Starting phenix.real_space_refine on Mon Dec 30 04:18:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yet_33777/12_2024/7yet_33777.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yet_33777/12_2024/7yet_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_33777/12_2024/7yet_33777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yet_33777/12_2024/7yet_33777.map" model { file = "/net/cci-nas-00/data/ceres_data/7yet_33777/12_2024/7yet_33777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yet_33777/12_2024/7yet_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 7.92, per 1000 atoms: 0.67 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: 2.79 Conformation dependent library (CDL) restraints added in 1.9 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: 1.13 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: 3.49 Time building geometry restraints manager: 3.25 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: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.310 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.070 ------------------------------------------------------------------------------- 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= 0.228 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 *********************** 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 : 1.458 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: 0.2555 time to fit residues: 69.3369 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 : 1.410 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 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= 0.211 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 *********************** 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 : 1.309 Fit side-chains revert: symmetry clash REVERT: A 238 ILE cc_start: 0.8620 (mm) cc_final: 0.8139 (mm) REVERT: A 663 ASN cc_start: 0.8729 (p0) cc_final: 0.8476 (p0) REVERT: A 846 ARG cc_start: 0.7870 (mtm-85) cc_final: 0.7603 (mtt-85) REVERT: A 1073 ARG cc_start: 0.6354 (ttt180) cc_final: 0.5820 (ttp-170) REVERT: B 201 ASN cc_start: 0.8805 (m-40) cc_final: 0.8497 (m-40) REVERT: B 216 LYS cc_start: 0.8208 (ttmm) cc_final: 0.7908 (mmmt) REVERT: B 309 LYS cc_start: 0.8348 (pttm) cc_final: 0.8107 (tmtt) REVERT: B 324 TRP cc_start: 0.6997 (m-90) cc_final: 0.6033 (m-90) REVERT: C 144 LEU cc_start: 0.8764 (mt) cc_final: 0.8405 (pp) REVERT: D 138 MET cc_start: 0.8319 (tmm) cc_final: 0.7871 (tmm) REVERT: E 138 MET cc_start: 0.7682 (ttp) cc_final: 0.7427 (ttt) outliers start: 6 outliers final: 5 residues processed: 163 average time/residue: 0.2546 time to fit residues: 59.0425 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 : 1.258 ------------------------------------------------------------------------------- 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 73 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 110 optimal weight: 0.0570 chunk 90 optimal weight: 0.6980 chunk 36 optimal weight: 0.0270 chunk 132 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12138 Z= 0.158 Angle : 0.592 15.054 16511 Z= 0.289 Chirality : 0.039 0.135 1880 Planarity : 0.004 0.079 2111 Dihedral : 4.625 62.560 1615 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.90 % Favored : 93.63 % Rotamer: Outliers : 0.91 % Allowed : 10.66 % Favored : 88.42 % 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: 2.26 (0.18), residues: 830 sheet: 0.71 (0.55), residues: 73 loop : -1.11 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 *********************** 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 173 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 1.300 Fit side-chains revert: symmetry clash REVERT: A 238 ILE cc_start: 0.8686 (mm) cc_final: 0.8222 (mm) REVERT: A 742 ASP cc_start: 0.7876 (p0) cc_final: 0.7653 (p0) REVERT: A 846 ARG cc_start: 0.7841 (mtm-85) cc_final: 0.7615 (mtt-85) REVERT: A 1073 ARG cc_start: 0.6432 (ttt180) cc_final: 0.5892 (ttp-170) REVERT: B 138 MET cc_start: 0.8576 (tmm) cc_final: 0.8317 (ttp) REVERT: B 201 ASN cc_start: 0.8829 (m-40) cc_final: 0.8587 (m110) REVERT: B 216 LYS cc_start: 0.8138 (ttmm) cc_final: 0.7858 (mmmt) REVERT: B 309 LYS cc_start: 0.8337 (pttm) cc_final: 0.8100 (tmtt) REVERT: C 144 LEU cc_start: 0.8745 (mt) cc_final: 0.8389 (pp) REVERT: D 138 MET cc_start: 0.8310 (tmm) cc_final: 0.7808 (tmm) REVERT: E 138 MET cc_start: 0.7477 (ttp) cc_final: 0.7273 (ttt) outliers start: 11 outliers final: 7 residues processed: 167 average time/residue: 0.2557 time to fit residues: 61.3085 Evaluate side-chains 152 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 131 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 133 optimal weight: 0.4980 chunk 141 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 126 optimal weight: 20.0000 chunk 38 optimal weight: 0.4980 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 814 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 12138 Z= 0.432 Angle : 0.716 14.897 16511 Z= 0.350 Chirality : 0.045 0.179 1880 Planarity : 0.005 0.075 2111 Dihedral : 4.900 58.975 1615 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.64 % Favored : 92.88 % Rotamer: Outliers : 1.75 % Allowed : 11.35 % Favored : 86.90 % 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: 1.11 (0.23), residues: 1487 helix: 1.93 (0.18), residues: 836 sheet: 0.57 (0.56), residues: 71 loop : -1.06 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 191 HIS 0.011 0.002 HIS A 864 PHE 0.027 0.002 PHE A 99 TYR 0.020 0.002 TYR C 142 ARG 0.003 0.001 ARG A 353 *********************** 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 176 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 1.372 Fit side-chains REVERT: A 71 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8552 (mp) REVERT: A 391 LYS cc_start: 0.8227 (tttp) cc_final: 0.7811 (ttpt) REVERT: A 742 ASP cc_start: 0.7974 (p0) cc_final: 0.7291 (p0) REVERT: A 766 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8064 (mm-30) REVERT: A 916 ASN cc_start: 0.8378 (p0) cc_final: 0.7922 (p0) REVERT: A 927 ASP cc_start: 0.7704 (t70) cc_final: 0.7497 (t70) REVERT: A 978 GLN cc_start: 0.7284 (mm-40) cc_final: 0.7062 (pp30) REVERT: A 1073 ARG cc_start: 0.6463 (ttt180) cc_final: 0.5891 (ttp-170) REVERT: B 201 ASN cc_start: 0.8871 (m-40) cc_final: 0.8662 (m110) REVERT: B 309 LYS cc_start: 0.8363 (pttm) cc_final: 0.8069 (tmtt) REVERT: D 138 MET cc_start: 0.8440 (tmm) cc_final: 0.7785 (tmm) outliers start: 22 outliers final: 13 residues processed: 167 average time/residue: 0.2735 time to fit residues: 64.9811 Evaluate side-chains 156 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 105 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1491 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= 0.207 Angle : 0.617 14.164 16511 Z= 0.301 Chirality : 0.040 0.164 1880 Planarity : 0.004 0.070 2111 Dihedral : 4.750 58.578 1615 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.51 % Favored : 93.08 % Rotamer: Outliers : 1.45 % Allowed : 12.80 % 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: 1.22 (0.23), residues: 1487 helix: 2.04 (0.18), residues: 835 sheet: 0.50 (0.56), residues: 71 loop : -1.04 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 191 HIS 0.004 0.001 HIS C 166 PHE 0.016 0.001 PHE A 548 TYR 0.021 0.001 TYR A 667 ARG 0.002 0.000 ARG A 546 *********************** 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: 18 poor density : 148 time to evaluate : 1.379 Fit side-chains REVERT: A 242 ASP cc_start: 0.8272 (m-30) cc_final: 0.8049 (m-30) REVERT: A 391 LYS cc_start: 0.8138 (tttp) cc_final: 0.7706 (ttpt) REVERT: A 742 ASP cc_start: 0.7689 (p0) cc_final: 0.7373 (p0) REVERT: A 916 ASN cc_start: 0.8272 (p0) cc_final: 0.7805 (p0) REVERT: A 927 ASP cc_start: 0.7680 (t70) cc_final: 0.7416 (t70) REVERT: A 1073 ARG cc_start: 0.6441 (ttt180) cc_final: 0.5900 (ttp-170) REVERT: B 138 MET cc_start: 0.8653 (tmm) cc_final: 0.8227 (ttp) REVERT: B 201 ASN cc_start: 0.8829 (m-40) cc_final: 0.8602 (m110) REVERT: B 309 LYS cc_start: 0.8318 (pttm) cc_final: 0.8065 (tmtt) outliers start: 18 outliers final: 12 residues processed: 159 average time/residue: 0.2704 time to fit residues: 61.4173 Evaluate side-chains 153 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 141 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1584 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= 0.249 Angle : 0.623 16.453 16511 Z= 0.302 Chirality : 0.041 0.167 1880 Planarity : 0.004 0.068 2111 Dihedral : 4.696 58.066 1615 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.24 % Favored : 93.29 % Rotamer: Outliers : 1.83 % Allowed : 12.87 % Favored : 85.30 % 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: 1.24 (0.23), residues: 1487 helix: 2.04 (0.18), residues: 835 sheet: 0.60 (0.57), residues: 71 loop : -1.02 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 191 HIS 0.005 0.001 HIS C 166 PHE 0.017 0.001 PHE A 99 TYR 0.015 0.001 TYR A 667 ARG 0.003 0.000 ARG A 357 *********************** 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 171 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 1.299 Fit side-chains REVERT: A 71 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8651 (mp) REVERT: A 391 LYS cc_start: 0.8131 (tttp) cc_final: 0.7728 (ttmt) REVERT: A 434 ASN cc_start: 0.7739 (m-40) cc_final: 0.7325 (t0) REVERT: A 544 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7812 (pt0) REVERT: A 742 ASP cc_start: 0.7655 (p0) cc_final: 0.7309 (p0) REVERT: A 916 ASN cc_start: 0.8249 (p0) cc_final: 0.7796 (p0) REVERT: A 927 ASP cc_start: 0.7699 (t70) cc_final: 0.7437 (t70) REVERT: A 1073 ARG cc_start: 0.6469 (ttt180) cc_final: 0.5933 (ttp-170) REVERT: B 138 MET cc_start: 0.8646 (tmm) cc_final: 0.8378 (ttp) REVERT: B 201 ASN cc_start: 0.8827 (m-40) cc_final: 0.8594 (m110) REVERT: B 309 LYS cc_start: 0.8323 (pttm) cc_final: 0.8079 (tmtt) outliers start: 22 outliers final: 17 residues processed: 164 average time/residue: 0.2546 time to fit residues: 59.8880 Evaluate side-chains 158 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 585 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 832 ASP 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 Chi-restraints excluded: chain E residue 131 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 103 optimal weight: 0.2980 chunk 79 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 64 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12138 Z= 0.177 Angle : 0.601 16.647 16511 Z= 0.292 Chirality : 0.039 0.157 1880 Planarity : 0.004 0.066 2111 Dihedral : 4.611 57.423 1615 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.51 % Favored : 93.02 % Rotamer: Outliers : 1.83 % Allowed : 13.10 % Favored : 85.07 % 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: 1.32 (0.23), residues: 1487 helix: 2.11 (0.18), residues: 835 sheet: 0.64 (0.57), residues: 71 loop : -0.98 (0.27), residues: 581 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 0.017 0.001 PHE B 214 TYR 0.022 0.001 TYR A 667 ARG 0.002 0.000 ARG A 357 *********************** 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 167 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 1.400 Fit side-chains REVERT: A 391 LYS cc_start: 0.8086 (tttp) cc_final: 0.7685 (ttmt) REVERT: A 544 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7732 (pt0) REVERT: A 916 ASN cc_start: 0.8240 (p0) cc_final: 0.7725 (p0) REVERT: A 927 ASP cc_start: 0.7723 (t70) cc_final: 0.7453 (t70) REVERT: A 1073 ARG cc_start: 0.6437 (ttt180) cc_final: 0.5925 (ttp-170) REVERT: B 138 MET cc_start: 0.8605 (tmm) cc_final: 0.8373 (ttp) REVERT: B 201 ASN cc_start: 0.8813 (m-40) cc_final: 0.8603 (m-40) REVERT: B 309 LYS cc_start: 0.8345 (pttm) cc_final: 0.8061 (tmtt) REVERT: D 138 MET cc_start: 0.8355 (tmm) cc_final: 0.7843 (tmm) outliers start: 22 outliers final: 15 residues processed: 160 average time/residue: 0.2569 time to fit residues: 58.8186 Evaluate side-chains 158 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 1.312 ------------------------------------------------------------------------------- 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 386 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 544 GLN 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 A residue 854 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 148 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 128 optimal weight: 0.4980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 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 : 0.004 0.046 12138 Z= 0.262 Angle : 0.636 15.760 16511 Z= 0.309 Chirality : 0.041 0.154 1880 Planarity : 0.004 0.066 2111 Dihedral : 4.628 56.987 1615 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.24 % Favored : 93.36 % Rotamer: Outliers : 1.75 % Allowed : 13.40 % 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: 1.26 (0.23), residues: 1487 helix: 2.07 (0.18), residues: 835 sheet: 0.62 (0.58), residues: 71 loop : -1.01 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 191 HIS 0.005 0.001 HIS A 864 PHE 0.020 0.002 PHE A 99 TYR 0.039 0.001 TYR A 667 ARG 0.002 0.000 ARG A 315 *********************** 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 165 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 1.609 Fit side-chains REVERT: A 391 LYS cc_start: 0.8137 (tttp) cc_final: 0.7727 (ttmt) REVERT: A 916 ASN cc_start: 0.8215 (p0) cc_final: 0.7729 (p0) REVERT: A 927 ASP cc_start: 0.7664 (t70) cc_final: 0.7396 (t70) REVERT: A 978 GLN cc_start: 0.7421 (mm-40) cc_final: 0.6925 (pt0) REVERT: A 1073 ARG cc_start: 0.6449 (ttt180) cc_final: 0.5949 (ttp-170) REVERT: B 138 MET cc_start: 0.8633 (tmm) cc_final: 0.8348 (ttp) REVERT: B 201 ASN cc_start: 0.8821 (m-40) cc_final: 0.8607 (m110) REVERT: B 309 LYS cc_start: 0.8363 (pttm) cc_final: 0.8116 (tmtt) REVERT: D 138 MET cc_start: 0.8302 (tmm) cc_final: 0.7761 (tmm) outliers start: 21 outliers final: 18 residues processed: 157 average time/residue: 0.2888 time to fit residues: 65.4777 Evaluate side-chains 161 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 585 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 832 ASP 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 Chi-restraints excluded: chain E residue 131 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 9.9990 chunk 122 optimal weight: 0.0010 chunk 131 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 40 optimal weight: 0.5980 chunk 118 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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** A 574 GLN ** A1318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 12138 Z= 0.250 Angle : 0.876 59.197 16511 Z= 0.483 Chirality : 0.041 0.469 1880 Planarity : 0.005 0.065 2111 Dihedral : 4.633 56.725 1615 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.31 % Favored : 93.22 % Rotamer: Outliers : 1.52 % Allowed : 13.86 % Favored : 84.62 % Cbeta Deviations : 0.07 % 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: 1.27 (0.23), residues: 1487 helix: 2.08 (0.18), residues: 835 sheet: 0.63 (0.58), residues: 71 loop : -1.02 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 191 HIS 0.005 0.001 HIS A 864 PHE 0.018 0.001 PHE A 99 TYR 0.033 0.001 TYR A 667 ARG 0.002 0.000 ARG A 571 *********************** 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 161 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 1.590 Fit side-chains REVERT: A 391 LYS cc_start: 0.8134 (tttp) cc_final: 0.7718 (ttmt) REVERT: A 916 ASN cc_start: 0.8213 (p0) cc_final: 0.7723 (p0) REVERT: A 927 ASP cc_start: 0.7669 (t70) cc_final: 0.7393 (t70) REVERT: A 978 GLN cc_start: 0.7411 (mm-40) cc_final: 0.6921 (pt0) REVERT: A 1073 ARG cc_start: 0.6445 (ttt180) cc_final: 0.5947 (ttp-170) REVERT: B 138 MET cc_start: 0.8621 (tmm) cc_final: 0.8336 (ttp) REVERT: B 201 ASN cc_start: 0.8822 (m-40) cc_final: 0.8605 (m110) REVERT: B 309 LYS cc_start: 0.8363 (pttm) cc_final: 0.8115 (tmtt) REVERT: D 138 MET cc_start: 0.8308 (tmm) cc_final: 0.7731 (tmm) outliers start: 18 outliers final: 18 residues processed: 152 average time/residue: 0.2778 time to fit residues: 61.2744 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 : 1.309 ------------------------------------------------------------------------------- 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 290 ASP Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 585 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 832 ASP 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 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 138 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 115 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 12138 Z= 0.250 Angle : 0.876 59.197 16511 Z= 0.483 Chirality : 0.041 0.469 1880 Planarity : 0.005 0.065 2111 Dihedral : 4.633 56.725 1615 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.31 % Favored : 93.22 % Rotamer: Outliers : 1.52 % Allowed : 13.86 % Favored : 84.62 % Cbeta Deviations : 0.07 % 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: 1.27 (0.23), residues: 1487 helix: 2.08 (0.18), residues: 835 sheet: 0.63 (0.58), residues: 71 loop : -1.02 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 191 HIS 0.005 0.001 HIS A 864 PHE 0.018 0.001 PHE A 99 TYR 0.033 0.001 TYR A 667 ARG 0.002 0.000 ARG A 571 ********************** 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 159 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 1.392 Fit side-chains REVERT: A 391 LYS cc_start: 0.8135 (tttp) cc_final: 0.7718 (ttmt) REVERT: A 916 ASN cc_start: 0.8214 (p0) cc_final: 0.7723 (p0) REVERT: A 927 ASP cc_start: 0.7668 (t70) cc_final: 0.7393 (t70) REVERT: A 978 GLN cc_start: 0.7412 (mm-40) cc_final: 0.6921 (pt0) REVERT: A 1073 ARG cc_start: 0.6445 (ttt180) cc_final: 0.5947 (ttp-170) REVERT: B 138 MET cc_start: 0.8621 (tmm) cc_final: 0.8336 (ttp) REVERT: B 201 ASN cc_start: 0.8822 (m-40) cc_final: 0.8605 (m110) REVERT: B 309 LYS cc_start: 0.8362 (pttm) cc_final: 0.8115 (tmtt) REVERT: D 138 MET cc_start: 0.8307 (tmm) cc_final: 0.7731 (tmm) outliers start: 18 outliers final: 18 residues processed: 150 average time/residue: 0.2632 time to fit residues: 56.8805 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 : 1.475 ------------------------------------------------------------------------------- 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 290 ASP Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 585 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 832 ASP 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 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 123 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.1980 chunk 101 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.151894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.106969 restraints weight = 56025.484| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 6.20 r_work: 0.2857 rms_B_bonded: 5.59 restraints_weight: 2.0000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 12138 Z= 0.250 Angle : 0.876 59.197 16511 Z= 0.483 Chirality : 0.041 0.469 1880 Planarity : 0.005 0.065 2111 Dihedral : 4.633 56.725 1615 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.31 % Favored : 93.22 % Rotamer: Outliers : 1.52 % Allowed : 13.86 % Favored : 84.62 % Cbeta Deviations : 0.07 % 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: 1.27 (0.23), residues: 1487 helix: 2.08 (0.18), residues: 835 sheet: 0.63 (0.58), residues: 71 loop : -1.02 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 191 HIS 0.005 0.001 HIS A 864 PHE 0.018 0.001 PHE A 99 TYR 0.033 0.001 TYR A 667 ARG 0.002 0.000 ARG A 571 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2550.06 seconds wall clock time: 47 minutes 51.96 seconds (2871.96 seconds total)