Starting phenix.real_space_refine on Wed Jul 30 08:40:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yet_33777/07_2025/7yet_33777.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yet_33777/07_2025/7yet_33777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yet_33777/07_2025/7yet_33777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yet_33777/07_2025/7yet_33777.map" model { file = "/net/cci-nas-00/data/ceres_data/7yet_33777/07_2025/7yet_33777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yet_33777/07_2025/7yet_33777.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 7588 2.51 5 N 1981 2.21 5 O 2227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11862 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 8038 Classifications: {'peptide': 999} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 53, 'TRANS': 945} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2011 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 260, 1983 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 242} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 260, 1983 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 242} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1990 Chain: "C" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 733 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 515 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 66} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 513 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 65} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'SVR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'SVR:plan-7': 1, 'SVR:plan-4': 1, 'SVR:plan-3': 1, 'SVR:plan-9': 1} Unresolved non-hydrogen planarities: 31 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AGLN B 244 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 244 " occ=0.50 residue: pdb=" N ASER B 266 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 266 " occ=0.50 residue: pdb=" N ACYS B 275 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 275 " occ=0.50 residue: pdb=" N ATHR B 335 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR B 335 " occ=0.50 Time building chain proxies: 8.25, per 1000 atoms: 0.70 Number of scatterers: 11862 At special positions: 0 Unit cell: (177.84, 132.08, 102.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2227 8.00 N 1981 7.00 C 7588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 1.8 seconds 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2856 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 6 sheets defined 60.7% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 21 through 29 removed outlier: 3.587A pdb=" N VAL A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.574A pdb=" N THR A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 removed outlier: 3.605A pdb=" N LYS A 82 " --> pdb=" O PRO A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 112 removed outlier: 3.533A pdb=" N ASP A 110 " --> pdb=" O TYR A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 122 Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 146 through 166 removed outlier: 3.664A pdb=" N ASN A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.816A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 221' Processing helix chain 'A' and resid 235 through 261 removed outlier: 3.719A pdb=" N GLU A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASP A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 288 Processing helix chain 'A' and resid 291 through 296 removed outlier: 3.655A pdb=" N ILE A 295 " --> pdb=" O GLY A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 308 Processing helix chain 'A' and resid 317 through 334 Processing helix chain 'A' and resid 341 through 348 Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 361 through 369 Processing helix chain 'A' and resid 381 through 392 removed outlier: 3.620A pdb=" N VAL A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HIS A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 422 Processing helix chain 'A' and resid 432 through 436 removed outlier: 3.716A pdb=" N LEU A 435 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 436 " --> pdb=" O ARG A 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 432 through 436' Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 450 through 454 removed outlier: 3.835A pdb=" N MET A 453 " --> pdb=" O PRO A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 464 removed outlier: 3.695A pdb=" N LEU A 464 " --> pdb=" O PHE A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 498 removed outlier: 3.615A pdb=" N TRP A 494 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ASP A 495 " --> pdb=" O THR A 492 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA A 496 " --> pdb=" O CYS A 493 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL A 497 " --> pdb=" O TRP A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 537 Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.614A pdb=" N LEU A 541 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 584 Processing helix chain 'A' and resid 634 through 640 removed outlier: 3.875A pdb=" N LEU A 638 " --> pdb=" O LYS A 635 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE A 640 " --> pdb=" O ASN A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 656 Proline residue: A 647 - end of helix removed outlier: 3.604A pdb=" N TYR A 656 " --> pdb=" O CYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 688 through 692 removed outlier: 3.668A pdb=" N ARG A 691 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN A 692 " --> pdb=" O GLU A 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 688 through 692' Processing helix chain 'A' and resid 712 through 731 removed outlier: 3.611A pdb=" N TRP A 716 " --> pdb=" O GLN A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.809A pdb=" N GLU A 762 " --> pdb=" O ALA A 758 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 763 " --> pdb=" O ASP A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 792 removed outlier: 3.791A pdb=" N THR A 792 " --> pdb=" O PRO A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 820 removed outlier: 3.569A pdb=" N THR A 820 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 850 removed outlier: 3.664A pdb=" N GLU A 850 " --> pdb=" O ARG A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 875 removed outlier: 3.714A pdb=" N PHE A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 889 removed outlier: 3.868A pdb=" N THR A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 903 removed outlier: 3.580A pdb=" N ILE A 899 " --> pdb=" O ASP A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 927 through 943 Processing helix chain 'A' and resid 949 through 954 removed outlier: 3.613A pdb=" N ILE A 953 " --> pdb=" O PHE A 949 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 949 through 954' Processing helix chain 'A' and resid 963 through 968 removed outlier: 3.998A pdb=" N LEU A 967 " --> pdb=" O ILE A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 978 Processing helix chain 'A' and resid 1069 through 1085 Processing helix chain 'A' and resid 1315 through 1331 removed outlier: 3.937A pdb=" N ILE A1320 " --> pdb=" O PHE A1316 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN A1321 " --> pdb=" O GLN A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1335 through 1339 Processing helix chain 'B' and resid 82 through 117 Processing helix chain 'B' and resid 118 through 125 removed outlier: 4.117A pdb=" N TYR B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP B 123 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 148 removed outlier: 3.987A pdb=" N SER B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU B 131 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.774A pdb=" N GLU B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 187 removed outlier: 3.547A pdb=" N GLU B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 206 removed outlier: 4.263A pdb=" N THR B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 230 Processing helix chain 'B' and resid 237 through 254 removed outlier: 3.759A pdb=" N GLN B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 270 Processing helix chain 'B' and resid 272 through 284 Processing helix chain 'B' and resid 306 through 309 removed outlier: 4.123A pdb=" N LYS B 309 " --> pdb=" O ALA B 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'C' and resid 82 through 118 removed outlier: 4.232A pdb=" N LEU C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 142 removed outlier: 3.739A pdb=" N SER C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 130 " --> pdb=" O LYS C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 165 removed outlier: 3.725A pdb=" N GLU C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 112 Processing helix chain 'D' and resid 114 through 146 Proline residue: D 120 - end of helix removed outlier: 4.028A pdb=" N SER D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER D 130 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU D 144 " --> pdb=" O ALA D 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 144 removed outlier: 4.842A pdb=" N LYS E 119 " --> pdb=" O GLU E 115 " (cutoff:3.500A) Proline residue: E 120 - end of helix removed outlier: 3.717A pdb=" N LEU E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 399 Processing sheet with id=AA3, first strand: chain 'A' and resid 562 through 565 Processing sheet with id=AA4, first strand: chain 'A' and resid 626 through 632 removed outlier: 3.819A pdb=" N LYS A 734 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 799 through 801 Processing sheet with id=AA6, first strand: chain 'B' and resid 294 through 297 removed outlier: 6.560A pdb=" N ILE B 295 " --> pdb=" O GLN B 329 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N CYS B 326 " --> pdb=" O LEU B 338 " (cutoff:3.500A) 640 hydrogen bonds defined for protein. 1831 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.18 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3803 1.34 - 1.46: 2046 1.46 - 1.58: 6196 1.58 - 1.70: 0 1.70 - 1.82: 93 Bond restraints: 12138 Sorted by residual: bond pdb=" O25 SVR A2301 " pdb=" S17 SVR A2301 " ideal model delta sigma weight residual 1.469 1.566 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" O30 SVR A2301 " pdb=" S21 SVR A2301 " ideal model delta sigma weight residual 1.472 1.566 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" C13 SVR A2301 " pdb=" C20 SVR A2301 " ideal model delta sigma weight residual 1.401 1.482 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" O24 SVR A2301 " pdb=" S17 SVR A2301 " ideal model delta sigma weight residual 1.485 1.429 0.056 2.00e-02 2.50e+03 7.84e+00 bond pdb=" O29 SVR A2301 " pdb=" S21 SVR A2301 " ideal model delta sigma weight residual 1.473 1.418 0.055 2.00e-02 2.50e+03 7.53e+00 ... (remaining 12133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 16069 1.68 - 3.35: 360 3.35 - 5.03: 55 5.03 - 6.71: 21 6.71 - 8.38: 6 Bond angle restraints: 16511 Sorted by residual: angle pdb=" N ILE A 963 " pdb=" CA ILE A 963 " pdb=" C ILE A 963 " ideal model delta sigma weight residual 112.96 109.00 3.96 1.00e+00 1.00e+00 1.57e+01 angle pdb=" N PHE A 113 " pdb=" CA PHE A 113 " pdb=" C PHE A 113 " ideal model delta sigma weight residual 110.80 118.23 -7.43 2.13e+00 2.20e-01 1.22e+01 angle pdb=" N ASN A 87 " pdb=" CA ASN A 87 " pdb=" C ASN A 87 " ideal model delta sigma weight residual 114.75 110.40 4.35 1.26e+00 6.30e-01 1.19e+01 angle pdb=" C ALA A 111 " pdb=" N LEU A 112 " pdb=" CA LEU A 112 " ideal model delta sigma weight residual 121.54 127.99 -6.45 1.91e+00 2.74e-01 1.14e+01 angle pdb=" N GLN B 100 " pdb=" CA GLN B 100 " pdb=" CB GLN B 100 " ideal model delta sigma weight residual 110.28 115.23 -4.95 1.55e+00 4.16e-01 1.02e+01 ... (remaining 16506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 6551 17.89 - 35.79: 587 35.79 - 53.68: 108 53.68 - 71.57: 25 71.57 - 89.46: 7 Dihedral angle restraints: 7278 sinusoidal: 2872 harmonic: 4406 Sorted by residual: dihedral pdb=" CA ASP A 110 " pdb=" C ASP A 110 " pdb=" N ALA A 111 " pdb=" CA ALA A 111 " ideal model delta harmonic sigma weight residual 180.00 154.93 25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA LEU A 112 " pdb=" C LEU A 112 " pdb=" N PHE A 113 " pdb=" CA PHE A 113 " ideal model delta harmonic sigma weight residual 180.00 -158.02 -21.98 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ALA A 111 " pdb=" C ALA A 111 " pdb=" N LEU A 112 " pdb=" CA LEU A 112 " ideal model delta harmonic sigma weight residual 180.00 159.08 20.92 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 7275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1484 0.047 - 0.093: 322 0.093 - 0.139: 70 0.139 - 0.186: 3 0.186 - 0.232: 1 Chirality restraints: 1880 Sorted by residual: chirality pdb=" CB ILE A 454 " pdb=" CA ILE A 454 " pdb=" CG1 ILE A 454 " pdb=" CG2 ILE A 454 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ASN A 681 " pdb=" N ASN A 681 " pdb=" C ASN A 681 " pdb=" CB ASN A 681 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" CA GLN B 99 " pdb=" N GLN B 99 " pdb=" C GLN B 99 " pdb=" CB GLN B 99 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 1877 not shown) Planarity restraints: 2111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 SVR A2301 " 0.316 2.00e-02 2.50e+03 2.60e-01 8.43e+02 pdb=" C26 SVR A2301 " -0.092 2.00e-02 2.50e+03 pdb=" C33 SVR A2301 " 0.194 2.00e-02 2.50e+03 pdb=" N19 SVR A2301 " -0.437 2.00e-02 2.50e+03 pdb=" O32 SVR A2301 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C39 SVR A2301 " 0.235 2.00e-02 2.50e+03 2.33e-01 8.17e+02 pdb=" C43 SVR A2301 " -0.016 2.00e-02 2.50e+03 pdb=" C46 SVR A2301 " -0.146 2.00e-02 2.50e+03 pdb=" N41 SVR A2301 " -0.335 2.00e-02 2.50e+03 pdb=" N44 SVR A2301 " 0.359 2.00e-02 2.50e+03 pdb=" O45 SVR A2301 " -0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 SVR A2301 " 0.050 2.00e-02 2.50e+03 1.96e-01 4.80e+02 pdb=" C3 SVR A2301 " -0.229 2.00e-02 2.50e+03 pdb=" C5 SVR A2301 " 0.010 2.00e-02 2.50e+03 pdb=" N1 SVR A2301 " 0.332 2.00e-02 2.50e+03 pdb=" O4 SVR A2301 " -0.163 2.00e-02 2.50e+03 ... (remaining 2108 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1150 2.74 - 3.28: 11973 3.28 - 3.82: 19536 3.82 - 4.36: 21928 4.36 - 4.90: 39195 Nonbonded interactions: 93782 Sorted by model distance: nonbonded pdb=" OG1 THR A 70 " pdb=" O VAL A 229 " model vdw 2.204 3.040 nonbonded pdb=" O TYR A 667 " pdb=" NE2 GLN A 671 " model vdw 2.214 3.120 nonbonded pdb=" OG1 THR A 687 " pdb=" OD1 ASN A 690 " model vdw 2.217 3.040 nonbonded pdb=" OD2 ASP A 20 " pdb=" ND2 ASN A 681 " model vdw 2.287 3.120 nonbonded pdb=" O GLU A 643 " pdb=" OG1 THR B 148 " model vdw 2.302 3.040 ... (remaining 93777 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 'D' and (resid 82 through 118 or (resid 119 and (name N or name CA or nam \ e C or name O or name CB )) or resid 120 through 146)) selection = (chain 'E' and (resid 82 through 132 or (resid 133 and (name N or name CA or nam \ e C or name O or name CB )) or resid 134 through 146)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.380 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 33.070 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:3.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 12138 Z= 0.168 Angle : 0.612 8.382 16511 Z= 0.318 Chirality : 0.039 0.232 1880 Planarity : 0.010 0.260 2111 Dihedral : 14.412 89.464 4422 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.90 % Favored : 93.69 % Rotamer: Outliers : 0.23 % Allowed : 0.15 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.23), residues: 1487 helix: 2.07 (0.19), residues: 837 sheet: 0.65 (0.55), residues: 73 loop : -0.94 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 191 HIS 0.004 0.001 HIS C 166 PHE 0.015 0.001 PHE A 867 TYR 0.019 0.001 TYR A 667 ARG 0.003 0.000 ARG A 654 Details of bonding type rmsd hydrogen bonds : bond 0.13548 ( 640) hydrogen bonds : angle 4.31909 ( 1831) covalent geometry : bond 0.00354 (12138) covalent geometry : angle 0.61235 (16511) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 187 time to evaluate : 1.380 Fit side-chains REVERT: A 108 MET cc_start: 0.8654 (mpp) cc_final: 0.7927 (mpp) REVERT: A 238 ILE cc_start: 0.8458 (mm) cc_final: 0.7851 (mm) REVERT: A 314 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7562 (tm-30) REVERT: A 559 VAL cc_start: 0.7457 (t) cc_final: 0.7181 (t) REVERT: A 663 ASN cc_start: 0.8741 (p0) cc_final: 0.8488 (p0) REVERT: A 846 ARG cc_start: 0.7848 (mtm-85) cc_final: 0.7567 (mtt-85) REVERT: B 201 ASN cc_start: 0.8813 (m-40) cc_final: 0.8388 (m110) REVERT: B 309 LYS cc_start: 0.8380 (pttm) cc_final: 0.8118 (tttt) REVERT: B 324 TRP cc_start: 0.6812 (m-90) cc_final: 0.5925 (m-90) REVERT: C 144 LEU cc_start: 0.8790 (mt) cc_final: 0.8378 (pp) outliers start: 2 outliers final: 0 residues processed: 187 average time/residue: 0.2909 time to fit residues: 80.1427 Evaluate side-chains 151 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.155258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.110798 restraints weight = 53135.461| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 6.18 r_work: 0.2907 rms_B_bonded: 5.64 restraints_weight: 2.0000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12138 Z= 0.141 Angle : 0.632 15.546 16511 Z= 0.310 Chirality : 0.040 0.147 1880 Planarity : 0.005 0.089 2111 Dihedral : 4.807 72.944 1615 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.37 % Favored : 93.15 % Rotamer: Outliers : 0.53 % Allowed : 7.69 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.23), residues: 1487 helix: 2.12 (0.18), residues: 842 sheet: 0.66 (0.55), residues: 73 loop : -1.11 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 191 HIS 0.005 0.001 HIS C 166 PHE 0.017 0.001 PHE A 949 TYR 0.012 0.001 TYR A 153 ARG 0.003 0.000 ARG A 546 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 640) hydrogen bonds : angle 3.60587 ( 1831) covalent geometry : bond 0.00324 (12138) covalent geometry : angle 0.63153 (16511) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 161 time to evaluate : 1.417 Fit side-chains revert: symmetry clash REVERT: A 108 MET cc_start: 0.9069 (mpp) cc_final: 0.8852 (mpp) REVERT: A 238 ILE cc_start: 0.8736 (mm) cc_final: 0.8445 (mm) REVERT: A 314 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8282 (tm-30) REVERT: A 663 ASN cc_start: 0.8981 (p0) cc_final: 0.8670 (p0) REVERT: A 846 ARG cc_start: 0.8068 (mtm-85) cc_final: 0.7808 (mtt-85) REVERT: A 1073 ARG cc_start: 0.6565 (ttt180) cc_final: 0.5930 (ttp-170) REVERT: B 201 ASN cc_start: 0.8910 (m-40) cc_final: 0.8654 (m-40) REVERT: B 216 LYS cc_start: 0.8182 (ttmm) cc_final: 0.7853 (mmmt) REVERT: B 309 LYS cc_start: 0.8365 (pttm) cc_final: 0.8095 (tmtt) REVERT: B 324 TRP cc_start: 0.7284 (m-90) cc_final: 0.6259 (m-90) REVERT: C 144 LEU cc_start: 0.8871 (mt) cc_final: 0.8362 (pp) REVERT: D 138 MET cc_start: 0.8398 (tmm) cc_final: 0.7864 (tmm) REVERT: E 138 MET cc_start: 0.7805 (ttp) cc_final: 0.7542 (ttt) outliers start: 6 outliers final: 5 residues processed: 163 average time/residue: 0.2540 time to fit residues: 59.4978 Evaluate side-chains 146 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 141 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain B residue 206 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 71 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 59 optimal weight: 0.0970 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.155800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.110648 restraints weight = 49451.171| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 5.91 r_work: 0.2926 rms_B_bonded: 5.38 restraints_weight: 2.0000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12138 Z= 0.121 Angle : 0.597 15.175 16511 Z= 0.291 Chirality : 0.039 0.136 1880 Planarity : 0.004 0.079 2111 Dihedral : 4.630 61.431 1615 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.76 % Favored : 93.76 % Rotamer: Outliers : 1.14 % Allowed : 10.36 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.23), residues: 1487 helix: 2.18 (0.18), residues: 836 sheet: 0.69 (0.55), residues: 73 loop : -1.06 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 191 HIS 0.004 0.001 HIS C 166 PHE 0.014 0.001 PHE A 369 TYR 0.011 0.001 TYR A 153 ARG 0.002 0.000 ARG A 571 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 640) hydrogen bonds : angle 3.44518 ( 1831) covalent geometry : bond 0.00277 (12138) covalent geometry : angle 0.59717 (16511) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 1.229 Fit side-chains revert: symmetry clash REVERT: A 238 ILE cc_start: 0.8770 (mm) cc_final: 0.8251 (mm) REVERT: A 314 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8211 (tm-30) REVERT: A 742 ASP cc_start: 0.8043 (p0) cc_final: 0.7773 (p0) REVERT: A 846 ARG cc_start: 0.8012 (mtm-85) cc_final: 0.7787 (mtt-85) REVERT: A 1073 ARG cc_start: 0.6651 (ttt180) cc_final: 0.6005 (ttp-170) REVERT: B 138 MET cc_start: 0.9031 (tmm) cc_final: 0.8802 (ttp) REVERT: B 201 ASN cc_start: 0.8924 (m-40) cc_final: 0.8670 (m110) REVERT: B 309 LYS cc_start: 0.8377 (pttm) cc_final: 0.8102 (tmtt) REVERT: C 144 LEU cc_start: 0.8821 (mt) cc_final: 0.8312 (pp) REVERT: D 138 MET cc_start: 0.8400 (tmm) cc_final: 0.7783 (tmm) outliers start: 14 outliers final: 8 residues processed: 168 average time/residue: 0.2394 time to fit residues: 57.9216 Evaluate side-chains 153 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 814 GLN Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 19 optimal weight: 0.0570 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 136 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 99 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 117 optimal weight: 0.6980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.155709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.110321 restraints weight = 53411.585| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 6.32 r_work: 0.2900 rms_B_bonded: 5.74 restraints_weight: 2.0000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12138 Z= 0.120 Angle : 0.593 13.947 16511 Z= 0.288 Chirality : 0.040 0.220 1880 Planarity : 0.004 0.074 2111 Dihedral : 4.582 60.688 1615 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.24 % Favored : 93.36 % Rotamer: Outliers : 1.07 % Allowed : 11.58 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.23), residues: 1487 helix: 2.20 (0.18), residues: 836 sheet: 0.68 (0.56), residues: 71 loop : -1.03 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 191 HIS 0.004 0.001 HIS C 166 PHE 0.014 0.001 PHE A 369 TYR 0.011 0.001 TYR A 667 ARG 0.002 0.000 ARG A 571 Details of bonding type rmsd hydrogen bonds : bond 0.03314 ( 640) hydrogen bonds : angle 3.43125 ( 1831) covalent geometry : bond 0.00276 (12138) covalent geometry : angle 0.59279 (16511) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 1.336 Fit side-chains revert: symmetry clash REVERT: A 108 MET cc_start: 0.9121 (mpp) cc_final: 0.8896 (mpp) REVERT: A 242 ASP cc_start: 0.8998 (m-30) cc_final: 0.8692 (m-30) REVERT: A 314 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8248 (tm-30) REVERT: A 1073 ARG cc_start: 0.6643 (ttt180) cc_final: 0.6008 (ttp-170) REVERT: B 138 MET cc_start: 0.9054 (tmm) cc_final: 0.8789 (ttp) REVERT: B 216 LYS cc_start: 0.8171 (ttmm) cc_final: 0.7788 (mmmt) REVERT: B 309 LYS cc_start: 0.8379 (pttm) cc_final: 0.8094 (tmtt) REVERT: C 144 LEU cc_start: 0.8818 (mt) cc_final: 0.8303 (pp) REVERT: D 138 MET cc_start: 0.8423 (tmm) cc_final: 0.7744 (tmm) outliers start: 13 outliers final: 11 residues processed: 161 average time/residue: 0.2506 time to fit residues: 59.1151 Evaluate side-chains 155 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 814 GLN Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 124 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 127 optimal weight: 6.9990 chunk 44 optimal weight: 0.2980 chunk 63 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.154768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.106208 restraints weight = 39171.152| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 4.45 r_work: 0.2950 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12138 Z= 0.137 Angle : 0.596 14.306 16511 Z= 0.289 Chirality : 0.040 0.177 1880 Planarity : 0.004 0.070 2111 Dihedral : 4.550 59.424 1615 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.58 % Favored : 93.02 % Rotamer: Outliers : 1.52 % Allowed : 12.19 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.23), residues: 1487 helix: 2.21 (0.18), residues: 836 sheet: 0.68 (0.56), residues: 71 loop : -1.00 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 191 HIS 0.005 0.001 HIS C 166 PHE 0.015 0.001 PHE A 99 TYR 0.011 0.001 TYR A 153 ARG 0.002 0.000 ARG A 546 Details of bonding type rmsd hydrogen bonds : bond 0.03322 ( 640) hydrogen bonds : angle 3.40543 ( 1831) covalent geometry : bond 0.00324 (12138) covalent geometry : angle 0.59602 (16511) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8113 (tm-30) REVERT: A 1073 ARG cc_start: 0.6594 (ttt180) cc_final: 0.5985 (ttp-170) REVERT: B 201 ASN cc_start: 0.8982 (m-40) cc_final: 0.8726 (m110) REVERT: B 309 LYS cc_start: 0.8361 (pttm) cc_final: 0.8088 (tmtt) REVERT: C 144 LEU cc_start: 0.8802 (mt) cc_final: 0.8268 (pp) REVERT: D 138 MET cc_start: 0.8440 (tmm) cc_final: 0.7711 (tmm) outliers start: 19 outliers final: 12 residues processed: 159 average time/residue: 0.2536 time to fit residues: 57.9874 Evaluate side-chains 156 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 814 GLN Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 69 optimal weight: 0.6980 chunk 122 optimal weight: 0.0570 chunk 132 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.0030 chunk 21 optimal weight: 3.9990 overall best weight: 0.4108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 ASN ** A1318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.156387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109400 restraints weight = 49292.471| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 5.55 r_work: 0.2942 rms_B_bonded: 5.20 restraints_weight: 2.0000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12138 Z= 0.109 Angle : 0.588 16.507 16511 Z= 0.284 Chirality : 0.039 0.163 1880 Planarity : 0.004 0.067 2111 Dihedral : 4.473 58.499 1615 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.37 % Favored : 93.22 % Rotamer: Outliers : 1.07 % Allowed : 13.18 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.23), residues: 1487 helix: 2.25 (0.18), residues: 838 sheet: 0.74 (0.57), residues: 71 loop : -0.96 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 191 HIS 0.004 0.000 HIS C 166 PHE 0.014 0.001 PHE A 369 TYR 0.010 0.001 TYR A 153 ARG 0.001 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03105 ( 640) hydrogen bonds : angle 3.35678 ( 1831) covalent geometry : bond 0.00242 (12138) covalent geometry : angle 0.58779 (16511) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 1.380 Fit side-chains revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8775 (pt0) cc_final: 0.8546 (pt0) REVERT: A 314 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8119 (tm-30) REVERT: A 548 PHE cc_start: 0.9007 (t80) cc_final: 0.8797 (t80) REVERT: A 571 ARG cc_start: 0.8257 (tmm-80) cc_final: 0.7781 (tpt170) REVERT: A 742 ASP cc_start: 0.7954 (p0) cc_final: 0.7640 (p0) REVERT: A 1073 ARG cc_start: 0.6579 (ttt180) cc_final: 0.5989 (ttp-170) REVERT: B 138 MET cc_start: 0.9030 (tmm) cc_final: 0.8811 (ttp) REVERT: B 309 LYS cc_start: 0.8365 (pttm) cc_final: 0.8042 (tmtt) REVERT: C 144 LEU cc_start: 0.8816 (mt) cc_final: 0.8289 (pp) REVERT: D 138 MET cc_start: 0.8371 (tmm) cc_final: 0.7860 (tmm) outliers start: 13 outliers final: 10 residues processed: 157 average time/residue: 0.2561 time to fit residues: 58.0669 Evaluate side-chains 151 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 814 GLN Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 96 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.152057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.105979 restraints weight = 51066.042| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 5.83 r_work: 0.2864 rms_B_bonded: 5.34 restraints_weight: 2.0000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12138 Z= 0.185 Angle : 0.642 15.184 16511 Z= 0.311 Chirality : 0.041 0.177 1880 Planarity : 0.004 0.066 2111 Dihedral : 4.574 57.443 1615 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.37 % Favored : 93.22 % Rotamer: Outliers : 1.29 % Allowed : 13.48 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.23), residues: 1487 helix: 2.20 (0.18), residues: 831 sheet: 0.72 (0.57), residues: 71 loop : -1.01 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 191 HIS 0.007 0.001 HIS A 864 PHE 0.022 0.002 PHE A 99 TYR 0.015 0.001 TYR C 142 ARG 0.002 0.000 ARG A 571 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 640) hydrogen bonds : angle 3.45338 ( 1831) covalent geometry : bond 0.00447 (12138) covalent geometry : angle 0.64163 (16511) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 1.359 Fit side-chains REVERT: A 314 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8155 (tm-30) REVERT: A 391 LYS cc_start: 0.8423 (tttp) cc_final: 0.7939 (ttmt) REVERT: A 916 ASN cc_start: 0.8531 (p0) cc_final: 0.8001 (p0) REVERT: A 927 ASP cc_start: 0.7668 (t70) cc_final: 0.7384 (t70) REVERT: A 1073 ARG cc_start: 0.6675 (ttt180) cc_final: 0.6070 (ttp-170) REVERT: B 309 LYS cc_start: 0.8390 (pttm) cc_final: 0.8108 (tmtt) REVERT: D 138 MET cc_start: 0.8417 (tmm) cc_final: 0.7861 (tmm) outliers start: 16 outliers final: 14 residues processed: 154 average time/residue: 0.3566 time to fit residues: 80.8103 Evaluate side-chains 153 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 814 GLN Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 113 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 chunk 84 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.153833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.107217 restraints weight = 46205.224| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 5.16 r_work: 0.2914 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12138 Z= 0.131 Angle : 0.619 17.102 16511 Z= 0.298 Chirality : 0.040 0.165 1880 Planarity : 0.004 0.064 2111 Dihedral : 4.534 56.829 1615 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.71 % Favored : 92.88 % Rotamer: Outliers : 1.52 % Allowed : 13.63 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.23), residues: 1487 helix: 2.20 (0.18), residues: 830 sheet: 0.72 (0.58), residues: 71 loop : -1.00 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 191 HIS 0.004 0.001 HIS C 166 PHE 0.018 0.001 PHE B 214 TYR 0.011 0.001 TYR A 153 ARG 0.002 0.000 ARG A 571 Details of bonding type rmsd hydrogen bonds : bond 0.03326 ( 640) hydrogen bonds : angle 3.43267 ( 1831) covalent geometry : bond 0.00306 (12138) covalent geometry : angle 0.61870 (16511) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8100 (tm-30) REVERT: A 916 ASN cc_start: 0.8531 (p0) cc_final: 0.7953 (p0) REVERT: A 927 ASP cc_start: 0.7670 (t70) cc_final: 0.7395 (t70) REVERT: A 1073 ARG cc_start: 0.6646 (ttt180) cc_final: 0.6055 (ttp-170) REVERT: B 138 MET cc_start: 0.9028 (tmm) cc_final: 0.8673 (ttp) REVERT: B 309 LYS cc_start: 0.8354 (pttm) cc_final: 0.8043 (tmtt) outliers start: 19 outliers final: 16 residues processed: 158 average time/residue: 0.2544 time to fit residues: 57.9881 Evaluate side-chains 152 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 814 GLN Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 56 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 92 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 ASN ** A1318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.152989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.105627 restraints weight = 46651.815| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 5.14 r_work: 0.2910 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12138 Z= 0.153 Angle : 0.631 16.242 16511 Z= 0.304 Chirality : 0.041 0.266 1880 Planarity : 0.004 0.064 2111 Dihedral : 4.533 56.483 1615 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.58 % Favored : 93.02 % Rotamer: Outliers : 1.45 % Allowed : 13.71 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.23), residues: 1487 helix: 2.17 (0.18), residues: 830 sheet: 0.75 (0.59), residues: 71 loop : -1.01 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 191 HIS 0.005 0.001 HIS C 166 PHE 0.018 0.001 PHE B 214 TYR 0.012 0.001 TYR C 142 ARG 0.002 0.000 ARG A 571 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 640) hydrogen bonds : angle 3.46010 ( 1831) covalent geometry : bond 0.00368 (12138) covalent geometry : angle 0.63079 (16511) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 1.660 Fit side-chains REVERT: A 314 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8121 (tm-30) REVERT: A 916 ASN cc_start: 0.8481 (p0) cc_final: 0.7923 (p0) REVERT: A 927 ASP cc_start: 0.7719 (t70) cc_final: 0.7435 (t70) REVERT: A 947 ASP cc_start: 0.7705 (m-30) cc_final: 0.7471 (p0) REVERT: A 1073 ARG cc_start: 0.6643 (ttt180) cc_final: 0.6061 (ttp-170) REVERT: B 138 MET cc_start: 0.9032 (tmm) cc_final: 0.8667 (ttp) REVERT: B 309 LYS cc_start: 0.8357 (pttm) cc_final: 0.8048 (tmtt) outliers start: 18 outliers final: 15 residues processed: 150 average time/residue: 0.3483 time to fit residues: 78.5729 Evaluate side-chains 156 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 814 GLN Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 67 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS ** A1318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.153050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.107907 restraints weight = 62681.055| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 6.64 r_work: 0.2853 rms_B_bonded: 5.90 restraints_weight: 2.0000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12138 Z= 0.144 Angle : 0.625 16.011 16511 Z= 0.302 Chirality : 0.041 0.246 1880 Planarity : 0.004 0.064 2111 Dihedral : 4.488 53.050 1615 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.78 % Favored : 92.81 % Rotamer: Outliers : 1.45 % Allowed : 13.86 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.23), residues: 1487 helix: 2.17 (0.18), residues: 830 sheet: 0.71 (0.59), residues: 71 loop : -1.03 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 191 HIS 0.005 0.001 HIS C 166 PHE 0.015 0.001 PHE A 99 TYR 0.011 0.001 TYR C 142 ARG 0.002 0.000 ARG A 571 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 640) hydrogen bonds : angle 3.44680 ( 1831) covalent geometry : bond 0.00344 (12138) covalent geometry : angle 0.62533 (16511) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 1.587 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8252 (tm-30) REVERT: A 434 ASN cc_start: 0.8364 (m-40) cc_final: 0.7847 (t0) REVERT: A 742 ASP cc_start: 0.8182 (p0) cc_final: 0.7848 (p0) REVERT: A 811 GLN cc_start: 0.8169 (tp40) cc_final: 0.7931 (tp40) REVERT: A 916 ASN cc_start: 0.8482 (p0) cc_final: 0.7947 (p0) REVERT: A 927 ASP cc_start: 0.7724 (t70) cc_final: 0.7410 (t70) REVERT: A 947 ASP cc_start: 0.7825 (m-30) cc_final: 0.7544 (p0) REVERT: A 1073 ARG cc_start: 0.6891 (ttt180) cc_final: 0.6214 (ttp-170) REVERT: B 138 MET cc_start: 0.9092 (tmm) cc_final: 0.8734 (ttp) REVERT: B 216 LYS cc_start: 0.8035 (ttmm) cc_final: 0.7732 (mmmt) REVERT: B 309 LYS cc_start: 0.8348 (pttm) cc_final: 0.8043 (tmtt) outliers start: 18 outliers final: 16 residues processed: 157 average time/residue: 0.2640 time to fit residues: 60.2345 Evaluate side-chains 159 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 814 GLN Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 121 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 85 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.153593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.105016 restraints weight = 41486.108| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 4.13 r_work: 0.2935 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12138 Z= 0.125 Angle : 0.619 15.835 16511 Z= 0.299 Chirality : 0.040 0.236 1880 Planarity : 0.004 0.063 2111 Dihedral : 4.450 52.995 1615 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.71 % Favored : 92.88 % Rotamer: Outliers : 1.37 % Allowed : 14.17 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.23), residues: 1487 helix: 2.17 (0.18), residues: 830 sheet: 0.73 (0.59), residues: 71 loop : -1.04 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 191 HIS 0.004 0.001 HIS C 166 PHE 0.015 0.001 PHE B 214 TYR 0.011 0.001 TYR A 153 ARG 0.002 0.000 ARG A 571 Details of bonding type rmsd hydrogen bonds : bond 0.03256 ( 640) hydrogen bonds : angle 3.42156 ( 1831) covalent geometry : bond 0.00291 (12138) covalent geometry : angle 0.61882 (16511) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8035.63 seconds wall clock time: 144 minutes 43.10 seconds (8683.10 seconds total)