Starting phenix.real_space_refine on Thu Jul 2 15:21:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mmp_48397/07_2026/9mmp_48397.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mmp_48397/07_2026/9mmp_48397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mmp_48397/07_2026/9mmp_48397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mmp_48397/07_2026/9mmp_48397.map" model { file = "/net/cci-nas-00/data/ceres_data/9mmp_48397/07_2026/9mmp_48397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mmp_48397/07_2026/9mmp_48397.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians I 1 10.91 5 Zn 2 6.06 5 P 8 5.49 5 S 53 5.16 5 C 5525 2.51 5 N 1509 2.21 5 O 1659 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8758 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1846 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 5, 'TRANS': 223} Chain: "D" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1833 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 223} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2815 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 14, 'TRANS': 333} Chain breaks: 2 Chain: "B" Number of atoms: 2175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2175 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 262} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' ZN': 2, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'AGS': 1, 'LCJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3914 SG CYS A 165 30.678 53.825 41.459 1.00129.08 S ATOM 3936 SG CYS A 168 31.574 52.862 44.904 1.00123.05 S ATOM 4064 SG CYS A 184 29.709 55.846 44.922 1.00156.08 S ATOM 3805 SG CYS A 152 24.813 41.636 44.174 1.00122.48 S ATOM 3827 SG CYS A 155 23.409 38.228 44.883 1.00112.97 S ATOM 4007 SG CYS A 176 21.264 40.742 43.151 1.00136.07 S Time building chain proxies: 1.53, per 1000 atoms: 0.17 Number of scatterers: 8758 At special positions: 0 Unit cell: (75.19, 89.06, 127.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) I 1 52.95 Zn 2 29.99 S 53 16.00 P 8 15.00 F 1 9.00 O 1659 8.00 N 1509 7.00 C 5525 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 319.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" ND1 HIS A 139 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 168 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 165 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 184 " pdb=" ZN A 703 " pdb="ZN ZN A 703 " - pdb=" ND1 HIS A 173 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 152 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 155 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 176 " Number of angles added : 6 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2058 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 5 sheets defined 62.3% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'C' and resid 2 through 16 removed outlier: 3.773A pdb=" N LEU C 6 " --> pdb=" O ASP C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 32 removed outlier: 3.756A pdb=" N MET C 22 " --> pdb=" O ARG C 18 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 70 removed outlier: 3.516A pdb=" N ARG C 55 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLU C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 105 Processing helix chain 'C' and resid 111 through 133 removed outlier: 3.508A pdb=" N VAL C 132 " --> pdb=" O TYR C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 160 removed outlier: 3.833A pdb=" N ASN C 139 " --> pdb=" O GLY C 135 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 181 Processing helix chain 'C' and resid 184 through 202 removed outlier: 3.629A pdb=" N ALA C 188 " --> pdb=" O SER C 184 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 230 removed outlier: 3.667A pdb=" N SER C 230 " --> pdb=" O THR C 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 16 Processing helix chain 'D' and resid 18 through 31 removed outlier: 3.841A pdb=" N MET D 22 " --> pdb=" O ARG D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 67 removed outlier: 3.864A pdb=" N ARG D 55 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 89 removed outlier: 3.857A pdb=" N MET D 78 " --> pdb=" O ARG D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 104 Processing helix chain 'D' and resid 111 through 133 removed outlier: 3.571A pdb=" N GLU D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 160 removed outlier: 3.508A pdb=" N ASN D 139 " --> pdb=" O GLY D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 181 Processing helix chain 'D' and resid 184 through 201 Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 211 through 228 removed outlier: 3.515A pdb=" N THR D 215 " --> pdb=" O TYR D 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.850A pdb=" N THR A 178 " --> pdb=" O HIS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 383 through 399 Processing helix chain 'A' and resid 428 through 434 Processing helix chain 'A' and resid 441 through 462 Processing helix chain 'A' and resid 470 through 472 No H-bonds generated for 'chain 'A' and resid 470 through 472' Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'A' and resid 513 through 519 Processing helix chain 'A' and resid 526 through 544 removed outlier: 3.534A pdb=" N ASP A 530 " --> pdb=" O SER A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 563 Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.772A pdb=" N LYS A 572 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 589 removed outlier: 3.559A pdb=" N VAL A 589 " --> pdb=" O VAL A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 613 Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 150 through 158 removed outlier: 3.755A pdb=" N VAL B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 184 Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 241 through 258 removed outlier: 3.835A pdb=" N ASP B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 331 through 342 Processing helix chain 'B' and resid 351 through 358 removed outlier: 3.520A pdb=" N VAL B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 367 Processing helix chain 'B' and resid 370 through 380 removed outlier: 3.787A pdb=" N TRP B 374 " --> pdb=" O ASP B 370 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 141 through 145 Processing sheet with id=AA2, first strand: chain 'A' and resid 351 through 357 removed outlier: 4.659A pdb=" N LYS A 365 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ARG A 354 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL A 363 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N GLY A 356 " --> pdb=" O GLY A 361 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLY A 361 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY A 410 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLN A 422 " --> pdb=" O PHE A 408 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N PHE A 408 " --> pdb=" O GLN A 422 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 474 through 477 Processing sheet with id=AA4, first strand: chain 'B' and resid 73 through 76 removed outlier: 6.796A pdb=" N VAL B 82 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ALA B 76 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 99 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY B 131 " --> pdb=" O CYS B 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 196 through 198 510 hydrogen bonds defined for protein. 1500 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: 1.38 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.37: 2954 1.37 - 1.54: 5711 1.54 - 1.70: 175 1.70 - 1.87: 84 1.87 - 2.03: 3 Bond restraints: 8927 Sorted by residual: bond pdb=" N VAL A 180 " pdb=" CA VAL A 180 " ideal model delta sigma weight residual 1.460 1.497 -0.038 7.50e-03 1.78e+04 2.50e+01 bond pdb=" O2G AGS A 701 " pdb=" PG AGS A 701 " ideal model delta sigma weight residual 1.604 1.508 0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" O3B AGS B 701 " pdb=" PB AGS B 701 " ideal model delta sigma weight residual 1.673 1.585 0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" O3A AGS B 701 " pdb=" PA AGS B 701 " ideal model delta sigma weight residual 1.664 1.581 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" O3B AGS A 701 " pdb=" PB AGS A 701 " ideal model delta sigma weight residual 1.673 1.599 0.074 2.00e-02 2.50e+03 1.36e+01 ... (remaining 8922 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 11798 2.58 - 5.16: 222 5.16 - 7.74: 19 7.74 - 10.32: 10 10.32 - 12.90: 3 Bond angle restraints: 12052 Sorted by residual: angle pdb=" CA GLN C 8 " pdb=" CB GLN C 8 " pdb=" CG GLN C 8 " ideal model delta sigma weight residual 114.10 124.50 -10.40 2.00e+00 2.50e-01 2.70e+01 angle pdb=" N GLU D 180 " pdb=" CA GLU D 180 " pdb=" C GLU D 180 " ideal model delta sigma weight residual 113.55 108.05 5.50 1.26e+00 6.30e-01 1.91e+01 angle pdb=" CB MET C 26 " pdb=" CG MET C 26 " pdb=" SD MET C 26 " ideal model delta sigma weight residual 112.70 125.60 -12.90 3.00e+00 1.11e-01 1.85e+01 angle pdb=" CB MET D 78 " pdb=" CG MET D 78 " pdb=" SD MET D 78 " ideal model delta sigma weight residual 112.70 125.33 -12.63 3.00e+00 1.11e-01 1.77e+01 angle pdb=" C VAL C 7 " pdb=" N GLN C 8 " pdb=" CA GLN C 8 " ideal model delta sigma weight residual 121.58 113.52 8.06 1.95e+00 2.63e-01 1.71e+01 ... (remaining 12047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.60: 5175 30.60 - 61.20: 292 61.20 - 91.79: 26 91.79 - 122.39: 1 122.39 - 152.99: 3 Dihedral angle restraints: 5497 sinusoidal: 2317 harmonic: 3180 Sorted by residual: dihedral pdb=" O1A AGS B 701 " pdb=" O3A AGS B 701 " pdb=" PA AGS B 701 " pdb=" PB AGS B 701 " ideal model delta sinusoidal sigma weight residual 82.37 -70.62 152.99 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" O5' AGS B 701 " pdb=" O3A AGS B 701 " pdb=" PA AGS B 701 " pdb=" PB AGS B 701 " ideal model delta sinusoidal sigma weight residual 193.20 45.49 147.71 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" O2A AGS B 701 " pdb=" O3A AGS B 701 " pdb=" PA AGS B 701 " pdb=" PB AGS B 701 " ideal model delta sinusoidal sigma weight residual 307.72 163.82 143.90 1 3.00e+01 1.11e-03 1.93e+01 ... (remaining 5494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1119 0.064 - 0.129: 181 0.129 - 0.193: 18 0.193 - 0.257: 1 0.257 - 0.321: 2 Chirality restraints: 1321 Sorted by residual: chirality pdb=" C3' AGS A 701 " pdb=" C2' AGS A 701 " pdb=" C4' AGS A 701 " pdb=" O3' AGS A 701 " both_signs ideal model delta sigma weight residual False -2.37 -2.69 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" C3' AGS B 701 " pdb=" C2' AGS B 701 " pdb=" C4' AGS B 701 " pdb=" O3' AGS B 701 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA ILE D 93 " pdb=" N ILE D 93 " pdb=" C ILE D 93 " pdb=" CB ILE D 93 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1318 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 627 " 0.368 9.50e-02 1.11e+02 1.65e-01 1.67e+01 pdb=" NE ARG A 627 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 627 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 627 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 627 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 156 " -0.260 9.50e-02 1.11e+02 1.17e-01 8.33e+00 pdb=" NE ARG A 156 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 156 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 156 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 156 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 370 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.78e+00 pdb=" CG ASP B 370 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP B 370 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP B 370 " -0.014 2.00e-02 2.50e+03 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.84: 2808 2.84 - 3.37: 9333 3.37 - 3.90: 15590 3.90 - 4.43: 18962 4.43 - 4.96: 30253 Nonbonded interactions: 76946 Sorted by model distance: nonbonded pdb=" O ASP A 371 " pdb=" OD1 ASP A 371 " model vdw 2.305 3.040 nonbonded pdb=" O03 LCJ B 702 " pdb=" O05 LCJ B 702 " model vdw 2.402 2.432 nonbonded pdb=" O ASP B 370 " pdb=" OD1 ASP B 370 " model vdw 2.461 3.040 nonbonded pdb=" NE2 GLN A 520 " pdb=" OE2 GLU B 312 " model vdw 2.515 3.120 nonbonded pdb=" O GLU C 4 " pdb=" OE1 GLN C 8 " model vdw 2.521 3.040 ... (remaining 76941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB or name CG )) or resid 6 through 195 or (resid 196 and (name \ N or name CA or name C or name O or name CB )) or resid 197 through 211 or (res \ id 212 and (name N or name CA or name C or name O or name CB )) or resid 213 thr \ ough 230)) selection = chain 'D' } 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: 3.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.000 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 8935 Z= 0.320 Angle : 0.855 14.155 12058 Z= 0.471 Chirality : 0.048 0.321 1321 Planarity : 0.007 0.165 1532 Dihedral : 17.883 152.990 3439 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.53 % Allowed : 27.35 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.25), residues: 1065 helix: 1.30 (0.21), residues: 627 sheet: -0.11 (0.62), residues: 50 loop : -1.09 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 363 TYR 0.015 0.001 TYR B 261 PHE 0.019 0.002 PHE C 196 TRP 0.006 0.001 TRP D 228 HIS 0.008 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.32 ( 8927) covalent geometry : angle 0.83423 / 0.47 (12052) hydrogen bonds : bond 0.11411 / 7.87 ( 510) hydrogen bonds : angle 5.76698 / 4.17 ( 1500) metal coordination : bond 0.02010 / 1.09 ( 8) metal coordination : angle 8.45205 / 6.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 170 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 40 GLU cc_start: 0.8741 (mp0) cc_final: 0.8239 (mp0) REVERT: A 538 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8519 (mp) REVERT: A 581 MET cc_start: 0.8455 (mmm) cc_final: 0.8232 (tpt) REVERT: A 611 HIS cc_start: 0.8932 (t-90) cc_final: 0.8704 (t70) REVERT: B 153 GLN cc_start: 0.8869 (mp10) cc_final: 0.8435 (mp10) REVERT: B 187 MET cc_start: 0.6908 (mmt) cc_final: 0.6672 (mmt) REVERT: B 319 ASN cc_start: 0.8612 (m110) cc_final: 0.8344 (m-40) REVERT: B 339 ASN cc_start: 0.8919 (m-40) cc_final: 0.8544 (m110) outliers start: 5 outliers final: 1 residues processed: 173 average time/residue: 0.0734 time to fit residues: 18.0316 Evaluate side-chains 137 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain B residue 178 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.0170 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 15 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN D 173 ASN A 501 GLN A 610 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.114492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.093892 restraints weight = 21209.523| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.64 r_work: 0.3441 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8935 Z= 0.122 Angle : 0.577 6.908 12058 Z= 0.294 Chirality : 0.040 0.154 1321 Planarity : 0.004 0.062 1532 Dihedral : 11.086 154.116 1276 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.38 % Allowed : 24.18 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.26), residues: 1065 helix: 1.71 (0.21), residues: 631 sheet: -0.24 (0.57), residues: 68 loop : -1.03 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 9 TYR 0.019 0.001 TYR D 179 PHE 0.012 0.001 PHE C 196 TRP 0.018 0.001 TRP D 228 HIS 0.007 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 8927) covalent geometry : angle 0.57325 / 0.29 (12052) hydrogen bonds : bond 0.03818 / 2.63 ( 510) hydrogen bonds : angle 4.52827 / 3.24 ( 1500) metal coordination : bond 0.00572 / 0.34 ( 8) metal coordination : angle 3.11003 / 1.77 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 18 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7486 (ptm160) REVERT: A 540 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7784 (pt0) REVERT: A 608 LEU cc_start: 0.8733 (mp) cc_final: 0.8405 (mt) REVERT: B 64 LYS cc_start: 0.8789 (mmmt) cc_final: 0.8400 (mmmt) REVERT: B 87 HIS cc_start: 0.7806 (OUTLIER) cc_final: 0.7385 (t-90) REVERT: B 116 GLN cc_start: 0.8697 (mm-40) cc_final: 0.8137 (mm-40) REVERT: B 118 LEU cc_start: 0.8401 (mt) cc_final: 0.8181 (mt) REVERT: B 153 GLN cc_start: 0.8897 (mp10) cc_final: 0.8442 (mp10) REVERT: B 256 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8074 (mmt) REVERT: B 316 TYR cc_start: 0.7626 (t80) cc_final: 0.7259 (t80) REVERT: B 319 ASN cc_start: 0.8662 (m110) cc_final: 0.8429 (m110) REVERT: B 339 ASN cc_start: 0.8811 (m-40) cc_final: 0.8487 (m110) outliers start: 32 outliers final: 13 residues processed: 169 average time/residue: 0.0700 time to fit residues: 17.2283 Evaluate side-chains 152 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 341 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 2 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 13 optimal weight: 0.1980 chunk 5 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 15 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN A 501 GLN B 358 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.114405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.093473 restraints weight = 21084.515| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.65 r_work: 0.3428 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8935 Z= 0.125 Angle : 0.541 7.738 12058 Z= 0.279 Chirality : 0.040 0.159 1321 Planarity : 0.004 0.066 1532 Dihedral : 9.623 147.913 1273 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.75 % Allowed : 24.60 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.26), residues: 1065 helix: 1.80 (0.21), residues: 631 sheet: -0.21 (0.56), residues: 73 loop : -1.04 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 41 TYR 0.012 0.001 TYR D 125 PHE 0.011 0.001 PHE A 599 TRP 0.037 0.002 TRP D 228 HIS 0.006 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 8927) covalent geometry : angle 0.53898 / 0.28 (12052) hydrogen bonds : bond 0.03592 / 2.46 ( 510) hydrogen bonds : angle 4.33084 / 3.10 ( 1500) metal coordination : bond 0.00644 / 0.35 ( 8) metal coordination : angle 2.38291 / 1.27 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLN cc_start: 0.7228 (OUTLIER) cc_final: 0.6773 (mp10) REVERT: B 64 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8554 (mmmt) REVERT: B 87 HIS cc_start: 0.7739 (OUTLIER) cc_final: 0.7344 (t-90) REVERT: B 116 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8190 (mm-40) REVERT: B 153 GLN cc_start: 0.8942 (mp10) cc_final: 0.8482 (mp10) REVERT: B 249 MET cc_start: 0.9145 (ttp) cc_final: 0.8738 (tmm) REVERT: B 310 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8059 (tp) REVERT: B 316 TYR cc_start: 0.7711 (t80) cc_final: 0.7329 (t80) REVERT: B 319 ASN cc_start: 0.8662 (m110) cc_final: 0.8441 (m110) REVERT: B 339 ASN cc_start: 0.8841 (m-40) cc_final: 0.8513 (m110) outliers start: 26 outliers final: 15 residues processed: 165 average time/residue: 0.0696 time to fit residues: 16.8923 Evaluate side-chains 151 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 341 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 82 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 15 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN A 501 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.113926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.093043 restraints weight = 21704.252| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.70 r_work: 0.3417 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8935 Z= 0.127 Angle : 0.556 8.849 12058 Z= 0.281 Chirality : 0.040 0.163 1321 Planarity : 0.004 0.064 1532 Dihedral : 9.173 144.405 1273 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.27 % Allowed : 24.18 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.26), residues: 1065 helix: 1.86 (0.21), residues: 630 sheet: -0.14 (0.57), residues: 73 loop : -1.06 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 167 TYR 0.012 0.001 TYR D 126 PHE 0.011 0.001 PHE A 599 TRP 0.028 0.001 TRP D 228 HIS 0.006 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 8927) covalent geometry : angle 0.55449 / 0.28 (12052) hydrogen bonds : bond 0.03449 / 2.37 ( 510) hydrogen bonds : angle 4.23537 / 3.01 ( 1500) metal coordination : bond 0.00734 / 0.39 ( 8) metal coordination : angle 2.14358 / 1.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLN cc_start: 0.7227 (OUTLIER) cc_final: 0.6817 (mp10) REVERT: A 457 ASP cc_start: 0.8387 (t0) cc_final: 0.8123 (t0) REVERT: A 469 MET cc_start: 0.7679 (tpt) cc_final: 0.6929 (tpt) REVERT: B 64 LYS cc_start: 0.8886 (mmmt) cc_final: 0.8638 (mmmt) REVERT: B 87 HIS cc_start: 0.7705 (OUTLIER) cc_final: 0.7485 (t-90) REVERT: B 119 HIS cc_start: 0.8555 (OUTLIER) cc_final: 0.7948 (m-70) REVERT: B 153 GLN cc_start: 0.8954 (mp10) cc_final: 0.8432 (mp10) REVERT: B 249 MET cc_start: 0.9110 (ttp) cc_final: 0.8669 (tmm) REVERT: B 256 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8015 (mmt) REVERT: B 310 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8078 (tp) REVERT: B 316 TYR cc_start: 0.7758 (t80) cc_final: 0.7382 (t80) REVERT: B 319 ASN cc_start: 0.8634 (m110) cc_final: 0.8421 (m110) REVERT: B 339 ASN cc_start: 0.8850 (m-40) cc_final: 0.8516 (m110) outliers start: 31 outliers final: 16 residues processed: 173 average time/residue: 0.0626 time to fit residues: 15.9502 Evaluate side-chains 156 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 341 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 15 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN A 501 GLN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.112154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.091300 restraints weight = 19888.483| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.54 r_work: 0.3381 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8935 Z= 0.175 Angle : 0.577 7.600 12058 Z= 0.294 Chirality : 0.041 0.175 1321 Planarity : 0.004 0.066 1532 Dihedral : 9.067 141.834 1273 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.80 % Allowed : 24.82 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.26), residues: 1065 helix: 1.78 (0.21), residues: 630 sheet: -0.16 (0.57), residues: 73 loop : -1.12 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 91 TYR 0.017 0.002 TYR D 179 PHE 0.012 0.001 PHE A 599 TRP 0.025 0.001 TRP D 228 HIS 0.006 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 ( 8927) covalent geometry : angle 0.57489 / 0.29 (12052) hydrogen bonds : bond 0.03687 / 2.53 ( 510) hydrogen bonds : angle 4.22914 / 3.01 ( 1500) metal coordination : bond 0.01340 / 0.72 ( 8) metal coordination : angle 2.13315 / 1.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 8 GLN cc_start: 0.8474 (pm20) cc_final: 0.8246 (pm20) REVERT: C 198 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8239 (t70) REVERT: A 255 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.6866 (mp10) REVERT: A 457 ASP cc_start: 0.8392 (t0) cc_final: 0.8143 (t0) REVERT: A 469 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7060 (tpt) REVERT: B 64 LYS cc_start: 0.8938 (mmmt) cc_final: 0.8649 (mmmt) REVERT: B 87 HIS cc_start: 0.7821 (OUTLIER) cc_final: 0.7520 (t-90) REVERT: B 119 HIS cc_start: 0.8609 (OUTLIER) cc_final: 0.8011 (m-70) REVERT: B 153 GLN cc_start: 0.8974 (mp10) cc_final: 0.8393 (mp10) REVERT: B 164 GLN cc_start: 0.9443 (mm110) cc_final: 0.9194 (mm110) REVERT: B 249 MET cc_start: 0.9166 (ttp) cc_final: 0.8674 (tmm) REVERT: B 256 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.7989 (mmt) REVERT: B 310 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8095 (tp) REVERT: B 316 TYR cc_start: 0.7793 (t80) cc_final: 0.7387 (t80) REVERT: B 319 ASN cc_start: 0.8617 (m110) cc_final: 0.8395 (m-40) REVERT: B 339 ASN cc_start: 0.8871 (m-40) cc_final: 0.8537 (m110) outliers start: 36 outliers final: 23 residues processed: 166 average time/residue: 0.0651 time to fit residues: 15.6984 Evaluate side-chains 161 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 341 CYS Chi-restraints excluded: chain B residue 356 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.0870 chunk 3 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 55 optimal weight: 0.1980 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 15 GLN C 42 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN A 501 GLN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.113102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.092391 restraints weight = 20128.332| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.53 r_work: 0.3411 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8935 Z= 0.120 Angle : 0.559 7.228 12058 Z= 0.282 Chirality : 0.040 0.183 1321 Planarity : 0.004 0.057 1532 Dihedral : 8.877 138.876 1273 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.17 % Allowed : 25.55 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.26), residues: 1065 helix: 1.83 (0.21), residues: 630 sheet: -0.19 (0.57), residues: 73 loop : -1.11 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 467 TYR 0.017 0.001 TYR D 179 PHE 0.011 0.001 PHE A 599 TRP 0.020 0.001 TRP D 228 HIS 0.008 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 8927) covalent geometry : angle 0.55741 / 0.28 (12052) hydrogen bonds : bond 0.03440 / 2.36 ( 510) hydrogen bonds : angle 4.16071 / 2.96 ( 1500) metal coordination : bond 0.00746 / 0.39 ( 8) metal coordination : angle 1.80668 / 1.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 8 GLN cc_start: 0.8426 (pm20) cc_final: 0.8200 (pm20) REVERT: C 198 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8238 (t70) REVERT: D 18 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7518 (ptm160) REVERT: A 255 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6911 (mp10) REVERT: A 457 ASP cc_start: 0.8410 (t0) cc_final: 0.8150 (t0) REVERT: A 469 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.6989 (tpt) REVERT: B 64 LYS cc_start: 0.8939 (mmmt) cc_final: 0.8679 (mmmt) REVERT: B 87 HIS cc_start: 0.7740 (OUTLIER) cc_final: 0.7356 (t-90) REVERT: B 119 HIS cc_start: 0.8639 (OUTLIER) cc_final: 0.8057 (m-70) REVERT: B 153 GLN cc_start: 0.8962 (mp10) cc_final: 0.8383 (mp10) REVERT: B 249 MET cc_start: 0.9158 (ttp) cc_final: 0.8683 (tmm) REVERT: B 256 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8020 (mmt) REVERT: B 310 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8071 (tp) REVERT: B 316 TYR cc_start: 0.7747 (t80) cc_final: 0.7355 (t80) REVERT: B 319 ASN cc_start: 0.8578 (m110) cc_final: 0.8369 (m110) REVERT: B 339 ASN cc_start: 0.8858 (m-40) cc_final: 0.8539 (m110) outliers start: 30 outliers final: 16 residues processed: 169 average time/residue: 0.0717 time to fit residues: 17.6957 Evaluate side-chains 159 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 341 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 23 optimal weight: 0.0980 chunk 2 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 15 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.113400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.093220 restraints weight = 19208.411| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.40 r_work: 0.3426 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8935 Z= 0.128 Angle : 0.570 8.816 12058 Z= 0.287 Chirality : 0.040 0.161 1321 Planarity : 0.004 0.070 1532 Dihedral : 8.699 135.024 1273 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.17 % Allowed : 25.03 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.26), residues: 1065 helix: 1.84 (0.21), residues: 630 sheet: -0.24 (0.57), residues: 73 loop : -1.10 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 467 TYR 0.018 0.001 TYR D 179 PHE 0.011 0.001 PHE A 599 TRP 0.018 0.001 TRP D 228 HIS 0.008 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 8927) covalent geometry : angle 0.56874 / 0.29 (12052) hydrogen bonds : bond 0.03432 / 2.35 ( 510) hydrogen bonds : angle 4.12856 / 2.94 ( 1500) metal coordination : bond 0.00866 / 0.46 ( 8) metal coordination : angle 1.78185 / 1.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 77 GLN cc_start: 0.8437 (mm-40) cc_final: 0.8161 (mp10) REVERT: C 198 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8178 (t70) REVERT: D 18 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7564 (ptm160) REVERT: A 255 GLN cc_start: 0.7237 (OUTLIER) cc_final: 0.6873 (mp10) REVERT: A 457 ASP cc_start: 0.8336 (t0) cc_final: 0.8085 (t0) REVERT: A 469 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.6982 (tpt) REVERT: A 581 MET cc_start: 0.8556 (mmm) cc_final: 0.8295 (tpt) REVERT: B 64 LYS cc_start: 0.8954 (mmmt) cc_final: 0.8703 (mmmt) REVERT: B 87 HIS cc_start: 0.7673 (OUTLIER) cc_final: 0.7392 (t-90) REVERT: B 119 HIS cc_start: 0.8568 (OUTLIER) cc_final: 0.7990 (m-70) REVERT: B 153 GLN cc_start: 0.8934 (mp10) cc_final: 0.8363 (mp10) REVERT: B 249 MET cc_start: 0.9136 (ttp) cc_final: 0.8671 (tmm) REVERT: B 256 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.7951 (mmt) REVERT: B 310 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8113 (tp) REVERT: B 316 TYR cc_start: 0.7776 (t80) cc_final: 0.7384 (t80) REVERT: B 335 GLN cc_start: 0.8231 (mt0) cc_final: 0.7983 (mt0) REVERT: B 339 ASN cc_start: 0.8859 (m-40) cc_final: 0.8542 (m110) outliers start: 30 outliers final: 16 residues processed: 161 average time/residue: 0.0771 time to fit residues: 17.8528 Evaluate side-chains 156 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 341 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 76 optimal weight: 3.9990 chunk 65 optimal weight: 0.0870 chunk 35 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 15 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.113272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.092786 restraints weight = 19856.673| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.50 r_work: 0.3406 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8935 Z= 0.128 Angle : 0.591 10.139 12058 Z= 0.297 Chirality : 0.040 0.230 1321 Planarity : 0.004 0.066 1532 Dihedral : 8.574 131.603 1273 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.27 % Allowed : 25.66 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.26), residues: 1065 helix: 1.83 (0.21), residues: 630 sheet: -0.25 (0.57), residues: 73 loop : -1.08 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 167 TYR 0.018 0.001 TYR D 179 PHE 0.010 0.001 PHE A 599 TRP 0.018 0.001 TRP D 228 HIS 0.009 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 8927) covalent geometry : angle 0.58945 / 0.30 (12052) hydrogen bonds : bond 0.03431 / 2.34 ( 510) hydrogen bonds : angle 4.13690 / 2.94 ( 1500) metal coordination : bond 0.00858 / 0.46 ( 8) metal coordination : angle 1.69240 / 0.96 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 77 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8178 (mp10) REVERT: C 198 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.8191 (t70) REVERT: D 18 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7578 (ptm160) REVERT: A 255 GLN cc_start: 0.7206 (OUTLIER) cc_final: 0.6834 (mp10) REVERT: A 457 ASP cc_start: 0.8371 (t0) cc_final: 0.8103 (t0) REVERT: A 469 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.6874 (tpt) REVERT: A 581 MET cc_start: 0.8523 (mmm) cc_final: 0.8282 (tpt) REVERT: B 64 LYS cc_start: 0.8982 (mmmt) cc_final: 0.8730 (mmmt) REVERT: B 119 HIS cc_start: 0.8586 (OUTLIER) cc_final: 0.7983 (m-70) REVERT: B 153 GLN cc_start: 0.8933 (mp10) cc_final: 0.8351 (mp10) REVERT: B 155 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7297 (mm) REVERT: B 249 MET cc_start: 0.9133 (ttp) cc_final: 0.8672 (tmm) REVERT: B 256 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.7855 (mmt) REVERT: B 310 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8195 (tp) REVERT: B 316 TYR cc_start: 0.7771 (t80) cc_final: 0.7398 (t80) REVERT: B 335 GLN cc_start: 0.8226 (mt0) cc_final: 0.7975 (mt0) REVERT: B 339 ASN cc_start: 0.8841 (m-40) cc_final: 0.8520 (m110) outliers start: 31 outliers final: 18 residues processed: 159 average time/residue: 0.0756 time to fit residues: 17.3401 Evaluate side-chains 157 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 341 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 65 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 15 GLN C 42 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN A 501 GLN B 236 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.112081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.091418 restraints weight = 19850.276| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.52 r_work: 0.3382 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8935 Z= 0.157 Angle : 0.619 9.905 12058 Z= 0.312 Chirality : 0.041 0.239 1321 Planarity : 0.004 0.075 1532 Dihedral : 8.501 127.430 1273 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.27 % Allowed : 26.40 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.26), residues: 1065 helix: 1.78 (0.21), residues: 629 sheet: -0.31 (0.57), residues: 73 loop : -1.10 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 227 TYR 0.020 0.002 TYR D 179 PHE 0.011 0.001 PHE A 599 TRP 0.023 0.001 TRP D 228 HIS 0.008 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 8927) covalent geometry : angle 0.61809 / 0.31 (12052) hydrogen bonds : bond 0.03584 / 2.43 ( 510) hydrogen bonds : angle 4.21343 / 3.00 ( 1500) metal coordination : bond 0.01390 / 0.74 ( 8) metal coordination : angle 1.95386 / 1.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: C 198 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8233 (t70) REVERT: D 18 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7577 (ptm160) REVERT: A 255 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6846 (mp10) REVERT: A 457 ASP cc_start: 0.8440 (t0) cc_final: 0.8183 (t0) REVERT: A 469 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.6830 (tpt) REVERT: B 64 LYS cc_start: 0.8988 (mmmt) cc_final: 0.8732 (mmmt) REVERT: B 119 HIS cc_start: 0.8634 (OUTLIER) cc_final: 0.8245 (m-70) REVERT: B 153 GLN cc_start: 0.8931 (mp10) cc_final: 0.8336 (mp10) REVERT: B 155 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7318 (mm) REVERT: B 249 MET cc_start: 0.9137 (ttp) cc_final: 0.8649 (tmm) REVERT: B 256 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.7819 (mmt) REVERT: B 310 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8202 (tp) REVERT: B 316 TYR cc_start: 0.7808 (t80) cc_final: 0.7428 (t80) REVERT: B 335 GLN cc_start: 0.8217 (mt0) cc_final: 0.7966 (mt0) REVERT: B 339 ASN cc_start: 0.8862 (m-40) cc_final: 0.8531 (m110) outliers start: 31 outliers final: 18 residues processed: 159 average time/residue: 0.0741 time to fit residues: 17.2115 Evaluate side-chains 154 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 341 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 93 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 0.0670 chunk 32 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 15 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN A 550 HIS B 116 GLN B 236 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.113034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.092497 restraints weight = 20518.574| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.53 r_work: 0.3418 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8935 Z= 0.129 Angle : 0.616 10.231 12058 Z= 0.310 Chirality : 0.041 0.199 1321 Planarity : 0.004 0.072 1532 Dihedral : 8.374 124.737 1273 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.75 % Allowed : 27.24 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.26), residues: 1065 helix: 1.80 (0.21), residues: 629 sheet: -0.23 (0.57), residues: 73 loop : -1.13 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 91 TYR 0.021 0.001 TYR D 179 PHE 0.010 0.001 PHE A 599 TRP 0.027 0.001 TRP D 228 HIS 0.010 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 8927) covalent geometry : angle 0.61496 / 0.31 (12052) hydrogen bonds : bond 0.03454 / 2.36 ( 510) hydrogen bonds : angle 4.19597 / 2.98 ( 1500) metal coordination : bond 0.00938 / 0.50 ( 8) metal coordination : angle 1.64844 / 0.94 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 198 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8188 (t70) REVERT: D 18 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7606 (ptm160) REVERT: A 255 GLN cc_start: 0.7159 (OUTLIER) cc_final: 0.6821 (mp10) REVERT: A 457 ASP cc_start: 0.8362 (t0) cc_final: 0.8100 (t0) REVERT: A 469 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6693 (tpt) REVERT: B 64 LYS cc_start: 0.8965 (mmmt) cc_final: 0.8709 (mmmt) REVERT: B 119 HIS cc_start: 0.8641 (OUTLIER) cc_final: 0.7781 (m-70) REVERT: B 153 GLN cc_start: 0.8907 (mp10) cc_final: 0.8272 (mp10) REVERT: B 155 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7275 (mm) REVERT: B 249 MET cc_start: 0.9130 (ttp) cc_final: 0.8681 (tmm) REVERT: B 256 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.7862 (mmt) REVERT: B 310 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8236 (tp) REVERT: B 316 TYR cc_start: 0.7759 (t80) cc_final: 0.7392 (t80) REVERT: B 335 GLN cc_start: 0.8220 (mt0) cc_final: 0.7965 (mt0) REVERT: B 339 ASN cc_start: 0.8848 (m-40) cc_final: 0.8524 (m110) outliers start: 26 outliers final: 17 residues processed: 153 average time/residue: 0.0670 time to fit residues: 15.1823 Evaluate side-chains 150 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 341 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 0.1980 chunk 57 optimal weight: 0.0980 chunk 92 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 15 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN A 501 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.113580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.093367 restraints weight = 17746.398| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.35 r_work: 0.3444 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8935 Z= 0.124 Angle : 0.610 10.004 12058 Z= 0.307 Chirality : 0.041 0.189 1321 Planarity : 0.004 0.071 1532 Dihedral : 8.182 120.439 1273 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.64 % Allowed : 27.03 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.26), residues: 1065 helix: 1.89 (0.21), residues: 629 sheet: -0.32 (0.57), residues: 73 loop : -1.14 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 467 TYR 0.021 0.001 TYR D 179 PHE 0.010 0.001 PHE A 599 TRP 0.032 0.001 TRP D 228 HIS 0.010 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 8927) covalent geometry : angle 0.60945 / 0.31 (12052) hydrogen bonds : bond 0.03389 / 2.30 ( 510) hydrogen bonds : angle 4.14778 / 2.96 ( 1500) metal coordination : bond 0.00815 / 0.43 ( 8) metal coordination : angle 1.56657 / 0.92 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1651.97 seconds wall clock time: 29 minutes 11.18 seconds (1751.18 seconds total)