Starting phenix.real_space_refine on Sun Aug 24 17:20:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ger_51305/08_2025/9ger_51305.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ger_51305/08_2025/9ger_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ger_51305/08_2025/9ger_51305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ger_51305/08_2025/9ger_51305.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ger_51305/08_2025/9ger_51305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ger_51305/08_2025/9ger_51305.map" } 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-2.0-5787/lib/python3.9/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: 4.80, per 1000 atoms: 0.23 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: 6.24 Conformation dependent library (CDL) restraints added in 607.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 2.03 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: 3.11 Time building geometry restraints manager: 2.64 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=" CA GLN N 193 " pdb=" CB GLN N 193 " ideal model delta sigma weight residual 1.531 1.627 -0.096 3.28e-02 9.30e+02 8.61e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.67e+00 bond pdb=" CB GLU G 61 " pdb=" CG GLU G 61 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.46e+00 bond pdb=" CB GLU G 64 " pdb=" CG GLU G 64 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.18e+00 bond pdb=" SD MET B 84 " pdb=" CE MET B 84 " ideal model delta sigma weight residual 1.791 1.764 0.027 2.50e-02 1.60e+03 1.13e+00 ... (remaining 22346 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 31212 2.35 - 4.70: 278 4.70 - 7.06: 37 7.06 - 9.41: 4 9.41 - 11.76: 2 Bond angle restraints: 31533 Sorted by residual: angle pdb=" CB MET B 84 " pdb=" CG MET B 84 " pdb=" SD MET B 84 " ideal model delta sigma weight residual 112.70 124.46 -11.76 3.00e+00 1.11e-01 1.54e+01 angle pdb=" C ILE F 29 " pdb=" N THR F 30 " pdb=" CA THR F 30 " ideal model delta sigma weight residual 121.54 128.06 -6.52 1.91e+00 2.74e-01 1.17e+01 angle pdb=" CA GLU C 41 " pdb=" CB GLU C 41 " pdb=" CG GLU C 41 " ideal model delta sigma weight residual 114.10 119.93 -5.83 2.00e+00 2.50e-01 8.50e+00 angle pdb=" CB MET L 287 " pdb=" CG MET L 287 " pdb=" SD MET L 287 " ideal model delta sigma weight residual 112.70 104.00 8.70 3.00e+00 1.11e-01 8.41e+00 angle pdb=" CA ARG C 99 " pdb=" CB ARG C 99 " pdb=" CG ARG C 99 " ideal model delta sigma weight residual 114.10 119.35 -5.25 2.00e+00 2.50e-01 6.89e+00 ... (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: 3066 0.049 - 0.099: 397 0.099 - 0.148: 66 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: 3.440 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 18.890 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 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 : 0.003 0.096 22376 Z= 0.137 Angle : 0.584 11.759 31583 Z= 0.313 Chirality : 0.035 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 aren 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 covalent geometry : bond 0.00292 (22351) covalent geometry : angle 0.58164 (31533) SS BOND : bond 0.00212 ( 10) SS BOND : angle 1.01909 ( 20) hydrogen bonds : bond 0.13113 ( 974) hydrogen bonds : angle 4.35973 ( 2509) Misc. bond : bond 0.04927 ( 5) link_ALPHA1-3 : bond 0.01009 ( 2) link_ALPHA1-3 : angle 1.75744 ( 6) link_ALPHA1-6 : bond 0.01180 ( 2) link_ALPHA1-6 : angle 1.42084 ( 6) link_BETA1-4 : bond 0.00380 ( 4) link_BETA1-4 : angle 1.74275 ( 12) link_BETA1-6 : bond 0.00342 ( 2) link_BETA1-6 : angle 1.27797 ( 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 : 0.411 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: 0.1492 time to fit residues: 61.5726 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 : 0.612 ------------------------------------------------------------------------------- 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: 10.0000 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: 10.0000 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3650 r_free = 0.3650 target = 0.104964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.080322 restraints weight = 50496.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.082353 restraints weight = 28010.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.082978 restraints weight = 17433.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.083096 restraints weight = 16019.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.083284 restraints weight = 15303.433| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.143 22376 Z= 0.220 Angle : 0.669 14.710 31583 Z= 0.354 Chirality : 0.039 0.232 3535 Planarity : 0.005 0.044 3036 Dihedral : 25.289 149.427 5685 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.90 % Favored : 94.05 % Rotamer: Outliers : 5.60 % Allowed : 27.98 % Favored : 66.42 % 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 aren not related in a simple way. whole: 0.24 (0.20), residues: 1865 helix: 2.08 (0.18), residues: 877 sheet: -1.96 (1.18), residues: 20 loop : -1.74 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 99 TYR 0.021 0.002 TYR D 80 PHE 0.016 0.002 PHE M 71 TRP 0.022 0.002 TRP N 271 HIS 0.004 0.001 HIS N 428 Details of bonding type rmsd covalent geometry : bond 0.00515 (22351) covalent geometry : angle 0.66560 (31533) SS BOND : bond 0.00329 ( 10) SS BOND : angle 1.45902 ( 20) hydrogen bonds : bond 0.07522 ( 974) hydrogen bonds : angle 3.53652 ( 2509) Misc. bond : bond 0.08371 ( 5) link_ALPHA1-3 : bond 0.00932 ( 2) link_ALPHA1-3 : angle 2.67140 ( 6) link_ALPHA1-6 : bond 0.01218 ( 2) link_ALPHA1-6 : angle 1.35184 ( 6) link_BETA1-4 : bond 0.00747 ( 4) link_BETA1-4 : angle 2.16670 ( 12) link_BETA1-6 : bond 0.00315 ( 2) link_BETA1-6 : angle 1.51223 ( 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 333 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 242 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 122 GLN cc_start: 0.7946 (pp30) cc_final: 0.7383 (pp30) REVERT: L 134 ASP cc_start: 0.7574 (t0) cc_final: 0.7233 (t70) REVERT: L 540 ASN cc_start: 0.7650 (m110) cc_final: 0.7047 (m110) REVERT: L 561 PHE cc_start: 0.7339 (m-80) cc_final: 0.6975 (m-80) REVERT: M 85 MET cc_start: 0.7810 (tpp) cc_final: 0.7586 (mmt) REVERT: N 175 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7256 (pmm) REVERT: N 271 TRP cc_start: 0.8343 (OUTLIER) cc_final: 0.7913 (m-10) REVERT: N 353 MET cc_start: 0.5831 (tpp) cc_final: 0.5612 (mpp) REVERT: N 412 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6817 (ptp-170) REVERT: B 27 GLN cc_start: 0.8364 (mm-40) cc_final: 0.7671 (tm-30) REVERT: B 88 TYR cc_start: 0.7707 (m-80) cc_final: 0.7304 (m-10) REVERT: C 15 LYS cc_start: 0.8873 (mtpt) cc_final: 0.8544 (mtmm) REVERT: D 102 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7372 (tm-30) REVERT: G 110 ASN cc_start: 0.8688 (t0) cc_final: 0.8299 (p0) outliers start: 91 outliers final: 60 residues processed: 320 average time/residue: 0.1430 time to fit residues: 67.3273 Evaluate side-chains 300 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 237 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 71 PHE 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 291 ILE 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 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 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 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 D residue 95 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 60 VAL 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 95 LYS 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: 3.9990 chunk 144 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 196 optimal weight: 8.9990 chunk 59 optimal weight: 0.0170 chunk 81 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.1420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 193 GLN L 330 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 = 0.3665 r_free = 0.3665 target = 0.104403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.080843 restraints weight = 47790.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.082777 restraints weight = 26855.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.084030 restraints weight = 18623.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.084796 restraints weight = 14961.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.085240 restraints weight = 13165.801| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.123 22376 Z= 0.139 Angle : 0.577 11.957 31583 Z= 0.310 Chirality : 0.035 0.203 3535 Planarity : 0.004 0.039 3036 Dihedral : 25.078 152.106 5640 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.22 % Favored : 96.73 % Rotamer: Outliers : 4.06 % Allowed : 29.52 % Favored : 66.42 % 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 aren not related in a simple way. whole: 0.48 (0.20), residues: 1865 helix: 2.30 (0.18), residues: 893 sheet: -2.04 (1.21), residues: 20 loop : -1.71 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 185 TYR 0.014 0.001 TYR F 88 PHE 0.015 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 covalent geometry : bond 0.00297 (22351) covalent geometry : angle 0.57444 (31533) SS BOND : bond 0.00230 ( 10) SS BOND : angle 0.97007 ( 20) hydrogen bonds : bond 0.05410 ( 974) hydrogen bonds : angle 3.17224 ( 2509) Misc. bond : bond 0.07347 ( 5) link_ALPHA1-3 : bond 0.00978 ( 2) link_ALPHA1-3 : angle 2.21678 ( 6) link_ALPHA1-6 : bond 0.01138 ( 2) link_ALPHA1-6 : angle 1.44938 ( 6) link_BETA1-4 : bond 0.00424 ( 4) link_BETA1-4 : angle 1.89718 ( 12) link_BETA1-6 : bond 0.00347 ( 2) link_BETA1-6 : angle 1.30791 ( 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 311 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 245 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 122 GLN cc_start: 0.7936 (pp30) cc_final: 0.7445 (pp30) REVERT: L 134 ASP cc_start: 0.7588 (t0) cc_final: 0.7256 (t70) REVERT: L 349 ARG cc_start: 0.7531 (ttp80) cc_final: 0.7303 (ttp80) REVERT: L 540 ASN cc_start: 0.7496 (m110) cc_final: 0.6992 (m110) REVERT: L 549 ASN cc_start: 0.7352 (p0) cc_final: 0.7144 (p0) REVERT: L 561 PHE cc_start: 0.7178 (m-80) cc_final: 0.6844 (m-80) REVERT: N 271 TRP cc_start: 0.8270 (OUTLIER) cc_final: 0.7889 (m-10) REVERT: N 412 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6803 (ptp-170) REVERT: B 27 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7350 (tm-30) REVERT: B 92 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8122 (ttp80) outliers start: 66 outliers final: 48 residues processed: 294 average time/residue: 0.1801 time to fit residues: 76.1119 Evaluate side-chains 284 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 233 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 238 THR 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 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 485 LEU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 86 PHE Chi-restraints excluded: chain N residue 130 ILE 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 448 VAL Chi-restraints excluded: chain N residue 511 ARG 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 70 VAL 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 E residue 51 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 130 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 98 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 39 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 193 GLN L 450 GLN N 133 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.108178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.083337 restraints weight = 49704.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.085621 restraints weight = 27106.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.086268 restraints weight = 16256.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.086563 restraints weight = 14419.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.086670 restraints weight = 13989.323| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 22376 Z= 0.150 Angle : 0.583 12.123 31583 Z= 0.312 Chirality : 0.036 0.206 3535 Planarity : 0.004 0.037 3036 Dihedral : 25.078 150.416 5636 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.88 % Favored : 95.07 % Rotamer: Outliers : 5.35 % Allowed : 27.80 % Favored : 66.85 % 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 aren not related in a simple way. whole: 0.48 (0.20), residues: 1865 helix: 2.27 (0.18), residues: 897 sheet: -1.91 (1.20), residues: 20 loop : -1.69 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 185 TYR 0.018 0.001 TYR D 80 PHE 0.014 0.001 PHE K 71 TRP 0.026 0.001 TRP N 271 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00332 (22351) covalent geometry : angle 0.58071 (31533) SS BOND : bond 0.00207 ( 10) SS BOND : angle 0.88188 ( 20) hydrogen bonds : bond 0.05625 ( 974) hydrogen bonds : angle 3.11477 ( 2509) Misc. bond : bond 0.07215 ( 5) link_ALPHA1-3 : bond 0.00994 ( 2) link_ALPHA1-3 : angle 2.31279 ( 6) link_ALPHA1-6 : bond 0.01150 ( 2) link_ALPHA1-6 : angle 1.36582 ( 6) link_BETA1-4 : bond 0.00351 ( 4) link_BETA1-4 : angle 1.93221 ( 12) link_BETA1-6 : bond 0.00284 ( 2) link_BETA1-6 : angle 1.38612 ( 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 326 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 239 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 80 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7868 (mt0) REVERT: L 122 GLN cc_start: 0.7900 (pp30) cc_final: 0.7390 (pp30) REVERT: L 134 ASP cc_start: 0.7657 (t0) cc_final: 0.7283 (t70) REVERT: L 193 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7829 (tp40) REVERT: L 540 ASN cc_start: 0.7542 (m110) cc_final: 0.7021 (m110) REVERT: L 561 PHE cc_start: 0.7208 (m-80) cc_final: 0.6873 (m-80) REVERT: N 175 MET cc_start: 0.7580 (pmm) cc_final: 0.7151 (pmm) REVERT: N 271 TRP cc_start: 0.8293 (OUTLIER) cc_final: 0.7961 (m-10) REVERT: N 412 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6783 (ptp-170) REVERT: N 549 ASN cc_start: 0.7240 (p0) cc_final: 0.7034 (p0) REVERT: B 27 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7337 (tm-30) REVERT: B 92 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8129 (ttp80) outliers start: 87 outliers final: 66 residues processed: 306 average time/residue: 0.1524 time to fit residues: 68.9346 Evaluate side-chains 304 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 233 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 80 GLN 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 193 GLN 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 410 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 86 PHE Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain N residue 130 ILE 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 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 491 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 70 VAL 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 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 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: 0.0980 chunk 69 optimal weight: 0.6980 chunk 187 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3742 r_free = 0.3742 target = 0.110114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.085546 restraints weight = 49854.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.087885 restraints weight = 26933.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.088508 restraints weight = 15955.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.088700 restraints weight = 14281.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.088802 restraints weight = 13815.217| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 22376 Z= 0.130 Angle : 0.560 10.713 31583 Z= 0.302 Chirality : 0.035 0.196 3535 Planarity : 0.004 0.035 3036 Dihedral : 25.030 150.463 5632 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.43 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 aren not related in a simple way. whole: 0.61 (0.20), residues: 1865 helix: 2.38 (0.18), residues: 897 sheet: -1.92 (1.24), residues: 20 loop : -1.62 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 349 TYR 0.020 0.001 TYR D 80 PHE 0.014 0.001 PHE K 71 TRP 0.023 0.001 TRP N 271 HIS 0.003 0.000 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00275 (22351) covalent geometry : angle 0.55752 (31533) SS BOND : bond 0.00209 ( 10) SS BOND : angle 0.77915 ( 20) hydrogen bonds : bond 0.04715 ( 974) hydrogen bonds : angle 3.00457 ( 2509) Misc. bond : bond 0.06798 ( 5) link_ALPHA1-3 : bond 0.01031 ( 2) link_ALPHA1-3 : angle 2.16309 ( 6) link_ALPHA1-6 : bond 0.01042 ( 2) link_ALPHA1-6 : angle 1.42110 ( 6) link_BETA1-4 : bond 0.00331 ( 4) link_BETA1-4 : angle 1.79016 ( 12) link_BETA1-6 : bond 0.00287 ( 2) link_BETA1-6 : angle 1.28292 ( 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 298 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 237 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 122 GLN cc_start: 0.7892 (pp30) cc_final: 0.7388 (pp30) REVERT: L 134 ASP cc_start: 0.7667 (t0) cc_final: 0.7304 (t70) REVERT: L 293 TYR cc_start: 0.6162 (OUTLIER) cc_final: 0.4205 (t80) REVERT: L 540 ASN cc_start: 0.7429 (m110) cc_final: 0.6927 (m110) REVERT: L 561 PHE cc_start: 0.7105 (m-80) cc_final: 0.6789 (m-80) REVERT: N 271 TRP cc_start: 0.8219 (OUTLIER) cc_final: 0.7921 (m-10) REVERT: N 412 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6760 (ptp-170) REVERT: B 27 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7853 (tm-30) REVERT: B 92 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8152 (ttp80) outliers start: 61 outliers final: 39 residues processed: 278 average time/residue: 0.1676 time to fit residues: 67.8639 Evaluate side-chains 272 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 229 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 71 PHE 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 293 TYR Chi-restraints excluded: chain L residue 297 LEU Chi-restraints excluded: chain L residue 327 VAL Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 353 MET Chi-restraints excluded: chain L residue 364 VAL Chi-restraints excluded: chain L residue 458 LEU Chi-restraints excluded: chain M residue 6 LYS 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 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 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 412 ARG Chi-restraints excluded: chain N residue 448 VAL Chi-restraints excluded: chain N residue 488 LYS 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 B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR 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 98 LEU Chi-restraints excluded: chain H residue 110 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 59 optimal weight: 0.9980 chunk 195 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 146 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 203 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 206 ASN M 15 ASN N 133 ASN D 106 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.103706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.079545 restraints weight = 47337.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.081578 restraints weight = 25629.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.082891 restraints weight = 17418.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.083702 restraints weight = 13793.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.084165 restraints weight = 12038.085| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.153 22376 Z= 0.204 Angle : 0.626 13.094 31583 Z= 0.335 Chirality : 0.038 0.216 3535 Planarity : 0.004 0.036 3036 Dihedral : 25.069 150.117 5629 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.52 % Favored : 94.42 % Rotamer: Outliers : 5.54 % Allowed : 28.35 % 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 aren not related in a simple way. whole: 0.45 (0.20), residues: 1865 helix: 2.29 (0.18), residues: 893 sheet: -1.73 (1.21), residues: 20 loop : -1.74 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 349 TYR 0.024 0.002 TYR D 80 PHE 0.013 0.002 PHE K 86 TRP 0.024 0.002 TRP N 271 HIS 0.003 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00473 (22351) covalent geometry : angle 0.62364 (31533) SS BOND : bond 0.00242 ( 10) SS BOND : angle 0.93564 ( 20) hydrogen bonds : bond 0.06529 ( 974) hydrogen bonds : angle 3.18993 ( 2509) Misc. bond : bond 0.09009 ( 5) link_ALPHA1-3 : bond 0.00987 ( 2) link_ALPHA1-3 : angle 2.56621 ( 6) link_ALPHA1-6 : bond 0.00907 ( 2) link_ALPHA1-6 : angle 1.26688 ( 6) link_BETA1-4 : bond 0.00411 ( 4) link_BETA1-4 : angle 2.02175 ( 12) link_BETA1-6 : bond 0.00354 ( 2) link_BETA1-6 : angle 1.53760 ( 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 322 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 232 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 80 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7922 (mt0) REVERT: L 122 GLN cc_start: 0.7831 (pp30) cc_final: 0.7222 (pp30) REVERT: L 134 ASP cc_start: 0.7626 (t0) cc_final: 0.7251 (t70) REVERT: L 525 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7346 (mtt90) REVERT: L 540 ASN cc_start: 0.7683 (m110) cc_final: 0.7167 (m110) REVERT: L 561 PHE cc_start: 0.7528 (m-80) cc_final: 0.7195 (m-80) REVERT: N 175 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7293 (pmm) REVERT: N 271 TRP cc_start: 0.8290 (OUTLIER) cc_final: 0.7984 (m-10) REVERT: N 549 ASN cc_start: 0.7546 (p0) cc_final: 0.7314 (p0) REVERT: A 62 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7707 (mt) REVERT: B 27 GLN cc_start: 0.8309 (mm-40) cc_final: 0.7335 (tm-30) outliers start: 90 outliers final: 69 residues processed: 297 average time/residue: 0.1619 time to fit residues: 70.5969 Evaluate side-chains 302 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 228 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 80 GLN 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 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 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 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 501 THR Chi-restraints excluded: chain L residue 525 ARG 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 125 CYS Chi-restraints excluded: chain N residue 130 ILE 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 347 ASP 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 488 LYS Chi-restraints excluded: chain N residue 491 VAL Chi-restraints excluded: chain N residue 511 ARG 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 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 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 E residue 107 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 18 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 175 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 93 optimal weight: 0.4980 chunk 42 optimal weight: 0.8980 chunk 44 optimal weight: 0.0060 chunk 35 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 133 ASN B 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.109134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.084350 restraints weight = 50025.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.086421 restraints weight = 26999.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.087417 restraints weight = 17692.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.087924 restraints weight = 13840.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.087995 restraints weight = 13816.769| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.143 22376 Z= 0.133 Angle : 0.574 10.947 31583 Z= 0.308 Chirality : 0.035 0.195 3535 Planarity : 0.004 0.034 3036 Dihedral : 24.998 149.851 5629 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.75 % Favored : 96.19 % Rotamer: Outliers : 3.81 % Allowed : 30.20 % 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 aren not related in a simple way. whole: 0.60 (0.20), residues: 1865 helix: 2.37 (0.18), residues: 897 sheet: -1.76 (1.23), residues: 20 loop : -1.65 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 349 TYR 0.010 0.001 TYR L 277 PHE 0.013 0.001 PHE K 71 TRP 0.023 0.001 TRP N 271 HIS 0.002 0.000 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00278 (22351) covalent geometry : angle 0.57122 (31533) SS BOND : bond 0.00213 ( 10) SS BOND : angle 0.75993 ( 20) hydrogen bonds : bond 0.04881 ( 974) hydrogen bonds : angle 3.01041 ( 2509) Misc. bond : bond 0.07919 ( 5) link_ALPHA1-3 : bond 0.01070 ( 2) link_ALPHA1-3 : angle 2.27866 ( 6) link_ALPHA1-6 : bond 0.01011 ( 2) link_ALPHA1-6 : angle 1.39890 ( 6) link_BETA1-4 : bond 0.00374 ( 4) link_BETA1-4 : angle 1.82487 ( 12) link_BETA1-6 : bond 0.00324 ( 2) link_BETA1-6 : angle 1.28827 ( 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 292 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 230 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: L 122 GLN cc_start: 0.7833 (pp30) cc_final: 0.7320 (pp30) REVERT: L 134 ASP cc_start: 0.7645 (t0) cc_final: 0.7288 (t70) REVERT: L 540 ASN cc_start: 0.7526 (m110) cc_final: 0.7038 (m110) REVERT: L 561 PHE cc_start: 0.7260 (m-80) cc_final: 0.6967 (m-80) REVERT: N 271 TRP cc_start: 0.8239 (OUTLIER) cc_final: 0.7705 (m-10) REVERT: N 353 MET cc_start: 0.5616 (OUTLIER) cc_final: 0.5065 (mmp) REVERT: N 577 GLU cc_start: 0.8067 (tp30) cc_final: 0.7661 (tt0) REVERT: B 27 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7827 (tm-30) REVERT: B 92 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8156 (ttp80) REVERT: F 23 ARG cc_start: 0.5444 (OUTLIER) cc_final: 0.4591 (tpp-160) outliers start: 62 outliers final: 44 residues processed: 276 average time/residue: 0.1667 time to fit residues: 66.8652 Evaluate side-chains 276 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 228 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 9 THR 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 264 LEU 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 448 VAL Chi-restraints excluded: chain L residue 458 LEU Chi-restraints excluded: chain M residue 6 LYS 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 300 VAL Chi-restraints excluded: chain N residue 304 THR Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 353 MET Chi-restraints excluded: chain N residue 402 ILE Chi-restraints excluded: chain N residue 488 LYS Chi-restraints excluded: chain N residue 543 ILE Chi-restraints excluded: chain A residue 100 LEU 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 F residue 23 ARG 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 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: 10.0000 chunk 50 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 85 optimal weight: 0.1980 chunk 74 optimal weight: 2.9990 chunk 116 optimal weight: 0.0870 chunk 190 optimal weight: 8.9990 chunk 68 optimal weight: 0.0040 chunk 167 optimal weight: 3.9990 overall best weight: 1.2574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 15 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 = 0.3712 r_free = 0.3712 target = 0.108114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.083368 restraints weight = 49863.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.085420 restraints weight = 26920.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.086379 restraints weight = 17695.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.087004 restraints weight = 13912.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.087054 restraints weight = 13836.095| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.123 22376 Z= 0.143 Angle : 0.585 11.701 31583 Z= 0.312 Chirality : 0.036 0.199 3535 Planarity : 0.004 0.034 3036 Dihedral : 24.997 149.306 5626 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.50 % Favored : 95.44 % Rotamer: Outliers : 3.87 % Allowed : 30.26 % 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 aren not related in a simple way. whole: 0.60 (0.20), residues: 1865 helix: 2.35 (0.18), residues: 897 sheet: -1.60 (1.24), residues: 20 loop : -1.62 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 349 TYR 0.013 0.001 TYR B 88 PHE 0.012 0.001 PHE K 71 TRP 0.023 0.001 TRP N 271 HIS 0.002 0.000 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00314 (22351) covalent geometry : angle 0.58279 (31533) SS BOND : bond 0.00216 ( 10) SS BOND : angle 0.84468 ( 20) hydrogen bonds : bond 0.05170 ( 974) hydrogen bonds : angle 3.01875 ( 2509) Misc. bond : bond 0.07211 ( 5) link_ALPHA1-3 : bond 0.01039 ( 2) link_ALPHA1-3 : angle 2.29885 ( 6) link_ALPHA1-6 : bond 0.01023 ( 2) link_ALPHA1-6 : angle 1.33360 ( 6) link_BETA1-4 : bond 0.00363 ( 4) link_BETA1-4 : angle 1.85265 ( 12) link_BETA1-6 : bond 0.00257 ( 2) link_BETA1-6 : angle 1.34632 ( 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 293 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 230 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: L 122 GLN cc_start: 0.7803 (pp30) cc_final: 0.7287 (pp30) REVERT: L 134 ASP cc_start: 0.7673 (t0) cc_final: 0.7332 (t70) REVERT: L 540 ASN cc_start: 0.7515 (m110) cc_final: 0.7014 (m110) REVERT: L 561 PHE cc_start: 0.7344 (m-80) cc_final: 0.6990 (m-80) REVERT: N 271 TRP cc_start: 0.8230 (OUTLIER) cc_final: 0.7930 (m-10) REVERT: B 27 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7830 (tm-30) REVERT: B 92 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8141 (ttp80) REVERT: F 23 ARG cc_start: 0.5435 (OUTLIER) cc_final: 0.4575 (tpp-160) outliers start: 63 outliers final: 53 residues processed: 276 average time/residue: 0.1598 time to fit residues: 63.9009 Evaluate side-chains 282 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 226 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 264 LEU 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 329 THR Chi-restraints excluded: chain L residue 364 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 474 ILE Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 11 THR 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 183 LEU 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 300 VAL Chi-restraints excluded: chain N residue 304 THR Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 402 ILE Chi-restraints excluded: chain N residue 425 SER Chi-restraints excluded: chain N residue 488 LYS Chi-restraints excluded: chain N residue 491 VAL Chi-restraints excluded: chain N residue 543 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 F residue 23 ARG 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 86 ILE Chi-restraints excluded: chain H residue 98 LEU 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: 10.0000 chunk 140 optimal weight: 5.9990 chunk 7 optimal weight: 0.2980 chunk 148 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 133 ASN B 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.106666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.081935 restraints weight = 49556.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.084306 restraints weight = 27228.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.084940 restraints weight = 16190.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.085237 restraints weight = 14210.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.085329 restraints weight = 13935.162| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 22376 Z= 0.165 Angle : 0.612 12.924 31583 Z= 0.325 Chirality : 0.037 0.207 3535 Planarity : 0.004 0.043 3036 Dihedral : 25.007 148.772 5626 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.83 % Favored : 95.12 % Rotamer: Outliers : 4.00 % Allowed : 30.26 % Favored : 65.74 % 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 aren not related in a simple way. whole: 0.54 (0.20), residues: 1865 helix: 2.30 (0.18), residues: 895 sheet: -1.49 (1.25), residues: 20 loop : -1.65 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 349 TYR 0.013 0.001 TYR D 80 PHE 0.011 0.001 PHE K 71 TRP 0.024 0.001 TRP N 271 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00375 (22351) covalent geometry : angle 0.60957 (31533) SS BOND : bond 0.00280 ( 10) SS BOND : angle 0.87434 ( 20) hydrogen bonds : bond 0.05932 ( 974) hydrogen bonds : angle 3.09028 ( 2509) Misc. bond : bond 0.08220 ( 5) link_ALPHA1-3 : bond 0.01014 ( 2) link_ALPHA1-3 : angle 2.49713 ( 6) link_ALPHA1-6 : bond 0.01038 ( 2) link_ALPHA1-6 : angle 1.32143 ( 6) link_BETA1-4 : bond 0.00388 ( 4) link_BETA1-4 : angle 1.94734 ( 12) link_BETA1-6 : bond 0.00216 ( 2) link_BETA1-6 : angle 1.43720 ( 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 289 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 224 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: L 122 GLN cc_start: 0.7812 (pp30) cc_final: 0.7280 (pp30) REVERT: L 134 ASP cc_start: 0.7680 (t0) cc_final: 0.7334 (t70) REVERT: L 540 ASN cc_start: 0.7601 (m110) cc_final: 0.7120 (m110) REVERT: L 561 PHE cc_start: 0.7427 (m-80) cc_final: 0.7156 (m-80) REVERT: M 6 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8041 (ptmt) REVERT: N 140 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.7866 (mm-40) REVERT: N 271 TRP cc_start: 0.8252 (OUTLIER) cc_final: 0.7919 (m-10) REVERT: N 353 MET cc_start: 0.5802 (mpp) cc_final: 0.5222 (mmp) REVERT: B 27 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7855 (tm-30) REVERT: B 92 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8137 (ttp80) REVERT: F 23 ARG cc_start: 0.5460 (OUTLIER) cc_final: 0.4643 (tpp-160) outliers start: 65 outliers final: 55 residues processed: 275 average time/residue: 0.1500 time to fit residues: 60.8235 Evaluate side-chains 283 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 223 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 264 LEU 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 329 THR Chi-restraints excluded: chain L residue 344 PHE Chi-restraints excluded: chain L residue 364 VAL Chi-restraints excluded: chain L residue 448 VAL Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 474 ILE 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 125 CYS Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 140 GLN Chi-restraints excluded: chain N residue 183 LEU 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 300 VAL Chi-restraints excluded: chain N residue 304 THR Chi-restraints excluded: chain N residue 402 ILE Chi-restraints excluded: chain N residue 425 SER Chi-restraints excluded: chain N residue 488 LYS Chi-restraints excluded: chain N residue 491 VAL Chi-restraints excluded: chain N residue 543 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 71 VAL Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 23 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 30.0000 chunk 68 optimal weight: 0.0040 chunk 57 optimal weight: 8.9990 chunk 180 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 202 optimal weight: 10.0000 chunk 151 optimal weight: 0.4980 chunk 75 optimal weight: 0.9990 chunk 183 optimal weight: 10.0000 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 133 ASN N 550 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.103867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.081248 restraints weight = 54306.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.083358 restraints weight = 29613.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.084714 restraints weight = 20257.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.085543 restraints weight = 16087.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.086043 restraints weight = 14047.767| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.134 22376 Z= 0.145 Angle : 0.593 12.176 31583 Z= 0.316 Chirality : 0.036 0.203 3535 Planarity : 0.004 0.035 3036 Dihedral : 24.962 148.203 5622 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.50 % Favored : 95.44 % Rotamer: Outliers : 3.81 % Allowed : 30.63 % Favored : 65.56 % 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 aren not related in a simple way. whole: 0.60 (0.20), residues: 1865 helix: 2.33 (0.18), residues: 898 sheet: -1.56 (1.25), residues: 20 loop : -1.60 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 349 TYR 0.032 0.001 TYR B 88 PHE 0.011 0.001 PHE K 71 TRP 0.023 0.001 TRP N 271 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00320 (22351) covalent geometry : angle 0.59030 (31533) SS BOND : bond 0.00253 ( 10) SS BOND : angle 0.76937 ( 20) hydrogen bonds : bond 0.05277 ( 974) hydrogen bonds : angle 3.02021 ( 2509) Misc. bond : bond 0.07602 ( 5) link_ALPHA1-3 : bond 0.01017 ( 2) link_ALPHA1-3 : angle 2.40370 ( 6) link_ALPHA1-6 : bond 0.00991 ( 2) link_ALPHA1-6 : angle 1.36004 ( 6) link_BETA1-4 : bond 0.00365 ( 4) link_BETA1-4 : angle 1.89008 ( 12) link_BETA1-6 : bond 0.00237 ( 2) link_BETA1-6 : angle 1.35530 ( 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 283 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 221 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: L 122 GLN cc_start: 0.7762 (pp30) cc_final: 0.7211 (pp30) REVERT: L 134 ASP cc_start: 0.7683 (t0) cc_final: 0.7319 (t70) REVERT: L 540 ASN cc_start: 0.7578 (m110) cc_final: 0.7043 (m110) REVERT: L 561 PHE cc_start: 0.7481 (m-80) cc_final: 0.7197 (m-80) REVERT: M 6 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8072 (ptmt) REVERT: N 140 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7872 (mm-40) REVERT: N 271 TRP cc_start: 0.8256 (OUTLIER) cc_final: 0.7901 (m-10) REVERT: B 27 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7809 (tm-30) REVERT: B 92 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8208 (ttp80) REVERT: F 23 ARG cc_start: 0.5456 (OUTLIER) cc_final: 0.4643 (tpp-160) outliers start: 62 outliers final: 56 residues processed: 270 average time/residue: 0.1616 time to fit residues: 63.9667 Evaluate side-chains 281 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 220 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 264 LEU 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 329 THR Chi-restraints excluded: chain L residue 344 PHE Chi-restraints excluded: chain L residue 364 VAL Chi-restraints excluded: chain L residue 373 LEU 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 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 125 CYS Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 140 GLN Chi-restraints excluded: chain N residue 183 LEU 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 300 VAL Chi-restraints excluded: chain N residue 304 THR 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 488 LYS Chi-restraints excluded: chain N residue 491 VAL Chi-restraints excluded: chain N residue 543 ILE 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 71 VAL Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 23 ARG 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 31 LYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 9 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 151 optimal weight: 0.9990 chunk 209 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 133 ASN N 193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.103824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.081244 restraints weight = 54255.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.083354 restraints weight = 29640.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.084715 restraints weight = 20208.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.085543 restraints weight = 16028.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.086000 restraints weight = 13991.569| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.126 22376 Z= 0.146 Angle : 0.592 12.142 31583 Z= 0.316 Chirality : 0.036 0.201 3535 Planarity : 0.004 0.040 3036 Dihedral : 24.965 147.459 5622 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.45 % Favored : 95.50 % Rotamer: Outliers : 3.87 % Allowed : 30.20 % 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 aren not related in a simple way. whole: 0.62 (0.20), residues: 1865 helix: 2.36 (0.18), residues: 895 sheet: -1.50 (1.26), residues: 20 loop : -1.60 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 349 TYR 0.013 0.001 TYR D 80 PHE 0.011 0.001 PHE K 71 TRP 0.023 0.001 TRP N 271 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00322 (22351) covalent geometry : angle 0.58929 (31533) SS BOND : bond 0.00238 ( 10) SS BOND : angle 0.75755 ( 20) hydrogen bonds : bond 0.05236 ( 974) hydrogen bonds : angle 3.01509 ( 2509) Misc. bond : bond 0.07260 ( 5) link_ALPHA1-3 : bond 0.01042 ( 2) link_ALPHA1-3 : angle 2.39864 ( 6) link_ALPHA1-6 : bond 0.01035 ( 2) link_ALPHA1-6 : angle 1.34335 ( 6) link_BETA1-4 : bond 0.00368 ( 4) link_BETA1-4 : angle 1.89621 ( 12) link_BETA1-6 : bond 0.00242 ( 2) link_BETA1-6 : angle 1.35869 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3111.38 seconds wall clock time: 54 minutes 31.16 seconds (3271.16 seconds total)