) REVERT: G 110 ASN cc_start: 0.8600 (OUTLIER) cc_final: 0.8394 (p0) outliers start: 70 outliers final: 50 residues processed: 290 average time/residue: 0.1669 time to fit residues: 71.2742 Evaluate side-chains 289 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 234 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 125 CYS Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain L residue 297 LEU Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 364 VAL Chi-restraints excluded: chain L residue 385 MET Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 448 VAL Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 458 LEU Chi-restraints excluded: chain L residue 485 LEU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 86 PHE Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 221 CYS Chi-restraints excluded: chain N residue 232 CYS Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 271 TRP Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 378 ASP Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 412 ARG Chi-restraints excluded: chain N residue 448 VAL Chi-restraints excluded: chain N residue 543 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 110 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 2 optimal weight: 0.0670 chunk 69 optimal weight: 4.9990 chunk 187 optimal weight: 30.0000 chunk 192 optimal weight: 30.0000 chunk 41 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 chunk 158 optimal weight: 0.0020 chunk 103 optimal weight: 0.0670 overall best weight: 1.8268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 450 GLN M 15 ASN N 133 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.104113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.080478 restraints weight = 47619.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.082375 restraints weight = 26848.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.083616 restraints weight = 18687.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.084385 restraints weight = 14968.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.084809 restraints weight = 13153.462| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 22376 Z= 0.157 Angle : 0.605 13.187 31583 Z= 0.330 Chirality : 0.041 0.237 3535 Planarity : 0.004 0.036 3036 Dihedral : 25.467 153.372 5637 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.72 % Favored : 95.23 % Rotamer: Outliers : 5.66 % Allowed : 27.68 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.49 (0.20), residues: 1865 helix: 2.28 (0.18), residues: 895 sheet: -1.93 (1.21), residues: 20 loop : -1.68 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 99 TYR 0.012 0.001 TYR D 80 PHE 0.014 0.001 PHE K 71 TRP 0.024 0.001 TRP N 271 HIS 0.003 0.001 HIS N 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (22351) covalent geometry : angle 0.60297 / 0.33 (31533) SS BOND : bond 0.00493 / 0.20 ( 10) SS BOND : angle 0.81912 / 0.51 ( 20) hydrogen bonds : bond 0.06163 / 4.00 ( 974) hydrogen bonds : angle 3.16485 / 2.29 ( 2509) Misc. bond : bond 0.06741 / 4.19 ( 5) link_ALPHA1-3 : bond 0.01028 / 0.53 ( 2) link_ALPHA1-3 : angle 2.26630 / 1.13 ( 6) link_ALPHA1-6 : bond 0.01114 / 0.58 ( 2) link_ALPHA1-6 : angle 1.37192 / 0.76 ( 6) link_BETA1-4 : bond 0.00418 / 0.21 ( 4) link_BETA1-4 : angle 1.94178 / 1.53 ( 12) link_BETA1-6 : bond 0.00254 / 0.12 ( 2) link_BETA1-6 : angle 1.41095 / 0.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 232 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 122 GLN cc_start: 0.7911 (pp30) cc_final: 0.7428 (pp30) REVERT: L 134 ASP cc_start: 0.7591 (t0) cc_final: 0.7249 (t70) REVERT: L 349 ARG cc_start: 0.7557 (ttp80) cc_final: 0.7338 (ttp80) REVERT: L 478 MET cc_start: 0.7775 (tpp) cc_final: 0.7503 (tpp) REVERT: L 540 ASN cc_start: 0.7498 (m110) cc_final: 0.6975 (m110) REVERT: L 549 ASN cc_start: 0.7450 (p0) cc_final: 0.7250 (p0) REVERT: L 561 PHE cc_start: 0.7195 (m-80) cc_final: 0.6842 (m-80) REVERT: N 175 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7222 (pmm) REVERT: N 271 TRP cc_start: 0.8228 (OUTLIER) cc_final: 0.7944 (m-10) REVERT: N 412 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6797 (ptp-170) REVERT: B 27 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7497 (tm-30) REVERT: B 92 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8117 (ttp80) outliers start: 92 outliers final: 74 residues processed: 299 average time/residue: 0.1497 time to fit residues: 66.9886 Evaluate side-chains 309 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 231 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 125 CYS Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 196 LEU Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain L residue 297 LEU Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 319 SER Chi-restraints excluded: chain L residue 327 VAL Chi-restraints excluded: chain L residue 364 VAL Chi-restraints excluded: chain L residue 373 LEU Chi-restraints excluded: chain L residue 385 MET Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 448 VAL Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 458 LEU Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain L residue 485 LEU Chi-restraints excluded: chain L residue 501 THR Chi-restraints excluded: chain L residue 565 SER Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 86 PHE Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 221 CYS Chi-restraints excluded: chain N residue 232 CYS Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 271 TRP Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 304 THR Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 378 ASP Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 412 ARG Chi-restraints excluded: chain N residue 425 SER Chi-restraints excluded: chain N residue 448 VAL Chi-restraints excluded: chain N residue 481 VAL Chi-restraints excluded: chain N residue 488 LYS Chi-restraints excluded: chain N residue 519 VAL Chi-restraints excluded: chain N residue 543 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 59 optimal weight: 3.9990 chunk 195 optimal weight: 40.0000 chunk 120 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 203 optimal weight: 20.0000 chunk 198 optimal weight: 30.0000 chunk 182 optimal weight: 30.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 330 ASN N 133 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.104069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.079816 restraints weight = 47329.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.081848 restraints weight = 25674.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.083143 restraints weight = 17459.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.083949 restraints weight = 13849.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.084423 restraints weight = 12095.856| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 22376 Z= 0.181 Angle : 0.644 13.820 31583 Z= 0.346 Chirality : 0.042 0.239 3535 Planarity : 0.004 0.034 3036 Dihedral : 25.481 153.974 5637 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.42 % Favored : 94.53 % Rotamer: Outliers : 5.78 % Allowed : 28.11 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.38 (0.20), residues: 1865 helix: 2.21 (0.18), residues: 891 sheet: -1.84 (1.21), residues: 20 loop : -1.75 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 76 TYR 0.016 0.001 TYR D 80 PHE 0.013 0.001 PHE K 71 TRP 0.024 0.001 TRP N 271 HIS 0.004 0.001 HIS N 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (22351) covalent geometry : angle 0.64170 / 0.35 (31533) SS BOND : bond 0.00287 / 0.19 ( 10) SS BOND : angle 0.90786 / 0.60 ( 20) hydrogen bonds : bond 0.06900 / 4.48 ( 974) hydrogen bonds : angle 3.25481 / 2.35 ( 2509) Misc. bond : bond 0.07724 / 4.94 ( 5) link_ALPHA1-3 : bond 0.00954 / 0.49 ( 2) link_ALPHA1-3 : angle 2.53001 / 1.25 ( 6) link_ALPHA1-6 : bond 0.01100 / 0.57 ( 2) link_ALPHA1-6 : angle 1.42159 / 0.79 ( 6) link_BETA1-4 : bond 0.00377 / 0.19 ( 4) link_BETA1-4 : angle 1.90011 / 1.56 ( 12) link_BETA1-6 : bond 0.00234 / 0.12 ( 2) link_BETA1-6 : angle 1.54858 / 0.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 236 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 122 GLN cc_start: 0.7861 (pp30) cc_final: 0.7319 (pp30) REVERT: L 134 ASP cc_start: 0.7596 (t0) cc_final: 0.7200 (t70) REVERT: L 540 ASN cc_start: 0.7670 (m110) cc_final: 0.7103 (m110) REVERT: L 549 ASN cc_start: 0.7794 (p0) cc_final: 0.7548 (p0) REVERT: L 561 PHE cc_start: 0.7555 (m-80) cc_final: 0.7246 (m-80) REVERT: N 271 TRP cc_start: 0.8351 (OUTLIER) cc_final: 0.8027 (m-10) REVERT: N 549 ASN cc_start: 0.7457 (p0) cc_final: 0.7224 (p0) REVERT: A 62 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7702 (mt) REVERT: B 27 GLN cc_start: 0.8289 (mm-40) cc_final: 0.7524 (tm-30) outliers start: 94 outliers final: 77 residues processed: 306 average time/residue: 0.1481 time to fit residues: 68.1613 Evaluate side-chains 311 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 232 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 125 CYS Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 196 LEU Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 264 LEU Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain L residue 297 LEU Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 312 THR Chi-restraints excluded: chain L residue 319 SER Chi-restraints excluded: chain L residue 327 VAL Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 364 VAL Chi-restraints excluded: chain L residue 373 LEU Chi-restraints excluded: chain L residue 385 MET Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 458 LEU Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain L residue 501 THR Chi-restraints excluded: chain L residue 565 SER Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 86 PHE Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 221 CYS Chi-restraints excluded: chain N residue 232 CYS Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 271 TRP Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 378 ASP Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 402 ILE Chi-restraints excluded: chain N residue 425 SER Chi-restraints excluded: chain N residue 448 VAL Chi-restraints excluded: chain N residue 453 THR Chi-restraints excluded: chain N residue 481 VAL Chi-restraints excluded: chain N residue 488 LYS Chi-restraints excluded: chain N residue 491 VAL Chi-restraints excluded: chain N residue 519 VAL Chi-restraints excluded: chain N residue 543 ILE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 18 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 35 optimal weight: 0.0570 chunk 39 optimal weight: 0.3980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 330 ASN N 133 ASN N 193 GLN B 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.107005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.083191 restraints weight = 47591.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.085265 restraints weight = 25448.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.086599 restraints weight = 17138.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.087442 restraints weight = 13509.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.087923 restraints weight = 11725.192| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.156 22376 Z= 0.130 Angle : 0.591 10.487 31583 Z= 0.324 Chirality : 0.040 0.240 3535 Planarity : 0.004 0.048 3036 Dihedral : 25.433 154.073 5636 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.49 % Favored : 96.46 % Rotamer: Outliers : 3.75 % Allowed : 30.07 % Favored : 66.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.54 (0.20), residues: 1865 helix: 2.33 (0.18), residues: 894 sheet: -1.93 (1.24), residues: 20 loop : -1.66 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 349 TYR 0.011 0.001 TYR L 277 PHE 0.013 0.001 PHE K 71 TRP 0.024 0.001 TRP N 271 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.13 (22351) covalent geometry : angle 0.58849 / 0.32 (31533) SS BOND : bond 0.00334 / 0.18 ( 10) SS BOND : angle 0.81168 / 0.53 ( 20) hydrogen bonds : bond 0.05272 / 3.39 ( 974) hydrogen bonds : angle 3.07045 / 2.23 ( 2509) Misc. bond : bond 0.08202 / 5.64 ( 5) link_ALPHA1-3 : bond 0.01022 / 0.53 ( 2) link_ALPHA1-3 : angle 2.30683 / 1.16 ( 6) link_ALPHA1-6 : bond 0.01050 / 0.54 ( 2) link_ALPHA1-6 : angle 1.41528 / 0.78 ( 6) link_BETA1-4 : bond 0.00372 / 0.18 ( 4) link_BETA1-4 : angle 1.77341 / 1.37 ( 12) link_BETA1-6 : bond 0.00429 / 0.21 ( 2) link_BETA1-6 : angle 1.25277 / 0.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 232 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: L 122 GLN cc_start: 0.7855 (pp30) cc_final: 0.7342 (pp30) REVERT: L 134 ASP cc_start: 0.7596 (t0) cc_final: 0.7226 (t70) REVERT: L 349 ARG cc_start: 0.7626 (ttp80) cc_final: 0.7358 (ttp80) REVERT: L 540 ASN cc_start: 0.7534 (m110) cc_final: 0.6987 (m110) REVERT: L 549 ASN cc_start: 0.7551 (p0) cc_final: 0.7332 (p0) REVERT: L 561 PHE cc_start: 0.7346 (m-80) cc_final: 0.7024 (m-80) REVERT: N 271 TRP cc_start: 0.8237 (OUTLIER) cc_final: 0.7944 (m-10) REVERT: N 549 ASN cc_start: 0.7467 (p0) cc_final: 0.7234 (p0) REVERT: B 27 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7866 (tm-30) REVERT: B 92 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8175 (ttp80) outliers start: 61 outliers final: 47 residues processed: 275 average time/residue: 0.1702 time to fit residues: 69.2085 Evaluate side-chains 273 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 224 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 125 CYS Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain L residue 297 LEU Chi-restraints excluded: chain L residue 312 THR Chi-restraints excluded: chain L residue 319 SER Chi-restraints excluded: chain L residue 327 VAL Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 458 LEU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 86 PHE Chi-restraints excluded: chain N residue 125 CYS Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 271 TRP Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 304 THR Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 488 LYS Chi-restraints excluded: chain N residue 543 ILE Chi-restraints excluded: chain N residue 551 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 110 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 40.0000 chunk 50 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 0.0370 chunk 190 optimal weight: 20.0000 chunk 68 optimal weight: 0.0070 chunk 167 optimal weight: 1.9990 overall best weight: 0.6076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 206 ASN N 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.110667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.086067 restraints weight = 49925.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.088586 restraints weight = 26712.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.089153 restraints weight = 15516.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.089387 restraints weight = 14007.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.089519 restraints weight = 13512.473| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.108 22376 Z= 0.126 Angle : 0.574 10.634 31583 Z= 0.316 Chirality : 0.039 0.239 3535 Planarity : 0.004 0.035 3036 Dihedral : 25.446 154.113 5630 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.18 % Favored : 95.76 % Rotamer: Outliers : 3.38 % Allowed : 30.50 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.64 (0.20), residues: 1865 helix: 2.37 (0.18), residues: 900 sheet: -1.85 (1.23), residues: 20 loop : -1.60 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 76 TYR 0.012 0.001 TYR D 80 PHE 0.013 0.001 PHE K 71 TRP 0.022 0.001 TRP N 271 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.13 (22351) covalent geometry : angle 0.57196 / 0.32 (31533) SS BOND : bond 0.00231 / 0.16 ( 10) SS BOND : angle 0.92098 / 0.65 ( 20) hydrogen bonds : bond 0.04951 / 3.20 ( 974) hydrogen bonds : angle 2.98446 / 2.17 ( 2509) Misc. bond : bond 0.06284 / 4.12 ( 5) link_ALPHA1-3 : bond 0.01043 / 0.53 ( 2) link_ALPHA1-3 : angle 2.11067 / 1.06 ( 6) link_ALPHA1-6 : bond 0.01043 / 0.54 ( 2) link_ALPHA1-6 : angle 1.36936 / 0.77 ( 6) link_BETA1-4 : bond 0.00302 / 0.15 ( 4) link_BETA1-4 : angle 1.76458 / 1.43 ( 12) link_BETA1-6 : bond 0.00332 / 0.16 ( 2) link_BETA1-6 : angle 1.23412 / 0.65 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 231 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: L 122 GLN cc_start: 0.7872 (pp30) cc_final: 0.7355 (pp30) REVERT: L 134 ASP cc_start: 0.7647 (t0) cc_final: 0.7306 (t70) REVERT: L 349 ARG cc_start: 0.7574 (ttp80) cc_final: 0.7304 (ttp80) REVERT: L 540 ASN cc_start: 0.7429 (m110) cc_final: 0.6932 (m110) REVERT: L 561 PHE cc_start: 0.7153 (m-80) cc_final: 0.6839 (m-80) REVERT: N 271 TRP cc_start: 0.8196 (OUTLIER) cc_final: 0.7923 (m-10) REVERT: N 347 ASP cc_start: 0.7213 (OUTLIER) cc_final: 0.6963 (p0) REVERT: N 353 MET cc_start: 0.3956 (mmp) cc_final: 0.3485 (mmp) REVERT: N 549 ASN cc_start: 0.7379 (p0) cc_final: 0.7161 (p0) REVERT: A 81 ASP cc_start: 0.8696 (p0) cc_final: 0.8460 (p0) REVERT: B 27 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7836 (tm-30) REVERT: B 92 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8172 (ttp80) outliers start: 55 outliers final: 45 residues processed: 274 average time/residue: 0.1853 time to fit residues: 74.3098 Evaluate side-chains 275 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 227 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain L residue 125 CYS Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 206 ASN Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain L residue 297 LEU Chi-restraints excluded: chain L residue 312 THR Chi-restraints excluded: chain L residue 319 SER Chi-restraints excluded: chain L residue 327 VAL Chi-restraints excluded: chain L residue 344 PHE Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 458 LEU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 86 PHE Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain N residue 125 CYS Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 271 TRP Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 304 THR Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 488 LYS Chi-restraints excluded: chain N residue 551 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 110 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 16 optimal weight: 0.8980 chunk 203 optimal weight: 20.0000 chunk 140 optimal weight: 0.1980 chunk 7 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 185 optimal weight: 30.0000 chunk 107 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 206 ASN N 133 ASN B 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.109937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.085230 restraints weight = 49793.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.087889 restraints weight = 26642.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.088403 restraints weight = 15245.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.088537 restraints weight = 13868.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.088650 restraints weight = 13368.652| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 22376 Z= 0.138 Angle : 0.590 11.509 31583 Z= 0.322 Chirality : 0.040 0.239 3535 Planarity : 0.004 0.034 3036 Dihedral : 25.447 154.311 5626 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.91 % Favored : 96.03 % Rotamer: Outliers : 3.32 % Allowed : 30.69 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.66 (0.20), residues: 1865 helix: 2.38 (0.18), residues: 900 sheet: -1.79 (1.23), residues: 20 loop : -1.58 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 349 TYR 0.022 0.001 TYR B 88 PHE 0.012 0.001 PHE K 71 TRP 0.022 0.001 TRP N 271 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (22351) covalent geometry : angle 0.58741 / 0.32 (31533) SS BOND : bond 0.00210 / 0.14 ( 10) SS BOND : angle 0.79186 / 0.51 ( 20) hydrogen bonds : bond 0.05226 / 3.39 ( 974) hydrogen bonds : angle 3.00929 / 2.19 ( 2509) Misc. bond : bond 0.05794 / 3.70 ( 5) link_ALPHA1-3 : bond 0.01057 / 0.54 ( 2) link_ALPHA1-3 : angle 2.18479 / 1.09 ( 6) link_ALPHA1-6 : bond 0.01038 / 0.54 ( 2) link_ALPHA1-6 : angle 1.37125 / 0.77 ( 6) link_BETA1-4 : bond 0.00362 / 0.18 ( 4) link_BETA1-4 : angle 1.80258 / 1.44 ( 12) link_BETA1-6 : bond 0.00322 / 0.15 ( 2) link_BETA1-6 : angle 1.29696 / 0.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 226 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: L 122 GLN cc_start: 0.7853 (pp30) cc_final: 0.7339 (pp30) REVERT: L 134 ASP cc_start: 0.7638 (t0) cc_final: 0.7291 (t70) REVERT: L 349 ARG cc_start: 0.7606 (ttp80) cc_final: 0.7297 (ttp80) REVERT: L 540 ASN cc_start: 0.7484 (m110) cc_final: 0.7024 (m110) REVERT: L 561 PHE cc_start: 0.7213 (m-80) cc_final: 0.6898 (m-80) REVERT: N 271 TRP cc_start: 0.8210 (OUTLIER) cc_final: 0.7939 (m-10) REVERT: N 347 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.7057 (p0) REVERT: N 353 MET cc_start: 0.4007 (mmp) cc_final: 0.3492 (mmp) REVERT: N 549 ASN cc_start: 0.7414 (p0) cc_final: 0.7186 (p0) REVERT: A 81 ASP cc_start: 0.8717 (p0) cc_final: 0.8494 (p0) REVERT: B 27 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7838 (tm-30) REVERT: B 92 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8161 (ttp80) outliers start: 54 outliers final: 47 residues processed: 266 average time/residue: 0.1694 time to fit residues: 66.2985 Evaluate side-chains 276 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 226 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain L residue 125 CYS Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 206 ASN Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain L residue 297 LEU Chi-restraints excluded: chain L residue 312 THR Chi-restraints excluded: chain L residue 319 SER Chi-restraints excluded: chain L residue 327 VAL Chi-restraints excluded: chain L residue 344 PHE Chi-restraints excluded: chain L residue 364 VAL Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 458 LEU Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 86 PHE Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain N residue 125 CYS Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 271 TRP Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 304 THR Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 488 LYS Chi-restraints excluded: chain N residue 551 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 110 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 59 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 57 optimal weight: 0.2980 chunk 180 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 202 optimal weight: 20.0000 chunk 151 optimal weight: 0.6980 chunk 75 optimal weight: 0.0870 chunk 183 optimal weight: 50.0000 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 206 ASN N 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.109956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.085239 restraints weight = 50035.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.087518 restraints weight = 26539.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.088397 restraints weight = 15848.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.088349 restraints weight = 14257.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.088493 restraints weight = 13778.765| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 22376 Z= 0.134 Angle : 0.590 11.479 31583 Z= 0.322 Chirality : 0.040 0.240 3535 Planarity : 0.004 0.034 3036 Dihedral : 25.442 154.491 5626 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.24 % Favored : 95.71 % Rotamer: Outliers : 3.38 % Allowed : 30.69 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.66 (0.20), residues: 1865 helix: 2.38 (0.18), residues: 899 sheet: -1.76 (1.24), residues: 20 loop : -1.57 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 349 TYR 0.033 0.001 TYR D 80 PHE 0.012 0.001 PHE K 71 TRP 0.022 0.001 TRP N 271 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (22351) covalent geometry : angle 0.58752 / 0.32 (31533) SS BOND : bond 0.00206 / 0.14 ( 10) SS BOND : angle 0.75270 / 0.46 ( 20) hydrogen bonds : bond 0.05269 / 3.42 ( 974) hydrogen bonds : angle 3.01483 / 2.19 ( 2509) Misc. bond : bond 0.06260 / 4.05 ( 5) link_ALPHA1-3 : bond 0.01043 / 0.54 ( 2) link_ALPHA1-3 : angle 2.21388 / 1.11 ( 6) link_ALPHA1-6 : bond 0.01038 / 0.54 ( 2) link_ALPHA1-6 : angle 1.34813 / 0.76 ( 6) link_BETA1-4 : bond 0.00363 / 0.18 ( 4) link_BETA1-4 : angle 1.80261 / 1.45 ( 12) link_BETA1-6 : bond 0.00341 / 0.16 ( 2) link_BETA1-6 : angle 1.28472 / 0.67 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 226 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: L 122 GLN cc_start: 0.7853 (pp30) cc_final: 0.7335 (pp30) REVERT: L 134 ASP cc_start: 0.7645 (t0) cc_final: 0.7287 (t70) REVERT: L 349 ARG cc_start: 0.7603 (ttp80) cc_final: 0.7283 (ttp80) REVERT: L 540 ASN cc_start: 0.7514 (m110) cc_final: 0.7057 (m110) REVERT: L 561 PHE cc_start: 0.7229 (m-80) cc_final: 0.6914 (m-80) REVERT: N 271 TRP cc_start: 0.8209 (OUTLIER) cc_final: 0.7935 (m-10) REVERT: N 347 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.7187 (p0) REVERT: N 353 MET cc_start: 0.4002 (mmp) cc_final: 0.3529 (mmp) REVERT: N 549 ASN cc_start: 0.7375 (p0) cc_final: 0.7114 (p0) REVERT: A 81 ASP cc_start: 0.8722 (p0) cc_final: 0.8499 (p0) REVERT: B 27 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7844 (tm-30) REVERT: B 92 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8156 (ttp80) outliers start: 55 outliers final: 50 residues processed: 266 average time/residue: 0.1666 time to fit residues: 65.6305 Evaluate side-chains 279 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 226 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 125 CYS Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain L residue 297 LEU Chi-restraints excluded: chain L residue 312 THR Chi-restraints excluded: chain L residue 319 SER Chi-restraints excluded: chain L residue 327 VAL Chi-restraints excluded: chain L residue 344 PHE Chi-restraints excluded: chain L residue 364 VAL Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 458 LEU Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 485 LEU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 86 PHE Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain N residue 125 CYS Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 271 TRP Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 304 THR Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 402 ILE Chi-restraints excluded: chain N residue 488 LYS Chi-restraints excluded: chain N residue 491 VAL Chi-restraints excluded: chain N residue 551 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 31 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 9 optimal weight: 4.9990 chunk 173 optimal weight: 0.2980 chunk 114 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 151 optimal weight: 0.7980 chunk 209 optimal weight: 30.0000 chunk 93 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 206 ASN N 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.106381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.082374 restraints weight = 47631.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.084486 restraints weight = 25332.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.085804 restraints weight = 16984.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.086666 restraints weight = 13375.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.087166 restraints weight = 11596.254| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 22376 Z= 0.141 Angle : 0.601 12.001 31583 Z= 0.326 Chirality : 0.040 0.242 3535 Planarity : 0.004 0.034 3036 Dihedral : 25.439 154.915 5626 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.45 % Favored : 95.50 % Rotamer: Outliers : 3.44 % Allowed : 30.69 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.64 (0.20), residues: 1865 helix: 2.37 (0.18), residues: 895 sheet: -1.68 (1.25), residues: 20 loop : -1.57 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 349 TYR 0.032 0.001 TYR D 80 PHE 0.012 0.001 PHE K 71 TRP 0.022 0.001 TRP N 271 HIS 0.003 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (22351) covalent geometry : angle 0.59847 / 0.33 (31533) SS BOND : bond 0.00211 / 0.14 ( 10) SS BOND : angle 0.76430 / 0.47 ( 20) hydrogen bonds : bond 0.05567 / 3.61 ( 974) hydrogen bonds : angle 3.04003 / 2.20 ( 2509) Misc. bond : bond 0.06622 / 4.28 ( 5) link_ALPHA1-3 : bond 0.01034 / 0.53 ( 2) link_ALPHA1-3 : angle 2.28175 / 1.14 ( 6) link_ALPHA1-6 : bond 0.01038 / 0.54 ( 2) link_ALPHA1-6 : angle 1.32976 / 0.75 ( 6) link_BETA1-4 : bond 0.00379 / 0.19 ( 4) link_BETA1-4 : angle 1.83957 / 1.47 ( 12) link_BETA1-6 : bond 0.00334 / 0.16 ( 2) link_BETA1-6 : angle 1.31988 / 0.69 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3278.02 seconds wall clock time: 57 minutes 6.92 seconds (3426.92 seconds total)