Starting phenix.real_space_refine on Wed Feb 4 05:38:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mmp_48397/02_2026/9mmp_48397.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mmp_48397/02_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_48397/02_2026/9mmp_48397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mmp_48397/02_2026/9mmp_48397.map" model { file = "/net/cci-nas-00/data/ceres_data/9mmp_48397/02_2026/9mmp_48397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mmp_48397/02_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-2.0-5952/lib/python3.9/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: 1.75, per 1000 atoms: 0.20 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: 0.73 Conformation dependent library (CDL) restraints added in 228.5 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: 0.16 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: 1.14 Time building geometry restraints manager: 0.85 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=" C23 LCJ B 702 " pdb=" I01 LCJ B 702 " ideal model delta sigma weight residual 2.099 2.032 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" N TYR D 179 " pdb=" CA TYR D 179 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.22e-02 6.72e+03 9.65e+00 bond pdb=" N ILE C 217 " pdb=" CA ILE C 217 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.56e+00 bond pdb=" N ILE D 93 " pdb=" CA ILE D 93 " ideal model delta sigma weight residual 1.461 1.493 -0.031 1.17e-02 7.31e+03 7.20e+00 ... (remaining 8922 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 11845 2.70 - 5.41: 179 5.41 - 8.11: 18 8.11 - 10.81: 6 10.81 - 13.51: 4 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=" PB AGS A 701 " pdb=" O3B AGS A 701 " pdb=" PG AGS A 701 " ideal model delta sigma weight residual 120.12 133.63 -13.51 3.00e+00 1.11e-01 2.03e+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 ... (remaining 12047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.06: 5178 31.06 - 62.12: 265 62.12 - 93.19: 16 93.19 - 124.25: 1 124.25 - 155.31: 1 Dihedral angle restraints: 5461 sinusoidal: 2281 harmonic: 3180 Sorted by residual: dihedral pdb=" O1A AGS A 701 " pdb=" O3A AGS A 701 " pdb=" PA AGS A 701 " pdb=" PB AGS A 701 " ideal model delta sinusoidal sigma weight residual 292.27 136.96 155.31 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" O1B AGS A 701 " pdb=" O3B AGS A 701 " pdb=" PB AGS A 701 " pdb=" PG AGS A 701 " ideal model delta sinusoidal sigma weight residual 68.91 -176.48 -114.61 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" CA TYR B 261 " pdb=" C TYR B 261 " pdb=" N PRO B 262 " pdb=" CA PRO B 262 " ideal model delta harmonic sigma weight residual -180.00 -160.92 -19.08 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 990 0.048 - 0.097: 257 0.097 - 0.145: 70 0.145 - 0.193: 7 0.193 - 0.242: 1 Chirality restraints: 1325 Sorted by residual: 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 chirality pdb=" CA ARG D 222 " pdb=" N ARG D 222 " pdb=" C ARG D 222 " pdb=" CB ARG D 222 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" CA MET D 160 " pdb=" N MET D 160 " pdb=" C MET D 160 " pdb=" CB MET D 160 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 1322 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: 3.970 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.540 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 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 0.067 8935 Z= 0.300 Angle : 0.843 14.155 12058 Z= 0.470 Chirality : 0.046 0.242 1325 Planarity : 0.007 0.165 1532 Dihedral : 16.963 155.312 3403 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 covalent geometry : bond 0.00497 ( 8927) covalent geometry : angle 0.82232 (12052) hydrogen bonds : bond 0.11411 ( 510) hydrogen bonds : angle 5.76698 ( 1500) metal coordination : bond 0.02010 ( 8) metal coordination : angle 8.45205 ( 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 : 0.350 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: 0.0784 time to fit residues: 19.0892 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 : 0.217 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3935 r_free = 0.3935 target = 0.114431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.093944 restraints weight = 20974.565| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.60 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: 0.7945 moved from start: 0.1209 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= 0.124 Angle : 0.574 6.874 12058 Z= 0.295 Chirality : 0.040 0.152 1325 Planarity : 0.004 0.063 1532 Dihedral : 9.198 152.035 1240 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.06 % Allowed : 24.39 % 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: 1.00 (0.26), residues: 1065 helix: 1.71 (0.21), residues: 630 sheet: -0.25 (0.57), residues: 68 loop : -1.00 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 363 TYR 0.017 0.001 TYR D 179 PHE 0.011 0.001 PHE C 196 TRP 0.022 0.001 TRP D 228 HIS 0.007 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8927) covalent geometry : angle 0.56973 (12052) hydrogen bonds : bond 0.03827 ( 510) hydrogen bonds : angle 4.54981 ( 1500) metal coordination : bond 0.00619 ( 8) metal coordination : angle 3.15523 ( 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 175 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 18 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7473 (ptm160) REVERT: A 540 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7778 (pt0) REVERT: A 608 LEU cc_start: 0.8731 (mp) cc_final: 0.8400 (mt) REVERT: B 64 LYS cc_start: 0.8769 (mmmt) cc_final: 0.8392 (mmmt) REVERT: B 87 HIS cc_start: 0.7852 (OUTLIER) cc_final: 0.7422 (t-90) REVERT: B 116 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8157 (mm-40) REVERT: B 118 LEU cc_start: 0.8413 (mt) cc_final: 0.8190 (mt) REVERT: B 153 GLN cc_start: 0.8890 (mp10) cc_final: 0.8430 (mp10) REVERT: B 187 MET cc_start: 0.6999 (mmt) cc_final: 0.6793 (mmt) REVERT: B 316 TYR cc_start: 0.7645 (t80) cc_final: 0.7279 (t80) REVERT: B 319 ASN cc_start: 0.8662 (m110) cc_final: 0.8441 (m110) REVERT: B 339 ASN cc_start: 0.8812 (m-40) cc_final: 0.8489 (m110) outliers start: 29 outliers final: 13 residues processed: 168 average time/residue: 0.0680 time to fit residues: 16.6594 Evaluate side-chains 151 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 94 CYS 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 B residue 87 HIS 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: 0.8980 chunk 91 optimal weight: 6.9990 chunk 52 optimal weight: 0.0570 chunk 45 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 0.0970 chunk 55 optimal weight: 0.3980 chunk 13 optimal weight: 0.0980 chunk 5 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN 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 = 0.3950 r_free = 0.3950 target = 0.115732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.095175 restraints weight = 20935.507| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.59 r_work: 0.3462 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8935 Z= 0.111 Angle : 0.537 7.669 12058 Z= 0.277 Chirality : 0.039 0.165 1325 Planarity : 0.004 0.064 1532 Dihedral : 8.922 154.979 1237 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.64 % Allowed : 24.71 % 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: 1.15 (0.26), residues: 1065 helix: 1.85 (0.21), residues: 630 sheet: -0.13 (0.57), residues: 68 loop : -1.00 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 83 TYR 0.011 0.001 TYR B 261 PHE 0.015 0.001 PHE B 371 TRP 0.031 0.001 TRP D 228 HIS 0.006 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8927) covalent geometry : angle 0.53444 (12052) hydrogen bonds : bond 0.03546 ( 510) hydrogen bonds : angle 4.36341 ( 1500) metal coordination : bond 0.00613 ( 8) metal coordination : angle 2.45991 ( 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 179 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 8 GLN cc_start: 0.8428 (pm20) cc_final: 0.8050 (pm20) REVERT: A 608 LEU cc_start: 0.8758 (mp) cc_final: 0.8456 (mt) REVERT: B 87 HIS cc_start: 0.7791 (OUTLIER) cc_final: 0.7416 (t-90) REVERT: B 116 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8153 (mm-40) REVERT: B 118 LEU cc_start: 0.8355 (mt) cc_final: 0.8155 (mt) REVERT: B 153 GLN cc_start: 0.8921 (mp10) cc_final: 0.8446 (mp10) REVERT: B 249 MET cc_start: 0.9182 (ttp) cc_final: 0.8710 (tmm) REVERT: B 256 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8070 (mmt) REVERT: B 310 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8039 (tp) REVERT: B 316 TYR cc_start: 0.7650 (t80) cc_final: 0.7286 (t80) REVERT: B 319 ASN cc_start: 0.8645 (m110) cc_final: 0.8422 (m110) REVERT: B 339 ASN cc_start: 0.8830 (m-40) cc_final: 0.8504 (m110) outliers start: 25 outliers final: 11 residues processed: 171 average time/residue: 0.0714 time to fit residues: 18.0517 Evaluate side-chains 147 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 GLU 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 140 SER 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 82 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 6 optimal weight: 0.0970 chunk 2 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 102 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN 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 = 0.3937 r_free = 0.3937 target = 0.114877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.094235 restraints weight = 21392.941| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.61 r_work: 0.3443 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8935 Z= 0.120 Angle : 0.544 8.655 12058 Z= 0.276 Chirality : 0.040 0.151 1325 Planarity : 0.004 0.064 1532 Dihedral : 8.739 155.472 1237 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.27 % Allowed : 25.03 % Favored : 71.70 % 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: 1.17 (0.26), residues: 1065 helix: 1.89 (0.21), residues: 630 sheet: -0.16 (0.57), residues: 73 loop : -1.04 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 167 TYR 0.014 0.001 TYR D 179 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 covalent geometry : bond 0.00264 ( 8927) covalent geometry : angle 0.54184 (12052) hydrogen bonds : bond 0.03442 ( 510) hydrogen bonds : angle 4.23338 ( 1500) metal coordination : bond 0.00590 ( 8) metal coordination : angle 2.21728 ( 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 180 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.8343 (t0) cc_final: 0.7998 (t0) REVERT: A 469 MET cc_start: 0.7553 (tpt) cc_final: 0.6823 (tpt) REVERT: A 608 LEU cc_start: 0.8783 (mp) cc_final: 0.8464 (mt) REVERT: B 87 HIS cc_start: 0.7824 (OUTLIER) cc_final: 0.7503 (t-90) REVERT: B 116 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8434 (mm-40) REVERT: B 119 HIS cc_start: 0.8547 (OUTLIER) cc_final: 0.8228 (m-70) REVERT: B 153 GLN cc_start: 0.8946 (mp10) cc_final: 0.8487 (mp10) REVERT: B 249 MET cc_start: 0.9148 (ttp) cc_final: 0.8697 (tmm) REVERT: B 256 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8043 (mmt) REVERT: B 310 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8041 (tp) REVERT: B 316 TYR cc_start: 0.7702 (t80) cc_final: 0.7343 (t80) REVERT: B 319 ASN cc_start: 0.8653 (m110) cc_final: 0.8435 (m110) REVERT: B 339 ASN cc_start: 0.8839 (m-40) cc_final: 0.8504 (m110) outliers start: 31 outliers final: 18 residues processed: 170 average time/residue: 0.0676 time to fit residues: 17.1576 Evaluate side-chains 159 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 400 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 463 ASN 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 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: 3.9990 chunk 53 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 78 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3908 r_free = 0.3908 target = 0.112998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.091872 restraints weight = 21718.726| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.72 r_work: 0.3394 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8935 Z= 0.161 Angle : 0.578 8.926 12058 Z= 0.294 Chirality : 0.041 0.183 1325 Planarity : 0.004 0.056 1532 Dihedral : 8.652 156.586 1237 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.27 % Allowed : 25.03 % Favored : 71.70 % 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: 1.85 (0.21), residues: 630 sheet: -0.23 (0.57), residues: 73 loop : -1.11 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 91 TYR 0.015 0.002 TYR D 125 PHE 0.012 0.001 PHE A 599 TRP 0.024 0.001 TRP D 228 HIS 0.007 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8927) covalent geometry : angle 0.57586 (12052) hydrogen bonds : bond 0.03606 ( 510) hydrogen bonds : angle 4.23973 ( 1500) metal coordination : bond 0.01154 ( 8) metal coordination : angle 2.13542 ( 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 172 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 198 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8231 (t70) REVERT: A 457 ASP cc_start: 0.8432 (t0) cc_final: 0.8091 (t0) REVERT: A 469 MET cc_start: 0.7761 (tpt) cc_final: 0.7063 (tpt) REVERT: B 64 LYS cc_start: 0.8926 (mmmt) cc_final: 0.8644 (mmmt) REVERT: B 87 HIS cc_start: 0.7756 (OUTLIER) cc_final: 0.7392 (t-90) REVERT: B 119 HIS cc_start: 0.8567 (OUTLIER) cc_final: 0.7947 (m-70) REVERT: B 153 GLN cc_start: 0.8965 (mp10) cc_final: 0.8416 (mp10) REVERT: B 249 MET cc_start: 0.9148 (ttp) cc_final: 0.8659 (tmm) REVERT: B 256 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8014 (mmt) REVERT: B 310 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8079 (tp) REVERT: B 316 TYR cc_start: 0.7808 (t80) cc_final: 0.7415 (t80) REVERT: B 319 ASN cc_start: 0.8633 (m110) cc_final: 0.8420 (m110) REVERT: B 339 ASN cc_start: 0.8860 (m-40) cc_final: 0.8520 (m110) outliers start: 31 outliers final: 19 residues processed: 164 average time/residue: 0.0752 time to fit residues: 17.9235 Evaluate side-chains 151 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 140 SER Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain A residue 184 CYS 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 3 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 GLN C 42 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.113854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.093401 restraints weight = 19653.245| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.50 r_work: 0.3435 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2001 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= 0.119 Angle : 0.560 9.058 12058 Z= 0.283 Chirality : 0.040 0.196 1325 Planarity : 0.004 0.067 1532 Dihedral : 8.634 158.427 1237 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % 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: 1.14 (0.26), residues: 1065 helix: 1.89 (0.21), residues: 630 sheet: -0.15 (0.58), 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 0.015 0.001 TYR D 179 PHE 0.012 0.001 PHE B 371 TRP 0.019 0.001 TRP D 228 HIS 0.007 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8927) covalent geometry : angle 0.55823 (12052) hydrogen bonds : bond 0.03396 ( 510) hydrogen bonds : angle 4.19423 ( 1500) metal coordination : bond 0.00657 ( 8) metal coordination : angle 1.79456 ( 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: 31 poor density : 147 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 8 GLN cc_start: 0.8407 (pm20) cc_final: 0.8175 (pm20) REVERT: C 198 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8197 (t70) REVERT: A 457 ASP cc_start: 0.8369 (t0) cc_final: 0.8057 (t0) REVERT: A 469 MET cc_start: 0.7691 (tpt) cc_final: 0.7064 (tpt) REVERT: A 608 LEU cc_start: 0.8762 (mp) cc_final: 0.8477 (mt) REVERT: B 64 LYS cc_start: 0.8914 (mmmt) cc_final: 0.8633 (mmmt) REVERT: B 87 HIS cc_start: 0.7648 (OUTLIER) cc_final: 0.7365 (t-90) REVERT: B 119 HIS cc_start: 0.8528 (OUTLIER) cc_final: 0.8237 (m-70) REVERT: B 153 GLN cc_start: 0.8941 (mp10) cc_final: 0.8357 (mp10) REVERT: B 249 MET cc_start: 0.9147 (ttp) cc_final: 0.8698 (tmm) REVERT: B 256 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8024 (mmt) REVERT: B 310 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8088 (tp) REVERT: B 316 TYR cc_start: 0.7717 (t80) cc_final: 0.7345 (t80) REVERT: B 339 ASN cc_start: 0.8837 (m-40) cc_final: 0.8516 (m110) outliers start: 31 outliers final: 21 residues processed: 168 average time/residue: 0.0725 time to fit residues: 17.5662 Evaluate side-chains 161 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN B 116 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 = 0.3914 r_free = 0.3914 target = 0.113376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.092827 restraints weight = 19837.125| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.52 r_work: 0.3412 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8935 Z= 0.131 Angle : 0.566 8.563 12058 Z= 0.288 Chirality : 0.040 0.174 1325 Planarity : 0.004 0.060 1532 Dihedral : 8.578 157.913 1237 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.96 % Allowed : 25.13 % Favored : 71.91 % 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: -0.17 (0.57), residues: 73 loop : -1.10 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 41 TYR 0.017 0.001 TYR D 179 PHE 0.010 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 covalent geometry : bond 0.00296 ( 8927) covalent geometry : angle 0.56487 (12052) hydrogen bonds : bond 0.03472 ( 510) hydrogen bonds : angle 4.17875 ( 1500) metal coordination : bond 0.00915 ( 8) metal coordination : angle 1.76154 ( 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 168 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 8 GLN cc_start: 0.8477 (pm20) cc_final: 0.8266 (pm20) REVERT: C 77 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8143 (mp10) REVERT: C 198 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8233 (t70) REVERT: A 457 ASP cc_start: 0.8430 (t0) cc_final: 0.8116 (t0) REVERT: A 469 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7048 (tpt) REVERT: A 581 MET cc_start: 0.8562 (mmm) cc_final: 0.8308 (tpt) REVERT: B 64 LYS cc_start: 0.8918 (mmmt) cc_final: 0.8684 (mmmt) REVERT: B 87 HIS cc_start: 0.7643 (OUTLIER) cc_final: 0.7370 (t-90) REVERT: B 153 GLN cc_start: 0.8943 (mp10) cc_final: 0.8316 (mp10) REVERT: B 249 MET cc_start: 0.9148 (ttp) cc_final: 0.8687 (tmm) REVERT: B 256 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.7968 (mmt) REVERT: B 310 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8118 (tp) REVERT: B 316 TYR cc_start: 0.7780 (t80) cc_final: 0.7413 (t80) REVERT: B 335 GLN cc_start: 0.8222 (mt0) cc_final: 0.7962 (mt0) REVERT: B 339 ASN cc_start: 0.8853 (m-40) cc_final: 0.8532 (m110) outliers start: 28 outliers final: 18 residues processed: 157 average time/residue: 0.0763 time to fit residues: 17.3008 Evaluate side-chains 156 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 400 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 76 optimal weight: 0.7980 chunk 65 optimal weight: 0.0050 chunk 35 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN A 501 GLN B 236 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 = 0.3917 r_free = 0.3917 target = 0.113766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.093456 restraints weight = 19598.108| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.46 r_work: 0.3424 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8935 Z= 0.124 Angle : 0.577 9.779 12058 Z= 0.292 Chirality : 0.040 0.164 1325 Planarity : 0.004 0.072 1532 Dihedral : 8.562 158.200 1237 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % 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: 1.12 (0.26), residues: 1065 helix: 1.85 (0.21), residues: 630 sheet: -0.16 (0.57), residues: 73 loop : -1.07 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 18 TYR 0.016 0.001 TYR D 179 PHE 0.010 0.001 PHE A 599 TRP 0.019 0.001 TRP D 228 HIS 0.009 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8927) covalent geometry : angle 0.57627 (12052) hydrogen bonds : bond 0.03379 ( 510) hydrogen bonds : angle 4.14808 ( 1500) metal coordination : bond 0.00778 ( 8) metal coordination : angle 1.71795 ( 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 171 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 77 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8172 (mp10) REVERT: C 198 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.8167 (t70) REVERT: D 18 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7519 (ptm160) REVERT: A 457 ASP cc_start: 0.8422 (t0) cc_final: 0.8101 (t0) REVERT: A 469 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.6893 (tpt) REVERT: A 581 MET cc_start: 0.8513 (mmm) cc_final: 0.8300 (tpt) REVERT: B 64 LYS cc_start: 0.8952 (mmmt) cc_final: 0.8697 (mmmt) REVERT: B 116 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8336 (mm-40) REVERT: B 119 HIS cc_start: 0.8592 (OUTLIER) cc_final: 0.7961 (m-70) REVERT: B 153 GLN cc_start: 0.8918 (mp10) cc_final: 0.8208 (mp10) REVERT: B 249 MET cc_start: 0.9136 (ttp) cc_final: 0.8669 (tmm) REVERT: B 256 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.7963 (mmt) REVERT: B 310 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8121 (tp) REVERT: B 316 TYR cc_start: 0.7710 (t80) cc_final: 0.7367 (t80) REVERT: B 335 GLN cc_start: 0.8203 (mt0) cc_final: 0.7938 (mt0) REVERT: B 339 ASN cc_start: 0.8834 (m-40) cc_final: 0.8503 (m110) outliers start: 31 outliers final: 20 residues processed: 160 average time/residue: 0.0717 time to fit residues: 16.4464 Evaluate side-chains 155 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 400 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 65 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 100 optimal weight: 0.0000 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3925 r_free = 0.3925 target = 0.113869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.093494 restraints weight = 20945.741| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.56 r_work: 0.3436 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2291 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 : 0.596 9.648 12058 Z= 0.302 Chirality : 0.040 0.165 1325 Planarity : 0.004 0.065 1532 Dihedral : 8.545 157.879 1237 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.75 % Allowed : 26.19 % 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: 1.11 (0.26), residues: 1065 helix: 1.86 (0.21), residues: 629 sheet: -0.26 (0.56), residues: 73 loop : -1.09 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 167 TYR 0.017 0.001 TYR D 179 PHE 0.010 0.001 PHE A 599 TRP 0.022 0.001 TRP D 228 HIS 0.008 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8927) covalent geometry : angle 0.59528 (12052) hydrogen bonds : bond 0.03372 ( 510) hydrogen bonds : angle 4.13621 ( 1500) metal coordination : bond 0.00779 ( 8) metal coordination : angle 1.65101 ( 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 164 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 77 GLN cc_start: 0.8400 (mm-40) cc_final: 0.8153 (mp10) REVERT: C 198 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8164 (t70) REVERT: D 18 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7615 (ptm160) REVERT: D 194 GLN cc_start: 0.7975 (pt0) cc_final: 0.7757 (pt0) REVERT: A 457 ASP cc_start: 0.8395 (t0) cc_final: 0.8077 (t0) REVERT: A 469 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.6868 (tpt) REVERT: A 581 MET cc_start: 0.8557 (mmm) cc_final: 0.8356 (tpt) REVERT: B 64 LYS cc_start: 0.8968 (mmmt) cc_final: 0.8714 (mmmt) REVERT: B 116 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8314 (mm-40) REVERT: B 119 HIS cc_start: 0.8517 (OUTLIER) cc_final: 0.7922 (m-70) REVERT: B 153 GLN cc_start: 0.8908 (mp10) cc_final: 0.8206 (mp10) REVERT: B 249 MET cc_start: 0.9123 (ttp) cc_final: 0.8666 (tmm) REVERT: B 256 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.7931 (mmt) REVERT: B 310 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8195 (tp) REVERT: B 316 TYR cc_start: 0.7710 (t80) cc_final: 0.7383 (t80) REVERT: B 335 GLN cc_start: 0.8218 (mt0) cc_final: 0.7962 (mt0) REVERT: B 339 ASN cc_start: 0.8834 (m-40) cc_final: 0.8517 (m110) outliers start: 26 outliers final: 17 residues processed: 152 average time/residue: 0.0731 time to fit residues: 16.3261 Evaluate side-chains 153 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 132 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain A residue 184 CYS 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 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 228 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 93 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN B 236 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 = 0.3917 r_free = 0.3917 target = 0.113414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.092787 restraints weight = 21208.163| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.63 r_work: 0.3422 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8935 Z= 0.133 Angle : 0.600 9.754 12058 Z= 0.303 Chirality : 0.041 0.148 1325 Planarity : 0.004 0.064 1532 Dihedral : 8.538 157.649 1237 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.85 % Allowed : 25.98 % Favored : 71.17 % 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: 1.15 (0.26), residues: 1065 helix: 1.89 (0.21), residues: 629 sheet: -0.25 (0.57), residues: 73 loop : -1.06 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 167 TYR 0.017 0.001 TYR D 179 PHE 0.010 0.001 PHE A 599 TRP 0.025 0.001 TRP D 228 HIS 0.009 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8927) covalent geometry : angle 0.59947 (12052) hydrogen bonds : bond 0.03430 ( 510) hydrogen bonds : angle 4.14308 ( 1500) metal coordination : bond 0.00957 ( 8) metal coordination : angle 1.68025 ( 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 159 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: C 77 GLN cc_start: 0.8382 (mm-40) cc_final: 0.8155 (mp10) REVERT: C 198 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8177 (t70) REVERT: D 194 GLN cc_start: 0.8007 (pt0) cc_final: 0.7790 (pt0) REVERT: A 457 ASP cc_start: 0.8363 (t0) cc_final: 0.8039 (t0) REVERT: A 469 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6689 (tpt) REVERT: B 64 LYS cc_start: 0.8943 (mmmt) cc_final: 0.8693 (mmmt) REVERT: B 116 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8373 (mm-40) REVERT: B 119 HIS cc_start: 0.8492 (OUTLIER) cc_final: 0.7874 (m-70) REVERT: B 153 GLN cc_start: 0.8899 (mp10) cc_final: 0.8204 (mp10) REVERT: B 155 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.7336 (mm) REVERT: B 249 MET cc_start: 0.9109 (ttp) cc_final: 0.8657 (tmm) REVERT: B 256 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.7832 (mmt) REVERT: B 310 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8229 (tp) REVERT: B 316 TYR cc_start: 0.7761 (t80) cc_final: 0.7435 (t80) REVERT: B 335 GLN cc_start: 0.8218 (mt0) cc_final: 0.7950 (mt0) REVERT: B 339 ASN cc_start: 0.8829 (m-40) cc_final: 0.8518 (m110) outliers start: 27 outliers final: 18 residues processed: 148 average time/residue: 0.0680 time to fit residues: 15.2889 Evaluate side-chains 151 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 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 400 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 538 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 65 optimal weight: 0.0770 chunk 101 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 GLN C 42 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 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 = 0.3898 r_free = 0.3898 target = 0.112737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.091443 restraints weight = 20217.977| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.58 r_work: 0.3387 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8935 Z= 0.154 Angle : 0.615 9.845 12058 Z= 0.311 Chirality : 0.041 0.156 1325 Planarity : 0.004 0.071 1532 Dihedral : 8.549 157.397 1237 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.64 % Allowed : 25.87 % Favored : 71.49 % 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: 1.07 (0.26), residues: 1065 helix: 1.84 (0.21), residues: 629 sheet: -0.27 (0.56), residues: 73 loop : -1.12 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 167 TYR 0.019 0.002 TYR D 179 PHE 0.010 0.001 PHE A 599 TRP 0.036 0.002 TRP D 228 HIS 0.009 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8927) covalent geometry : angle 0.61340 (12052) hydrogen bonds : bond 0.03542 ( 510) hydrogen bonds : angle 4.18356 ( 1500) metal coordination : bond 0.01394 ( 8) metal coordination : angle 1.86408 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1783.15 seconds wall clock time: 31 minutes 26.46 seconds (1886.46 seconds total)