Starting phenix.real_space_refine on Thu Feb 15 22:50:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzw_24780/02_2024/7rzw_24780_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzw_24780/02_2024/7rzw_24780.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzw_24780/02_2024/7rzw_24780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzw_24780/02_2024/7rzw_24780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzw_24780/02_2024/7rzw_24780_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzw_24780/02_2024/7rzw_24780_updated.pdb" } 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= 0.004 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 105 5.16 5 C 8675 2.51 5 N 2336 2.21 5 O 2500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 129": "NH1" <-> "NH2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ARG 320": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A ARG 352": "NH1" <-> "NH2" Residue "A TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 504": "OE1" <-> "OE2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 554": "NH1" <-> "NH2" Residue "A ARG 582": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 876": "NH1" <-> "NH2" Residue "A ARG 920": "NH1" <-> "NH2" Residue "A GLU 960": "OE1" <-> "OE2" Residue "A ARG 978": "NH1" <-> "NH2" Residue "A ARG 997": "NH1" <-> "NH2" Residue "A GLU 1036": "OE1" <-> "OE2" Residue "A ARG 1057": "NH1" <-> "NH2" Residue "A GLU 1086": "OE1" <-> "OE2" Residue "A GLU 1094": "OE1" <-> "OE2" Residue "A ARG 1102": "NH1" <-> "NH2" Residue "A ARG 1122": "NH1" <-> "NH2" Residue "A ARG 1136": "NH1" <-> "NH2" Residue "A ARG 1140": "NH1" <-> "NH2" Residue "A GLU 1148": "OE1" <-> "OE2" Residue "B TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B ARG 320": "NH1" <-> "NH2" Residue "B ARG 352": "NH1" <-> "NH2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B ARG 554": "NH1" <-> "NH2" Residue "B ARG 582": "NH1" <-> "NH2" Residue "B ARG 615": "NH1" <-> "NH2" Residue "B GLU 806": "OE1" <-> "OE2" Residue "B ARG 890": "NH1" <-> "NH2" Residue "B ARG 920": "NH1" <-> "NH2" Residue "B GLU 954": "OE1" <-> "OE2" Residue "B ARG 978": "NH1" <-> "NH2" Residue "B GLU 1030": "OE1" <-> "OE2" Residue "B ARG 1102": "NH1" <-> "NH2" Residue "B ARG 1122": "NH1" <-> "NH2" Residue "B ARG 1136": "NH1" <-> "NH2" Residue "B GLU 1137": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13616 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6749 Classifications: {'peptide': 859} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 821} Chain breaks: 5 Chain: "B" Number of atoms: 6781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 864, 6781 Classifications: {'peptide': 864} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 826} Chain breaks: 4 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.64, per 1000 atoms: 0.56 Number of scatterers: 13616 At special positions: 0 Unit cell: (124.509, 119.364, 113.19, 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 105 16.00 O 2500 8.00 N 2336 7.00 C 8675 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 - 3.50 Amino acid : False - 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.49 Conformation dependent library (CDL) restraints added in 2.6 seconds 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3226 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 17 sheets defined 36.4% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.67 Creating SS restraints... Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.570A pdb=" N GLN A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 140 No H-bonds generated for 'chain 'A' and resid 137 through 140' Processing helix chain 'A' and resid 163 through 166 Processing helix chain 'A' and resid 169 through 179 Processing helix chain 'A' and resid 231 through 246 removed outlier: 3.965A pdb=" N LEU A 237 " --> pdb=" O GLN A 233 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 310 through 319 Processing helix chain 'A' and resid 356 through 365 Processing helix chain 'A' and resid 412 through 455 removed outlier: 3.871A pdb=" N LEU A 435 " --> pdb=" O MET A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 465 removed outlier: 3.595A pdb=" N VAL A 464 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 473 No H-bonds generated for 'chain 'A' and resid 470 through 473' Processing helix chain 'A' and resid 496 through 508 Processing helix chain 'A' and resid 521 through 524 No H-bonds generated for 'chain 'A' and resid 521 through 524' Processing helix chain 'A' and resid 529 through 532 No H-bonds generated for 'chain 'A' and resid 529 through 532' Processing helix chain 'A' and resid 534 through 536 No H-bonds generated for 'chain 'A' and resid 534 through 536' Processing helix chain 'A' and resid 601 through 620 Processing helix chain 'A' and resid 815 through 821 Processing helix chain 'A' and resid 825 through 828 No H-bonds generated for 'chain 'A' and resid 825 through 828' Processing helix chain 'A' and resid 836 through 839 No H-bonds generated for 'chain 'A' and resid 836 through 839' Processing helix chain 'A' and resid 849 through 862 Processing helix chain 'A' and resid 909 through 919 removed outlier: 3.792A pdb=" N GLN A 918 " --> pdb=" O ALA A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 953 removed outlier: 4.857A pdb=" N LYS A 940 " --> pdb=" O CYS A 936 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN A 941 " --> pdb=" O GLN A 937 " (cutoff:3.500A) Proline residue: A 942 - end of helix Processing helix chain 'A' and resid 960 through 982 removed outlier: 3.722A pdb=" N GLN A 975 " --> pdb=" O SER A 971 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 976 " --> pdb=" O CYS A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1006 No H-bonds generated for 'chain 'A' and resid 1003 through 1006' Processing helix chain 'A' and resid 1014 through 1019 Processing helix chain 'A' and resid 1041 through 1057 removed outlier: 3.781A pdb=" N SER A1054 " --> pdb=" O GLU A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1104 removed outlier: 4.020A pdb=" N ARG A1102 " --> pdb=" O PRO A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1126 removed outlier: 3.644A pdb=" N LEU A1125 " --> pdb=" O CYS A1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 135 through 141 removed outlier: 4.217A pdb=" N ARG B 138 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 139 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU B 141 " --> pdb=" O ARG B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 169 through 180 removed outlier: 3.725A pdb=" N ILE B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 187 No H-bonds generated for 'chain 'B' and resid 184 through 187' Processing helix chain 'B' and resid 231 through 244 removed outlier: 4.226A pdb=" N LEU B 237 " --> pdb=" O GLN B 233 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ARG B 240 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 267 removed outlier: 3.698A pdb=" N VAL B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU B 262 " --> pdb=" O ASP B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 316 Processing helix chain 'B' and resid 356 through 365 Processing helix chain 'B' and resid 412 through 455 Processing helix chain 'B' and resid 460 through 463 removed outlier: 3.952A pdb=" N ILE B 463 " --> pdb=" O PRO B 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 460 through 463' Processing helix chain 'B' and resid 470 through 473 No H-bonds generated for 'chain 'B' and resid 470 through 473' Processing helix chain 'B' and resid 496 through 508 Processing helix chain 'B' and resid 521 through 524 No H-bonds generated for 'chain 'B' and resid 521 through 524' Processing helix chain 'B' and resid 529 through 532 No H-bonds generated for 'chain 'B' and resid 529 through 532' Processing helix chain 'B' and resid 601 through 619 removed outlier: 3.760A pdb=" N LYS B 619 " --> pdb=" O ARG B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 820 Processing helix chain 'B' and resid 825 through 828 No H-bonds generated for 'chain 'B' and resid 825 through 828' Processing helix chain 'B' and resid 849 through 861 Processing helix chain 'B' and resid 909 through 952 removed outlier: 4.509A pdb=" N ASP B 922 " --> pdb=" O GLN B 918 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR B 923 " --> pdb=" O ARG B 919 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE B 926 " --> pdb=" O ASP B 922 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 927 " --> pdb=" O THR B 923 " (cutoff:3.500A) Proline residue: B 942 - end of helix Processing helix chain 'B' and resid 960 through 979 Processing helix chain 'B' and resid 1002 through 1020 removed outlier: 4.796A pdb=" N PHE B1015 " --> pdb=" O SER B1011 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LEU B1016 " --> pdb=" O GLN B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1058 Processing helix chain 'B' and resid 1098 through 1106 Processing helix chain 'B' and resid 1113 through 1127 removed outlier: 3.832A pdb=" N LEU B1125 " --> pdb=" O CYS B1121 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 190 through 193 removed outlier: 3.820A pdb=" N VAL A 190 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ASP A 124 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE A 130 " --> pdb=" O ASP A 124 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 284 through 289 removed outlier: 6.227A pdb=" N VAL A 275 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU A 289 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL A 273 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP A 397 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A 375 " --> pdb=" O TRP A 397 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU A 399 " --> pdb=" O MET A 373 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N MET A 373 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL A 401 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU A 371 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N HIS A 403 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA A 369 " --> pdb=" O HIS A 403 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 488 through 491 removed outlier: 3.573A pdb=" N ASP A 548 " --> pdb=" O ILE A 544 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 560 through 564 Processing sheet with id= E, first strand: chain 'A' and resid 869 through 874 Processing sheet with id= F, first strand: chain 'A' and resid 998 through 1000 removed outlier: 3.912A pdb=" N PHE A1000 " --> pdb=" O VAL A1037 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A1037 " --> pdb=" O PHE A1000 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1023 through 1027 removed outlier: 3.703A pdb=" N VAL A1065 " --> pdb=" O GLN A1023 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A1027 " --> pdb=" O ILE A1067 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1071 through 1075 Processing sheet with id= I, first strand: chain 'B' and resid 190 through 192 removed outlier: 4.052A pdb=" N VAL B 190 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N MET B 120 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 321 through 324 Processing sheet with id= K, first strand: chain 'B' and resid 488 through 491 Processing sheet with id= L, first strand: chain 'B' and resid 515 through 518 Processing sheet with id= M, first strand: chain 'B' and resid 884 through 889 removed outlier: 3.667A pdb=" N GLU B 812 " --> pdb=" O ALA B 803 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 1023 through 1025 removed outlier: 3.682A pdb=" N GLU B1148 " --> pdb=" O ILE B1083 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B1085 " --> pdb=" O ILE B1146 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 1071 through 1074 removed outlier: 3.593A pdb=" N LYS B1074 " --> pdb=" O ALA B1082 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 272 through 278 removed outlier: 3.812A pdb=" N ALA B 288 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS B 277 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N VAL B 286 " --> pdb=" O LYS B 277 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 374 through 377 removed outlier: 3.741A pdb=" N GLY B 398 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE B 377 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU B 396 " --> pdb=" O ILE B 377 " (cutoff:3.500A) 571 hydrogen bonds defined for protein. 1614 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: 4.85 Time building geometry restraints manager: 5.89 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: 3878 1.34 - 1.45: 2307 1.45 - 1.57: 7534 1.57 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 13887 Sorted by residual: bond pdb=" CAO O6E A1201 " pdb=" CBO O6E A1201 " ideal model delta sigma weight residual 1.397 1.528 -0.131 2.00e-02 2.50e+03 4.31e+01 bond pdb=" CAO O6E B1201 " pdb=" CBO O6E B1201 " ideal model delta sigma weight residual 1.397 1.517 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" CAP O6E B1201 " pdb=" CBL O6E B1201 " ideal model delta sigma weight residual 1.448 1.530 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" CAV O6E B1201 " pdb=" NAE O6E B1201 " ideal model delta sigma weight residual 1.374 1.456 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" CAY O6E A1201 " pdb=" NAN O6E A1201 " ideal model delta sigma weight residual 1.346 1.423 -0.077 2.00e-02 2.50e+03 1.47e+01 ... (remaining 13882 not shown) Histogram of bond angle deviations from ideal: 98.66 - 105.86: 342 105.86 - 113.06: 7366 113.06 - 120.26: 5342 120.26 - 127.46: 5578 127.46 - 134.66: 142 Bond angle restraints: 18770 Sorted by residual: angle pdb=" C CYS A 842 " pdb=" N MET A 843 " pdb=" CA MET A 843 " ideal model delta sigma weight residual 121.56 127.70 -6.14 1.56e+00 4.11e-01 1.55e+01 angle pdb=" N MET A 843 " pdb=" CA MET A 843 " pdb=" C MET A 843 " ideal model delta sigma weight residual 110.42 115.85 -5.43 1.46e+00 4.69e-01 1.38e+01 angle pdb=" C ASP B 281 " pdb=" N GLU B 282 " pdb=" CA GLU B 282 " ideal model delta sigma weight residual 121.54 128.45 -6.91 1.91e+00 2.74e-01 1.31e+01 angle pdb=" N GLY B 846 " pdb=" CA GLY B 846 " pdb=" C GLY B 846 " ideal model delta sigma weight residual 115.22 119.80 -4.58 1.27e+00 6.20e-01 1.30e+01 angle pdb=" C SER B1107 " pdb=" N SER B1108 " pdb=" CA SER B1108 " ideal model delta sigma weight residual 124.82 131.20 -6.38 1.78e+00 3.16e-01 1.28e+01 ... (remaining 18765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7477 17.98 - 35.95: 772 35.95 - 53.93: 163 53.93 - 71.91: 28 71.91 - 89.89: 16 Dihedral angle restraints: 8456 sinusoidal: 3478 harmonic: 4978 Sorted by residual: dihedral pdb=" CA GLU A1031 " pdb=" C GLU A1031 " pdb=" N ILE A1032 " pdb=" CA ILE A1032 " ideal model delta harmonic sigma weight residual 180.00 154.36 25.64 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA SER A1034 " pdb=" C SER A1034 " pdb=" N ILE A1035 " pdb=" CA ILE A1035 " ideal model delta harmonic sigma weight residual -180.00 -156.69 -23.31 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA MET A1128 " pdb=" C MET A1128 " pdb=" N ASN A1129 " pdb=" CA ASN A1129 " ideal model delta harmonic sigma weight residual 180.00 157.18 22.82 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 8453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1670 0.066 - 0.133: 365 0.133 - 0.199: 45 0.199 - 0.265: 18 0.265 - 0.331: 3 Chirality restraints: 2101 Sorted by residual: chirality pdb=" CG LEU B 187 " pdb=" CB LEU B 187 " pdb=" CD1 LEU B 187 " pdb=" CD2 LEU B 187 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA PHE B 838 " pdb=" N PHE B 838 " pdb=" C PHE B 838 " pdb=" CB PHE B 838 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA LEU A1116 " pdb=" N LEU A1116 " pdb=" C LEU A1116 " pdb=" CB LEU A1116 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2098 not shown) Planarity restraints: 2413 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAB O6E A1201 " 0.207 2.00e-02 2.50e+03 2.11e-01 1.11e+03 pdb=" CAP O6E A1201 " -0.323 2.00e-02 2.50e+03 pdb=" CAS O6E A1201 " -0.018 2.00e-02 2.50e+03 pdb=" CAW O6E A1201 " -0.186 2.00e-02 2.50e+03 pdb=" CBC O6E A1201 " -0.053 2.00e-02 2.50e+03 pdb=" CBI O6E A1201 " 0.049 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " 0.475 2.00e-02 2.50e+03 pdb=" CBM O6E A1201 " -0.020 2.00e-02 2.50e+03 pdb=" NAJ O6E A1201 " -0.169 2.00e-02 2.50e+03 pdb=" OAK O6E A1201 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAB O6E B1201 " -0.198 2.00e-02 2.50e+03 1.98e-01 9.82e+02 pdb=" CAP O6E B1201 " 0.300 2.00e-02 2.50e+03 pdb=" CAS O6E B1201 " 0.010 2.00e-02 2.50e+03 pdb=" CAW O6E B1201 " 0.178 2.00e-02 2.50e+03 pdb=" CBC O6E B1201 " 0.045 2.00e-02 2.50e+03 pdb=" CBI O6E B1201 " -0.048 2.00e-02 2.50e+03 pdb=" CBL O6E B1201 " -0.446 2.00e-02 2.50e+03 pdb=" CBM O6E B1201 " 0.022 2.00e-02 2.50e+03 pdb=" NAJ O6E B1201 " 0.164 2.00e-02 2.50e+03 pdb=" OAK O6E B1201 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAQ O6E A1201 " -0.067 2.00e-02 2.50e+03 6.56e-02 5.39e+01 pdb=" CAY O6E A1201 " 0.070 2.00e-02 2.50e+03 pdb=" CBJ O6E A1201 " 0.072 2.00e-02 2.50e+03 pdb=" CBN O6E A1201 " -0.083 2.00e-02 2.50e+03 pdb=" NBP O6E A1201 " 0.009 2.00e-02 2.50e+03 ... (remaining 2410 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 4184 2.84 - 3.35: 12480 3.35 - 3.87: 23205 3.87 - 4.38: 26578 4.38 - 4.90: 45480 Nonbonded interactions: 111927 Sorted by model distance: nonbonded pdb=" O THR B 168 " pdb=" OG SER B 172 " model vdw 2.321 2.440 nonbonded pdb=" O SER B 393 " pdb=" OG SER B 393 " model vdw 2.326 2.440 nonbonded pdb=" O VAL B 264 " pdb=" OG1 THR B 268 " model vdw 2.327 2.440 nonbonded pdb=" O ASN B 378 " pdb=" ND2 ASN B 430 " model vdw 2.328 2.520 nonbonded pdb=" O ILE A 470 " pdb=" NE1 TRP A 552 " model vdw 2.347 2.520 ... (remaining 111922 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 102 through 220 or resid 227 through 620 or resid 778 thro \ ugh 1151 or resid 1201)) selection = (chain 'B' and (resid 102 through 378 or resid 393 through 986 or resid 993 thro \ ugh 1151 or resid 1201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.510 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: 0.020 Extract box with map and model: 4.030 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 40.180 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.080 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 13887 Z= 0.423 Angle : 1.006 10.201 18770 Z= 0.553 Chirality : 0.058 0.331 2101 Planarity : 0.010 0.211 2413 Dihedral : 15.417 89.886 5230 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.88 % Allowed : 11.61 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -2.54 (0.18), residues: 1701 helix: -1.21 (0.18), residues: 670 sheet: -1.56 (0.27), residues: 344 loop : -2.08 (0.21), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 563 HIS 0.012 0.002 HIS B1106 PHE 0.041 0.003 PHE B1080 TYR 0.039 0.003 TYR A 487 ARG 0.008 0.001 ARG A 554 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 301 time to evaluate : 1.603 Fit side-chains REVERT: A 979 ILE cc_start: 0.7161 (mt) cc_final: 0.6817 (mt) REVERT: B 336 GLN cc_start: 0.5618 (pt0) cc_final: 0.5227 (pm20) REVERT: B 431 MET cc_start: 0.7140 (mtp) cc_final: 0.6934 (mtt) REVERT: B 466 GLN cc_start: 0.5340 (tp40) cc_final: 0.5095 (tp40) REVERT: B 483 TYR cc_start: 0.5268 (t80) cc_final: 0.4865 (t80) REVERT: B 611 GLN cc_start: 0.6386 (OUTLIER) cc_final: 0.6107 (pt0) REVERT: B 817 MET cc_start: 0.7298 (mmm) cc_final: 0.7013 (mmm) REVERT: B 823 TRP cc_start: 0.7205 (m100) cc_final: 0.6848 (m100) REVERT: B 940 LYS cc_start: 0.7472 (mttp) cc_final: 0.7108 (tptm) REVERT: B 983 MET cc_start: 0.3602 (ptm) cc_final: 0.3397 (ptm) REVERT: B 1127 LEU cc_start: 0.7764 (tp) cc_final: 0.7297 (mt) outliers start: 13 outliers final: 4 residues processed: 311 average time/residue: 0.2820 time to fit residues: 123.7763 Evaluate side-chains 189 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 184 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 611 GLN Chi-restraints excluded: chain B residue 917 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.7980 chunk 129 optimal weight: 0.0980 chunk 71 optimal weight: 4.9990 chunk 44 optimal weight: 0.0570 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 HIS A 782 ASN A 882 GLN A 888 ASN B 556 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13887 Z= 0.174 Angle : 0.619 10.935 18770 Z= 0.310 Chirality : 0.041 0.177 2101 Planarity : 0.005 0.067 2413 Dihedral : 6.774 86.303 1942 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.17 % Favored : 96.71 % Rotamer: Outliers : 2.57 % Allowed : 15.46 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.69 (0.19), residues: 1701 helix: -0.20 (0.19), residues: 673 sheet: -1.51 (0.25), residues: 364 loop : -1.72 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 599 HIS 0.008 0.001 HIS B1106 PHE 0.019 0.002 PHE B 948 TYR 0.018 0.002 TYR B 113 ARG 0.004 0.000 ARG B1109 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 195 time to evaluate : 1.735 Fit side-chains revert: symmetry clash REVERT: A 323 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.7026 (ttp) REVERT: A 998 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6779 (pm20) REVERT: A 1014 MET cc_start: 0.6974 (tpp) cc_final: 0.6375 (ttt) REVERT: A 1072 LEU cc_start: 0.6045 (OUTLIER) cc_final: 0.5743 (pt) REVERT: A 1076 MET cc_start: 0.6865 (mtp) cc_final: 0.6465 (mtm) REVERT: A 1140 ARG cc_start: 0.6538 (mtt90) cc_final: 0.5889 (mtp180) REVERT: B 291 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7988 (pttp) REVERT: B 336 GLN cc_start: 0.5665 (pt0) cc_final: 0.5429 (pm20) REVERT: B 541 VAL cc_start: 0.7647 (t) cc_final: 0.7239 (t) REVERT: B 823 TRP cc_start: 0.7129 (m100) cc_final: 0.6752 (m100) REVERT: B 881 VAL cc_start: 0.7164 (OUTLIER) cc_final: 0.6945 (p) REVERT: B 896 LYS cc_start: 0.5142 (OUTLIER) cc_final: 0.4831 (ptpt) REVERT: B 940 LYS cc_start: 0.7361 (mttp) cc_final: 0.6963 (tptm) REVERT: B 1015 PHE cc_start: 0.7093 (t80) cc_final: 0.6724 (m-80) REVERT: B 1127 LEU cc_start: 0.7871 (tp) cc_final: 0.7415 (mt) outliers start: 38 outliers final: 15 residues processed: 219 average time/residue: 0.2790 time to fit residues: 87.7504 Evaluate side-chains 197 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 176 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 888 ASN Chi-restraints excluded: chain A residue 998 GLU Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 896 LYS Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 969 SER Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1099 GLU Chi-restraints excluded: chain B residue 1142 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 168 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 154 optimal weight: 0.0670 chunk 53 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 302 HIS A 319 ASN A 355 HIS A 782 ASN ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13887 Z= 0.222 Angle : 0.607 8.684 18770 Z= 0.303 Chirality : 0.041 0.157 2101 Planarity : 0.004 0.068 2413 Dihedral : 6.417 88.121 1936 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.24 % Allowed : 17.35 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.19), residues: 1701 helix: 0.13 (0.19), residues: 678 sheet: -1.45 (0.25), residues: 354 loop : -1.58 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1110 HIS 0.006 0.001 HIS B1106 PHE 0.020 0.002 PHE A 903 TYR 0.017 0.001 TYR A 487 ARG 0.004 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 177 time to evaluate : 1.717 Fit side-chains revert: symmetry clash REVERT: A 965 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7604 (tt) REVERT: A 1014 MET cc_start: 0.7153 (tpp) cc_final: 0.6633 (ttt) REVERT: A 1072 LEU cc_start: 0.6135 (OUTLIER) cc_final: 0.5838 (pt) REVERT: A 1076 MET cc_start: 0.6945 (mtp) cc_final: 0.6559 (mtm) REVERT: A 1140 ARG cc_start: 0.6633 (mtt90) cc_final: 0.5926 (mtp180) REVERT: B 291 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8036 (pttp) REVERT: B 336 GLN cc_start: 0.5880 (pt0) cc_final: 0.5585 (pm20) REVERT: B 823 TRP cc_start: 0.7275 (m100) cc_final: 0.6931 (m100) REVERT: B 881 VAL cc_start: 0.7563 (OUTLIER) cc_final: 0.7345 (p) REVERT: B 896 LYS cc_start: 0.5513 (OUTLIER) cc_final: 0.5261 (ptpt) REVERT: B 940 LYS cc_start: 0.7373 (mttp) cc_final: 0.6943 (tptm) REVERT: B 1015 PHE cc_start: 0.7116 (t80) cc_final: 0.6739 (m-80) REVERT: B 1096 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7185 (tp) REVERT: B 1114 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7352 (tt0) outliers start: 48 outliers final: 29 residues processed: 211 average time/residue: 0.2691 time to fit residues: 83.1688 Evaluate side-chains 205 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 170 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 888 ASN Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 972 CYS Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1119 SER Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 888 ASN Chi-restraints excluded: chain B residue 896 LYS Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 969 SER Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1085 THR Chi-restraints excluded: chain B residue 1096 LEU Chi-restraints excluded: chain B residue 1099 GLU Chi-restraints excluded: chain B residue 1142 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN ** A 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 GLN A 792 HIS B 959 ASN ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 13887 Z= 0.362 Angle : 0.679 7.922 18770 Z= 0.340 Chirality : 0.044 0.168 2101 Planarity : 0.005 0.072 2413 Dihedral : 6.589 89.798 1936 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.65 % Allowed : 18.50 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.19), residues: 1701 helix: -0.08 (0.19), residues: 688 sheet: -1.38 (0.25), residues: 354 loop : -1.56 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 813 HIS 0.008 0.001 HIS B1106 PHE 0.018 0.002 PHE A 551 TYR 0.018 0.002 TYR A 487 ARG 0.003 0.000 ARG B 272 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 181 time to evaluate : 1.778 Fit side-chains REVERT: A 293 ASP cc_start: 0.4787 (OUTLIER) cc_final: 0.4579 (p0) REVERT: A 437 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8011 (tt) REVERT: A 486 LYS cc_start: 0.7847 (ttpt) cc_final: 0.7606 (tptt) REVERT: A 965 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7674 (tt) REVERT: A 979 ILE cc_start: 0.7829 (mt) cc_final: 0.7577 (mt) REVERT: A 1014 MET cc_start: 0.7391 (tpp) cc_final: 0.7164 (ttt) REVERT: A 1072 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.5928 (pt) REVERT: A 1140 ARG cc_start: 0.6854 (mtt90) cc_final: 0.5985 (mtp180) REVERT: B 291 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8271 (pttp) REVERT: B 336 GLN cc_start: 0.6117 (pt0) cc_final: 0.5648 (pm20) REVERT: B 443 ARG cc_start: 0.7285 (mtp-110) cc_final: 0.7009 (ttp-110) REVERT: B 604 MET cc_start: 0.7135 (OUTLIER) cc_final: 0.6711 (tpp) REVERT: B 823 TRP cc_start: 0.7341 (m100) cc_final: 0.7090 (m100) REVERT: B 896 LYS cc_start: 0.5747 (OUTLIER) cc_final: 0.5487 (ptpt) REVERT: B 983 MET cc_start: 0.3737 (ptm) cc_final: 0.3520 (ptm) REVERT: B 1114 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7350 (tt0) REVERT: B 1142 TYR cc_start: 0.7793 (OUTLIER) cc_final: 0.7486 (t80) outliers start: 54 outliers final: 33 residues processed: 221 average time/residue: 0.2723 time to fit residues: 87.2856 Evaluate side-chains 210 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 169 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 809 CYS Chi-restraints excluded: chain A residue 888 ASN Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 972 CYS Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1119 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 604 MET Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 888 ASN Chi-restraints excluded: chain B residue 896 LYS Chi-restraints excluded: chain B residue 944 SER Chi-restraints excluded: chain B residue 969 SER Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1085 THR Chi-restraints excluded: chain B residue 1099 GLU Chi-restraints excluded: chain B residue 1142 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 2 optimal weight: 0.1980 chunk 123 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 141 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN B 360 GLN ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13887 Z= 0.199 Angle : 0.583 8.235 18770 Z= 0.290 Chirality : 0.041 0.167 2101 Planarity : 0.004 0.068 2413 Dihedral : 6.291 89.334 1936 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.38 % Allowed : 19.65 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.12 (0.20), residues: 1701 helix: 0.26 (0.19), residues: 690 sheet: -1.25 (0.26), residues: 360 loop : -1.40 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 813 HIS 0.005 0.001 HIS B1106 PHE 0.017 0.002 PHE A 551 TYR 0.022 0.001 TYR B 487 ARG 0.007 0.000 ARG B 615 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 179 time to evaluate : 1.740 Fit side-chains REVERT: A 486 LYS cc_start: 0.7821 (ttpt) cc_final: 0.7552 (tptt) REVERT: A 798 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7519 (pt) REVERT: A 979 ILE cc_start: 0.7777 (mt) cc_final: 0.7567 (mt) REVERT: A 1002 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8385 (tt) REVERT: A 1072 LEU cc_start: 0.6016 (OUTLIER) cc_final: 0.5679 (pt) REVERT: A 1110 TRP cc_start: 0.6482 (p-90) cc_final: 0.6214 (p-90) REVERT: A 1140 ARG cc_start: 0.6916 (mtt90) cc_final: 0.6064 (mtp180) REVERT: B 274 MET cc_start: 0.8151 (ptp) cc_final: 0.7936 (ptp) REVERT: B 291 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8044 (pttp) REVERT: B 336 GLN cc_start: 0.6082 (pt0) cc_final: 0.5625 (pm20) REVERT: B 604 MET cc_start: 0.6942 (OUTLIER) cc_final: 0.6554 (tpp) REVERT: B 823 TRP cc_start: 0.7338 (m100) cc_final: 0.7082 (m100) REVERT: B 913 GLN cc_start: 0.7289 (mt0) cc_final: 0.7039 (mt0) REVERT: B 983 MET cc_start: 0.3765 (ptm) cc_final: 0.3530 (ptm) REVERT: B 1015 PHE cc_start: 0.6818 (t80) cc_final: 0.6403 (m-80) REVERT: B 1114 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7337 (tt0) REVERT: B 1127 LEU cc_start: 0.8019 (tp) cc_final: 0.7554 (mt) outliers start: 50 outliers final: 32 residues processed: 211 average time/residue: 0.2606 time to fit residues: 80.6015 Evaluate side-chains 209 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 172 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 809 CYS Chi-restraints excluded: chain A residue 810 CYS Chi-restraints excluded: chain A residue 888 ASN Chi-restraints excluded: chain A residue 972 CYS Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 998 GLU Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1119 SER Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 604 MET Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 888 ASN Chi-restraints excluded: chain B residue 969 SER Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1085 THR Chi-restraints excluded: chain B residue 1099 GLU Chi-restraints excluded: chain B residue 1142 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 54 optimal weight: 0.0270 chunk 86 optimal weight: 1.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN A 882 GLN ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13887 Z= 0.188 Angle : 0.587 8.307 18770 Z= 0.289 Chirality : 0.041 0.163 2101 Planarity : 0.004 0.067 2413 Dihedral : 6.166 88.124 1936 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.24 % Allowed : 20.93 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.95 (0.20), residues: 1701 helix: 0.42 (0.19), residues: 690 sheet: -1.19 (0.26), residues: 357 loop : -1.30 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 813 HIS 0.006 0.001 HIS B1106 PHE 0.017 0.001 PHE A 551 TYR 0.027 0.001 TYR B 487 ARG 0.005 0.000 ARG B 615 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 178 time to evaluate : 1.750 Fit side-chains REVERT: A 199 LYS cc_start: 0.8181 (ttmt) cc_final: 0.7414 (ptmm) REVERT: A 486 LYS cc_start: 0.7828 (ttpt) cc_final: 0.7562 (tptt) REVERT: A 798 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7528 (pt) REVERT: A 979 ILE cc_start: 0.7743 (mt) cc_final: 0.7493 (mt) REVERT: A 1002 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8285 (tt) REVERT: A 1072 LEU cc_start: 0.5953 (OUTLIER) cc_final: 0.5620 (pt) REVERT: A 1110 TRP cc_start: 0.6284 (p-90) cc_final: 0.5971 (p-90) REVERT: A 1140 ARG cc_start: 0.6965 (mtt90) cc_final: 0.6104 (mtp180) REVERT: B 291 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8040 (pttp) REVERT: B 486 LYS cc_start: 0.7765 (tptm) cc_final: 0.7492 (tptm) REVERT: B 539 MET cc_start: 0.8719 (tmm) cc_final: 0.8430 (tmm) REVERT: B 604 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.6535 (tpp) REVERT: B 823 TRP cc_start: 0.7354 (m100) cc_final: 0.7097 (m100) REVERT: B 881 VAL cc_start: 0.7792 (OUTLIER) cc_final: 0.7574 (p) REVERT: B 896 LYS cc_start: 0.5400 (OUTLIER) cc_final: 0.5110 (mmtm) REVERT: B 1015 PHE cc_start: 0.6665 (t80) cc_final: 0.6388 (m-80) REVERT: B 1114 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7324 (tt0) REVERT: B 1127 LEU cc_start: 0.8036 (tp) cc_final: 0.7550 (mt) REVERT: B 1142 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.7597 (t80) outliers start: 48 outliers final: 32 residues processed: 211 average time/residue: 0.2679 time to fit residues: 82.6748 Evaluate side-chains 206 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 166 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 810 CYS Chi-restraints excluded: chain A residue 888 ASN Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 972 CYS Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1119 SER Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 604 MET Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 896 LYS Chi-restraints excluded: chain B residue 969 SER Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1085 THR Chi-restraints excluded: chain B residue 1142 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 120 optimal weight: 0.4980 chunk 93 optimal weight: 0.5980 chunk 139 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 164 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 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 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13887 Z= 0.193 Angle : 0.579 9.915 18770 Z= 0.287 Chirality : 0.041 0.162 2101 Planarity : 0.004 0.066 2413 Dihedral : 6.089 87.489 1936 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.44 % Allowed : 21.47 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.81 (0.20), residues: 1701 helix: 0.55 (0.19), residues: 690 sheet: -1.15 (0.26), residues: 359 loop : -1.24 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 505 HIS 0.005 0.001 HIS B1106 PHE 0.016 0.001 PHE A 551 TYR 0.026 0.001 TYR B 487 ARG 0.004 0.000 ARG B 615 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 175 time to evaluate : 1.660 Fit side-chains revert: symmetry clash REVERT: A 199 LYS cc_start: 0.8149 (ttmt) cc_final: 0.7412 (ptmm) REVERT: A 486 LYS cc_start: 0.7807 (ttpt) cc_final: 0.7592 (tptt) REVERT: A 979 ILE cc_start: 0.7757 (mt) cc_final: 0.7502 (mt) REVERT: A 1002 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8234 (tt) REVERT: A 1061 SER cc_start: 0.7693 (p) cc_final: 0.7428 (t) REVERT: A 1072 LEU cc_start: 0.5932 (OUTLIER) cc_final: 0.5611 (pt) REVERT: A 1110 TRP cc_start: 0.6265 (p-90) cc_final: 0.5966 (p-90) REVERT: A 1140 ARG cc_start: 0.7113 (mtt90) cc_final: 0.6230 (mtp180) REVERT: B 120 MET cc_start: 0.8027 (tmm) cc_final: 0.7533 (ttt) REVERT: B 291 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7965 (pttp) REVERT: B 539 MET cc_start: 0.8707 (tmm) cc_final: 0.8371 (tmm) REVERT: B 604 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6511 (tpp) REVERT: B 823 TRP cc_start: 0.7352 (m100) cc_final: 0.7102 (m100) REVERT: B 881 VAL cc_start: 0.7755 (OUTLIER) cc_final: 0.7545 (p) REVERT: B 896 LYS cc_start: 0.5382 (OUTLIER) cc_final: 0.5111 (mmtm) REVERT: B 940 LYS cc_start: 0.7527 (mttp) cc_final: 0.6793 (tptm) REVERT: B 1114 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7426 (tt0) outliers start: 51 outliers final: 36 residues processed: 211 average time/residue: 0.2617 time to fit residues: 80.7512 Evaluate side-chains 211 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 169 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 809 CYS Chi-restraints excluded: chain A residue 810 CYS Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 888 ASN Chi-restraints excluded: chain A residue 972 CYS Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1119 SER Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 604 MET Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 888 ASN Chi-restraints excluded: chain B residue 896 LYS Chi-restraints excluded: chain B residue 969 SER Chi-restraints excluded: chain B residue 1085 THR Chi-restraints excluded: chain B residue 1135 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13887 Z= 0.183 Angle : 0.571 10.988 18770 Z= 0.281 Chirality : 0.041 0.156 2101 Planarity : 0.004 0.066 2413 Dihedral : 6.018 87.164 1936 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.31 % Allowed : 22.15 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.70 (0.20), residues: 1701 helix: 0.63 (0.20), residues: 692 sheet: -1.04 (0.27), residues: 357 loop : -1.21 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 505 HIS 0.005 0.001 HIS B1106 PHE 0.016 0.001 PHE A 551 TYR 0.024 0.001 TYR B 487 ARG 0.005 0.000 ARG B 615 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 175 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 LYS cc_start: 0.8038 (ttmt) cc_final: 0.7421 (ptmm) REVERT: A 798 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7517 (pt) REVERT: A 979 ILE cc_start: 0.7787 (mt) cc_final: 0.7582 (mt) REVERT: A 1002 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8254 (tt) REVERT: A 1061 SER cc_start: 0.7601 (p) cc_final: 0.7270 (t) REVERT: A 1072 LEU cc_start: 0.5998 (OUTLIER) cc_final: 0.5662 (pt) REVERT: A 1110 TRP cc_start: 0.6289 (p-90) cc_final: 0.5994 (p-90) REVERT: A 1140 ARG cc_start: 0.7086 (mtt90) cc_final: 0.6268 (mtp180) REVERT: B 291 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7938 (pttp) REVERT: B 365 MET cc_start: 0.8991 (ttp) cc_final: 0.8697 (ttp) REVERT: B 539 MET cc_start: 0.8674 (tmm) cc_final: 0.8346 (tmm) REVERT: B 604 MET cc_start: 0.6929 (OUTLIER) cc_final: 0.6472 (tpp) REVERT: B 823 TRP cc_start: 0.7353 (m100) cc_final: 0.7100 (m100) REVERT: B 881 VAL cc_start: 0.7730 (OUTLIER) cc_final: 0.7524 (p) REVERT: B 940 LYS cc_start: 0.7514 (mttp) cc_final: 0.6763 (tptm) REVERT: B 1114 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7545 (tt0) REVERT: B 1127 LEU cc_start: 0.7825 (tt) cc_final: 0.7199 (mt) outliers start: 49 outliers final: 35 residues processed: 211 average time/residue: 0.2610 time to fit residues: 81.1258 Evaluate side-chains 207 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 166 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 809 CYS Chi-restraints excluded: chain A residue 810 CYS Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 888 ASN Chi-restraints excluded: chain A residue 972 CYS Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1119 SER Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 604 MET Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 888 ASN Chi-restraints excluded: chain B residue 969 SER Chi-restraints excluded: chain B residue 1085 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 92 optimal weight: 0.2980 chunk 66 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13887 Z= 0.206 Angle : 0.577 8.610 18770 Z= 0.285 Chirality : 0.041 0.158 2101 Planarity : 0.004 0.066 2413 Dihedral : 6.040 88.305 1936 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.97 % Allowed : 22.48 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.68 (0.20), residues: 1701 helix: 0.62 (0.19), residues: 694 sheet: -0.98 (0.27), residues: 350 loop : -1.21 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 505 HIS 0.005 0.001 HIS B1106 PHE 0.016 0.001 PHE A 903 TYR 0.023 0.001 TYR B 487 ARG 0.005 0.000 ARG B 947 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 167 time to evaluate : 1.594 Fit side-chains revert: symmetry clash REVERT: A 199 LYS cc_start: 0.8038 (ttmt) cc_final: 0.7420 (ptmm) REVERT: A 798 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7502 (pt) REVERT: A 979 ILE cc_start: 0.7819 (mt) cc_final: 0.7587 (mt) REVERT: A 1002 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8242 (tt) REVERT: A 1061 SER cc_start: 0.7472 (p) cc_final: 0.7215 (t) REVERT: A 1072 LEU cc_start: 0.6064 (OUTLIER) cc_final: 0.5732 (pt) REVERT: A 1110 TRP cc_start: 0.6336 (p-90) cc_final: 0.6019 (p-90) REVERT: A 1140 ARG cc_start: 0.7097 (mtt90) cc_final: 0.6259 (mtp180) REVERT: B 120 MET cc_start: 0.7941 (tmm) cc_final: 0.7627 (ttt) REVERT: B 291 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7954 (pttp) REVERT: B 365 MET cc_start: 0.8986 (ttp) cc_final: 0.8675 (ttp) REVERT: B 505 TRP cc_start: 0.7868 (t60) cc_final: 0.7579 (t60) REVERT: B 539 MET cc_start: 0.8669 (tmm) cc_final: 0.8313 (tmm) REVERT: B 604 MET cc_start: 0.6955 (OUTLIER) cc_final: 0.6506 (tpp) REVERT: B 823 TRP cc_start: 0.7382 (m100) cc_final: 0.7110 (m100) REVERT: B 881 VAL cc_start: 0.7780 (OUTLIER) cc_final: 0.7566 (p) REVERT: B 940 LYS cc_start: 0.7489 (mttp) cc_final: 0.6778 (tptm) REVERT: B 1127 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7166 (mt) outliers start: 44 outliers final: 35 residues processed: 199 average time/residue: 0.2504 time to fit residues: 74.1457 Evaluate side-chains 204 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 162 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 809 CYS Chi-restraints excluded: chain A residue 810 CYS Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 888 ASN Chi-restraints excluded: chain A residue 972 CYS Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1119 SER Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 604 MET Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 888 ASN Chi-restraints excluded: chain B residue 969 SER Chi-restraints excluded: chain B residue 1085 THR Chi-restraints excluded: chain B residue 1127 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 77 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 135 optimal weight: 0.4980 chunk 14 optimal weight: 0.0970 chunk 104 optimal weight: 0.7980 chunk 83 optimal weight: 0.4980 chunk 107 optimal weight: 0.0470 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13887 Z= 0.154 Angle : 0.554 8.720 18770 Z= 0.273 Chirality : 0.040 0.158 2101 Planarity : 0.004 0.065 2413 Dihedral : 5.902 86.960 1936 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.63 % Allowed : 23.02 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.51 (0.20), residues: 1701 helix: 0.79 (0.20), residues: 692 sheet: -0.87 (0.27), residues: 348 loop : -1.16 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 505 HIS 0.005 0.001 HIS B1106 PHE 0.015 0.001 PHE B 948 TYR 0.022 0.001 TYR B 487 ARG 0.005 0.000 ARG B 947 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 174 time to evaluate : 1.729 Fit side-chains revert: symmetry clash REVERT: A 199 LYS cc_start: 0.8010 (ttmt) cc_final: 0.7369 (ptmm) REVERT: A 208 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7347 (mt) REVERT: A 798 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7481 (pt) REVERT: A 1061 SER cc_start: 0.7411 (p) cc_final: 0.7190 (t) REVERT: A 1072 LEU cc_start: 0.6009 (OUTLIER) cc_final: 0.5682 (pt) REVERT: A 1110 TRP cc_start: 0.6217 (p-90) cc_final: 0.5940 (p-90) REVERT: A 1140 ARG cc_start: 0.7059 (mtt90) cc_final: 0.6354 (mtp180) REVERT: B 291 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7835 (pttp) REVERT: B 365 MET cc_start: 0.8922 (ttp) cc_final: 0.8624 (ttp) REVERT: B 505 TRP cc_start: 0.7786 (t60) cc_final: 0.7539 (t60) REVERT: B 539 MET cc_start: 0.8671 (tmm) cc_final: 0.8351 (tmm) REVERT: B 604 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.6432 (tpp) REVERT: B 823 TRP cc_start: 0.7387 (m100) cc_final: 0.7111 (m100) REVERT: B 881 VAL cc_start: 0.7622 (OUTLIER) cc_final: 0.7412 (p) REVERT: B 940 LYS cc_start: 0.7333 (mttp) cc_final: 0.6713 (tptm) REVERT: B 1068 HIS cc_start: 0.6773 (t70) cc_final: 0.5949 (t-170) REVERT: B 1127 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7212 (mt) outliers start: 39 outliers final: 26 residues processed: 201 average time/residue: 0.2690 time to fit residues: 79.5040 Evaluate side-chains 196 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 163 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 809 CYS Chi-restraints excluded: chain A residue 810 CYS Chi-restraints excluded: chain A residue 888 ASN Chi-restraints excluded: chain A residue 972 CYS Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 604 MET Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 888 ASN Chi-restraints excluded: chain B residue 969 SER Chi-restraints excluded: chain B residue 1085 THR Chi-restraints excluded: chain B residue 1127 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1133 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.157904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.132642 restraints weight = 18623.451| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.87 r_work: 0.3571 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13887 Z= 0.248 Angle : 0.591 8.843 18770 Z= 0.292 Chirality : 0.041 0.157 2101 Planarity : 0.004 0.066 2413 Dihedral : 6.071 89.592 1936 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.70 % Allowed : 23.09 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.61 (0.20), residues: 1701 helix: 0.65 (0.19), residues: 698 sheet: -0.86 (0.27), residues: 345 loop : -1.20 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 505 HIS 0.006 0.001 HIS B1106 PHE 0.018 0.002 PHE A 903 TYR 0.023 0.002 TYR B 487 ARG 0.009 0.000 ARG B 947 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3095.71 seconds wall clock time: 56 minutes 52.06 seconds (3412.06 seconds total)