Starting phenix.real_space_refine on Fri Jul 3 02:50:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l48_23157/07_2026/7l48_23157.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l48_23157/07_2026/7l48_23157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l48_23157/07_2026/7l48_23157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l48_23157/07_2026/7l48_23157.map" model { file = "/net/cci-nas-00/data/ceres_data/7l48_23157/07_2026/7l48_23157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l48_23157/07_2026/7l48_23157.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7l48_23157/07_2026/7l48_23157.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l48_23157/07_2026/7l48_23157.cif" } resolution = 3.9 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 144 5.49 5 S 37 5.16 5 C 6739 2.51 5 N 2052 2.21 5 O 2512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s 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: 11488 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4229 Classifications: {'peptide': 522} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 17, 'TRANS': 504} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 4181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4181 Classifications: {'peptide': 519} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 17, 'TRANS': 501} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 3074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 3074 Classifications: {'RNA': 144} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 4, 'rna3p_pur': 67, 'rna3p_pyr': 61} Link IDs: {'rna2p': 16, 'rna3p': 127} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3837 SG CYS A 475 13.590 59.792 45.199 1.00144.72 S ATOM 4048 SG CYS A 500 11.483 59.182 41.090 1.00168.30 S ATOM 364 SG CYS A 50 53.063 98.075 78.234 1.00132.99 S ATOM 502 SG CYS A 69 56.898 98.778 78.930 1.00109.77 S ATOM 527 SG CYS A 72 55.165 95.811 80.252 1.00111.13 S ATOM 8022 SG CYS B 475 60.243 58.550 15.167 1.00129.53 S ATOM 8043 SG CYS B 478 59.669 57.064 10.831 1.00129.65 S ATOM 4570 SG CYS B 50 29.666 39.470 31.268 1.00448.64 S Time building chain proxies: 2.37, per 1000 atoms: 0.21 Number of scatterers: 11488 At special positions: 0 Unit cell: (101.85, 119.7, 111.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 37 16.00 P 144 15.00 O 2512 8.00 N 2052 7.00 C 6739 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: 0.87 Conformation dependent library (CDL) restraints added in 519.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 500 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 475 " pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" ND1 HIS A 53 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 72 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 69 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 50 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 478 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 475 " pdb=" ZN B 602 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 50 " Number of angles added : 3 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1990 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 7 sheets defined 43.8% alpha, 9.3% beta 47 base pairs and 84 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 21 through 42 removed outlier: 3.665A pdb=" N ASN A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 55 removed outlier: 4.335A pdb=" N LYS A 55 " --> pdb=" O SER A 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 51 through 55' Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 79 through 89 Processing helix chain 'A' and resid 94 through 126 Processing helix chain 'A' and resid 133 through 153 removed outlier: 4.472A pdb=" N TYR A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 168 Processing helix chain 'A' and resid 171 through 177 removed outlier: 3.629A pdb=" N LEU A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 261 removed outlier: 3.855A pdb=" N ARG A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 280 removed outlier: 3.597A pdb=" N GLU A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 367 Processing helix chain 'A' and resid 382 through 414 Processing helix chain 'A' and resid 423 through 428 Processing helix chain 'A' and resid 444 through 458 removed outlier: 3.857A pdb=" N MET A 448 " --> pdb=" O PRO A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 493 Processing helix chain 'A' and resid 508 through 519 removed outlier: 4.673A pdb=" N ILE A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 42 Processing helix chain 'B' and resid 52 through 58 removed outlier: 3.720A pdb=" N ALA B 57 " --> pdb=" O HIS B 53 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 76 removed outlier: 4.242A pdb=" N LYS B 73 " --> pdb=" O CYS B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 89 Processing helix chain 'B' and resid 94 through 126 Processing helix chain 'B' and resid 133 through 144 removed outlier: 3.831A pdb=" N VAL B 137 " --> pdb=" O ASN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 155 through 170 removed outlier: 3.807A pdb=" N ALA B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.585A pdb=" N LEU B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 281 removed outlier: 3.998A pdb=" N GLY B 281 " --> pdb=" O LYS B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 366 Processing helix chain 'B' and resid 382 through 415 removed outlier: 3.954A pdb=" N THR B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE B 387 " --> pdb=" O LYS B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 429 removed outlier: 3.572A pdb=" N ARG B 429 " --> pdb=" O GLU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 459 Processing helix chain 'B' and resid 486 through 493 Processing helix chain 'B' and resid 510 through 518 removed outlier: 3.743A pdb=" N ILE B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 214 through 218 removed outlier: 4.215A pdb=" N PHE A 214 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N SER A 251 " --> pdb=" O PRO A 17 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU A 253 " --> pdb=" O VAL A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 3.931A pdb=" N ALA A 49 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 64 " --> pdb=" O ALA A 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 343 through 345 removed outlier: 7.032A pdb=" N GLY A 323 " --> pdb=" O GLN A 420 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 208 through 209 removed outlier: 3.649A pdb=" N TYR B 287 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 258 through 259 Processing sheet with id=AA6, first strand: chain 'B' and resid 344 through 345 removed outlier: 5.507A pdb=" N THR B 418 " --> pdb=" O PRO B 319 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE B 321 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N GLN B 420 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLY B 323 " --> pdb=" O GLN B 420 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU B 462 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 498 through 500 365 hydrogen bonds defined for protein. 1065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 114 hydrogen bonds 216 hydrogen bond angles 0 basepair planarities 47 basepair parallelities 84 stacking parallelities Total time for adding SS restraints: 2.01 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2651 1.34 - 1.46: 3594 1.46 - 1.58: 5439 1.58 - 1.71: 286 1.71 - 1.83: 51 Bond restraints: 12021 Sorted by residual: bond pdb=" CA SER B 51 " pdb=" CB SER B 51 " ideal model delta sigma weight residual 1.529 1.455 0.074 1.59e-02 3.96e+03 2.17e+01 bond pdb=" N LYS A 383 " pdb=" CA LYS A 383 " ideal model delta sigma weight residual 1.461 1.495 -0.034 9.20e-03 1.18e+04 1.36e+01 bond pdb=" N LYS B 383 " pdb=" CA LYS B 383 " ideal model delta sigma weight residual 1.461 1.494 -0.033 9.20e-03 1.18e+04 1.30e+01 bond pdb=" N LEU A 194 " pdb=" CA LEU A 194 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.79e+00 bond pdb=" N LEU A 382 " pdb=" CA LEU A 382 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.14e-02 7.69e+03 7.94e+00 ... (remaining 12016 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 16212 2.23 - 4.46: 550 4.46 - 6.69: 87 6.69 - 8.92: 19 8.92 - 11.15: 7 Bond angle restraints: 16875 Sorted by residual: angle pdb=" N GLU B 390 " pdb=" CA GLU B 390 " pdb=" CB GLU B 390 " ideal model delta sigma weight residual 110.12 118.78 -8.66 1.47e+00 4.63e-01 3.47e+01 angle pdb=" C PHE A 435 " pdb=" N ASN A 436 " pdb=" CA ASN A 436 " ideal model delta sigma weight residual 121.54 132.69 -11.15 1.91e+00 2.74e-01 3.41e+01 angle pdb=" N GLN B 88 " pdb=" CA GLN B 88 " pdb=" CB GLN B 88 " ideal model delta sigma weight residual 110.13 118.64 -8.51 1.48e+00 4.57e-01 3.31e+01 angle pdb=" C PRO B 219 " pdb=" N PHE B 220 " pdb=" CA PHE B 220 " ideal model delta sigma weight residual 122.20 130.82 -8.62 1.72e+00 3.38e-01 2.51e+01 angle pdb=" CA GLU A 123 " pdb=" CB GLU A 123 " pdb=" CG GLU A 123 " ideal model delta sigma weight residual 114.10 123.94 -9.84 2.00e+00 2.50e-01 2.42e+01 ... (remaining 16870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 6754 35.72 - 71.44: 222 71.44 - 107.16: 19 107.16 - 142.88: 2 142.88 - 178.60: 3 Dihedral angle restraints: 7000 sinusoidal: 3933 harmonic: 3067 Sorted by residual: dihedral pdb=" O4' U E 92 " pdb=" C1' U E 92 " pdb=" N1 U E 92 " pdb=" C2 U E 92 " ideal model delta sinusoidal sigma weight residual 232.00 53.40 178.60 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C E 77 " pdb=" C1' C E 77 " pdb=" N1 C E 77 " pdb=" C2 C E 77 " ideal model delta sinusoidal sigma weight residual 232.00 55.26 176.74 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U E 110 " pdb=" C1' U E 110 " pdb=" N1 U E 110 " pdb=" C2 U E 110 " ideal model delta sinusoidal sigma weight residual -160.00 -56.82 -103.18 1 1.50e+01 4.44e-03 5.24e+01 ... (remaining 6997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1733 0.089 - 0.179: 181 0.179 - 0.268: 26 0.268 - 0.357: 2 0.357 - 0.446: 2 Chirality restraints: 1944 Sorted by residual: chirality pdb=" CB ILE B 131 " pdb=" CA ILE B 131 " pdb=" CG1 ILE B 131 " pdb=" CG2 ILE B 131 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 4.98e+00 chirality pdb=" CA CYS A 50 " pdb=" N CYS A 50 " pdb=" C CYS A 50 " pdb=" CB CYS A 50 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" C3' A E 129 " pdb=" C4' A E 129 " pdb=" O3' A E 129 " pdb=" C2' A E 129 " both_signs ideal model delta sigma weight residual False -2.48 -2.76 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1941 not shown) Planarity restraints: 1620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 52 " 0.025 2.00e-02 2.50e+03 5.20e-02 2.71e+01 pdb=" C LYS B 52 " -0.090 2.00e-02 2.50e+03 pdb=" O LYS B 52 " 0.033 2.00e-02 2.50e+03 pdb=" N HIS B 53 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 48 " -0.018 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C GLU B 48 " 0.065 2.00e-02 2.50e+03 pdb=" O GLU B 48 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA B 49 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 84 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C LYS B 84 " -0.062 2.00e-02 2.50e+03 pdb=" O LYS B 84 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU B 85 " 0.021 2.00e-02 2.50e+03 ... (remaining 1617 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2561 2.79 - 3.32: 10342 3.32 - 3.85: 21243 3.85 - 4.37: 24108 4.37 - 4.90: 36428 Nonbonded interactions: 94682 Sorted by model distance: nonbonded pdb=" OG SER B 51 " pdb=" CD ARG B 66 " model vdw 2.263 3.440 nonbonded pdb=" O ASN A 133 " pdb=" OG SER A 136 " model vdw 2.273 3.040 nonbonded pdb=" N6 A E 100 " pdb=" O2 C E 123 " model vdw 2.283 3.120 nonbonded pdb=" OG SER A 476 " pdb=" ND2 ASN A 512 " model vdw 2.298 3.120 nonbonded pdb=" C SER B 51 " pdb=" OG SER B 51 " model vdw 2.302 2.616 ... (remaining 94677 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 'A' and (resid 7 through 260 or (resid 261 through 262 and (name N or nam \ e CA or name C or name O or name CB )) or resid 263 through 294 or (resid 295 th \ rough 297 and (name N or name CA or name C or name O or name CB )) or resid 298 \ or (resid 299 and (name N or name CA or name C or name O or name CB )) or resid \ 300 through 491 or (resid 492 and (name N or name CA or name C or name O or name \ CB )) or resid 493 through 602)) selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.390 Find NCS groups from input model: 0.180 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 : 0.008 0.692 12030 Z= 0.335 Angle : 0.969 11.153 16878 Z= 0.548 Chirality : 0.058 0.446 1944 Planarity : 0.006 0.061 1620 Dihedral : 16.897 178.601 5010 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 0.22 % Allowed : 3.56 % Favored : 96.21 % Cbeta Deviations : 0.20 % 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: -3.57 (0.21), residues: 1037 helix: -1.48 (0.20), residues: 441 sheet: -2.30 (0.40), residues: 132 loop : -3.27 (0.22), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 363 TYR 0.032 0.002 TYR B 121 PHE 0.060 0.003 PHE A 354 TRP 0.035 0.003 TRP B 223 HIS 0.028 0.003 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.26 (12021) covalent geometry : angle 0.96488 / 0.55 (16875) hydrogen bonds : bond 0.14342 / 9.59 ( 479) hydrogen bonds : angle 6.55054 / 4.88 ( 1281) metal coordination : bond 0.23892 / 15.57 ( 9) metal coordination : angle 6.88555 / 4.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8106 (t80) cc_final: 0.7831 (t80) REVERT: A 421 MET cc_start: 0.7801 (tmm) cc_final: 0.7521 (tmm) REVERT: A 510 ASP cc_start: 0.8498 (m-30) cc_final: 0.8219 (m-30) REVERT: B 353 HIS cc_start: 0.8389 (t-90) cc_final: 0.8095 (t-170) REVERT: B 358 MET cc_start: 0.8598 (tpt) cc_final: 0.8078 (tpp) outliers start: 2 outliers final: 0 residues processed: 88 average time/residue: 0.1129 time to fit residues: 14.2472 Evaluate side-chains 53 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.0670 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 overall best weight: 4.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 ASN A 516 ASN A 519 ASN B 32 ASN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN B 189 ASN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.068335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.049503 restraints weight = 62802.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.050785 restraints weight = 34279.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.051432 restraints weight = 23881.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.051904 restraints weight = 19856.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.052121 restraints weight = 17693.992| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 12030 Z= 0.308 Angle : 0.740 7.556 16878 Z= 0.391 Chirality : 0.043 0.185 1944 Planarity : 0.006 0.053 1620 Dihedral : 16.087 165.154 2858 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 2.00 % Allowed : 12.69 % Favored : 85.30 % 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: -2.38 (0.24), residues: 1037 helix: -0.16 (0.23), residues: 457 sheet: -2.30 (0.40), residues: 141 loop : -2.89 (0.26), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 438 TYR 0.020 0.002 TYR A 434 PHE 0.025 0.002 PHE B 220 TRP 0.014 0.002 TRP B 443 HIS 0.006 0.001 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.31 (12021) covalent geometry : angle 0.73782 / 0.39 (16875) hydrogen bonds : bond 0.05900 / 4.19 ( 479) hydrogen bonds : angle 4.98098 / 3.62 ( 1281) metal coordination : bond 0.01891 / 0.96 ( 9) metal coordination : angle 4.30805 / 3.97 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8646 (ttt) cc_final: 0.8242 (tpp) REVERT: A 354 PHE cc_start: 0.8661 (t80) cc_final: 0.8368 (t80) REVERT: A 357 LYS cc_start: 0.9174 (pptt) cc_final: 0.8959 (pptt) REVERT: A 510 ASP cc_start: 0.8706 (m-30) cc_final: 0.8349 (m-30) REVERT: B 353 HIS cc_start: 0.8908 (t-90) cc_final: 0.8463 (t-170) REVERT: B 421 MET cc_start: 0.6907 (tmm) cc_final: 0.6666 (tmm) outliers start: 18 outliers final: 10 residues processed: 77 average time/residue: 0.1098 time to fit residues: 12.1792 Evaluate side-chains 59 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 489 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 63 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN A 169 ASN A 210 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** 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 = 0.3640 r_free = 0.3640 target = 0.069952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.050428 restraints weight = 63173.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.051828 restraints weight = 32848.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.052534 restraints weight = 22307.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.053036 restraints weight = 18281.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.053261 restraints weight = 16156.324| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12030 Z= 0.175 Angle : 0.598 6.655 16878 Z= 0.314 Chirality : 0.038 0.165 1944 Planarity : 0.004 0.040 1620 Dihedral : 15.822 168.004 2858 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 2.12 % Allowed : 14.70 % Favored : 83.18 % 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: -1.87 (0.25), residues: 1037 helix: 0.39 (0.23), residues: 461 sheet: -2.14 (0.41), residues: 143 loop : -2.78 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 440 TYR 0.013 0.002 TYR B 445 PHE 0.021 0.002 PHE A 341 TRP 0.012 0.001 TRP B 443 HIS 0.002 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (12021) covalent geometry : angle 0.59701 / 0.31 (16875) hydrogen bonds : bond 0.04922 / 3.42 ( 479) hydrogen bonds : angle 4.52068 / 3.26 ( 1281) metal coordination : bond 0.00964 / 0.48 ( 9) metal coordination : angle 2.26103 / 2.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8701 (ttt) cc_final: 0.8443 (ttt) REVERT: A 346 ILE cc_start: 0.6632 (OUTLIER) cc_final: 0.6229 (mp) REVERT: A 510 ASP cc_start: 0.8528 (m-30) cc_final: 0.8152 (m-30) REVERT: B 353 HIS cc_start: 0.9031 (t-90) cc_final: 0.8552 (t-170) REVERT: B 358 MET cc_start: 0.8728 (tpp) cc_final: 0.8424 (tpp) REVERT: B 421 MET cc_start: 0.7131 (tmm) cc_final: 0.6718 (tmm) outliers start: 19 outliers final: 12 residues processed: 68 average time/residue: 0.0864 time to fit residues: 9.0813 Evaluate side-chains 58 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 489 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 80 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 72 optimal weight: 0.0970 chunk 48 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.069661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.050138 restraints weight = 63618.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.051547 restraints weight = 32920.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.052264 restraints weight = 22300.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.052767 restraints weight = 18178.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.052987 restraints weight = 16064.154| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12030 Z= 0.173 Angle : 0.578 8.485 16878 Z= 0.302 Chirality : 0.038 0.163 1944 Planarity : 0.004 0.037 1620 Dihedral : 15.687 167.398 2858 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 2.78 % Allowed : 17.04 % Favored : 80.18 % 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: -1.44 (0.26), residues: 1037 helix: 0.83 (0.24), residues: 461 sheet: -1.95 (0.43), residues: 142 loop : -2.64 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 438 TYR 0.012 0.002 TYR A 82 PHE 0.018 0.002 PHE A 214 TRP 0.010 0.001 TRP B 223 HIS 0.002 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (12021) covalent geometry : angle 0.57757 / 0.30 (16875) hydrogen bonds : bond 0.04807 / 3.36 ( 479) hydrogen bonds : angle 4.29784 / 3.09 ( 1281) metal coordination : bond 0.01103 / 0.55 ( 9) metal coordination : angle 1.84398 / 1.72 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8201 (tpp) REVERT: A 346 ILE cc_start: 0.6810 (OUTLIER) cc_final: 0.6471 (mp) REVERT: A 448 MET cc_start: 0.7820 (ttp) cc_final: 0.7471 (ptm) REVERT: A 510 ASP cc_start: 0.8501 (m-30) cc_final: 0.8219 (m-30) REVERT: B 303 MET cc_start: 0.0845 (ppp) cc_final: 0.0602 (tmm) REVERT: B 353 HIS cc_start: 0.9018 (t-90) cc_final: 0.8570 (t-170) REVERT: B 358 MET cc_start: 0.8774 (tpp) cc_final: 0.8544 (tpp) REVERT: B 421 MET cc_start: 0.7277 (tmm) cc_final: 0.6886 (tmm) REVERT: B 443 TRP cc_start: 0.8955 (t-100) cc_final: 0.8635 (t-100) outliers start: 25 outliers final: 12 residues processed: 78 average time/residue: 0.0865 time to fit residues: 10.1788 Evaluate side-chains 63 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 489 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 65 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 HIS ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B 516 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.065788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.047188 restraints weight = 64587.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.048387 restraints weight = 35265.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.049028 restraints weight = 24754.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.049482 restraints weight = 20536.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.049619 restraints weight = 18263.696| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 12030 Z= 0.389 Angle : 0.800 8.345 16878 Z= 0.418 Chirality : 0.045 0.202 1944 Planarity : 0.006 0.056 1620 Dihedral : 16.638 167.228 2858 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 26.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 3.67 % Allowed : 18.04 % Favored : 78.29 % 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: -1.93 (0.25), residues: 1037 helix: 0.29 (0.23), residues: 464 sheet: -2.30 (0.41), residues: 147 loop : -2.70 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 438 TYR 0.022 0.003 TYR B 445 PHE 0.022 0.003 PHE B 495 TRP 0.013 0.002 TRP A 223 HIS 0.006 0.002 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00798 / 0.39 (12021) covalent geometry : angle 0.79843 / 0.42 (16875) hydrogen bonds : bond 0.06512 / 4.63 ( 479) hydrogen bonds : angle 5.08165 / 3.61 ( 1281) metal coordination : bond 0.02861 / 1.40 ( 9) metal coordination : angle 3.57639 / 3.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 41 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 346 ILE cc_start: 0.7395 (OUTLIER) cc_final: 0.6987 (mp) REVERT: A 510 ASP cc_start: 0.8810 (m-30) cc_final: 0.8538 (m-30) REVERT: B 78 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7641 (t70) outliers start: 33 outliers final: 21 residues processed: 68 average time/residue: 0.0807 time to fit residues: 8.7517 Evaluate side-chains 59 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 36 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 510 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 47 optimal weight: 0.4980 chunk 95 optimal weight: 0.5980 chunk 11 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 HIS A 369 ASN A 512 ASN A 516 ASN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN B 450 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.069653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.050245 restraints weight = 62850.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.051646 restraints weight = 32169.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.052421 restraints weight = 21760.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.052857 restraints weight = 17560.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.053058 restraints weight = 15650.327| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12030 Z= 0.134 Angle : 0.600 9.656 16878 Z= 0.306 Chirality : 0.038 0.181 1944 Planarity : 0.004 0.041 1620 Dihedral : 15.800 169.558 2858 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.78 % Allowed : 20.27 % Favored : 76.95 % 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: -1.35 (0.26), residues: 1037 helix: 0.82 (0.24), residues: 470 sheet: -1.88 (0.44), residues: 142 loop : -2.56 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 34 TYR 0.014 0.001 TYR A 82 PHE 0.013 0.002 PHE A 190 TRP 0.013 0.001 TRP B 223 HIS 0.003 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (12021) covalent geometry : angle 0.59923 / 0.31 (16875) hydrogen bonds : bond 0.04765 / 3.33 ( 479) hydrogen bonds : angle 4.41522 / 3.18 ( 1281) metal coordination : bond 0.00725 / 0.35 ( 9) metal coordination : angle 1.49127 / 1.40 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 121 TYR cc_start: 0.8814 (t80) cc_final: 0.8210 (t80) REVERT: A 309 ASP cc_start: 0.8757 (m-30) cc_final: 0.8549 (m-30) REVERT: A 510 ASP cc_start: 0.8468 (m-30) cc_final: 0.8194 (m-30) outliers start: 25 outliers final: 17 residues processed: 74 average time/residue: 0.0770 time to fit residues: 9.1487 Evaluate side-chains 66 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 489 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 40 optimal weight: 0.0570 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 0.0030 chunk 27 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 81 optimal weight: 0.2980 chunk 49 optimal weight: 30.0000 chunk 112 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.4510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN A 177 ASN A 210 HIS A 512 ASN A 516 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.071711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.052405 restraints weight = 63709.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.053840 restraints weight = 32416.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.054671 restraints weight = 21793.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.055137 restraints weight = 17474.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.055326 restraints weight = 15547.577| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12030 Z= 0.113 Angle : 0.582 11.709 16878 Z= 0.297 Chirality : 0.037 0.173 1944 Planarity : 0.004 0.037 1620 Dihedral : 15.130 168.589 2858 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.45 % Allowed : 20.16 % Favored : 77.39 % 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: -1.05 (0.27), residues: 1037 helix: 1.13 (0.24), residues: 465 sheet: -1.96 (0.43), residues: 150 loop : -2.35 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 163 TYR 0.013 0.001 TYR B 146 PHE 0.012 0.001 PHE A 94 TRP 0.012 0.001 TRP A 443 HIS 0.003 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (12021) covalent geometry : angle 0.58145 / 0.30 (16875) hydrogen bonds : bond 0.04614 / 3.14 ( 479) hydrogen bonds : angle 4.14371 / 2.98 ( 1281) metal coordination : bond 0.00365 / 0.18 ( 9) metal coordination : angle 1.15819 / 1.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TYR cc_start: 0.8837 (t80) cc_final: 0.8317 (t80) REVERT: A 510 ASP cc_start: 0.8350 (m-30) cc_final: 0.8133 (m-30) REVERT: B 358 MET cc_start: 0.8713 (tpp) cc_final: 0.8461 (tpp) outliers start: 22 outliers final: 14 residues processed: 83 average time/residue: 0.0828 time to fit residues: 10.4197 Evaluate side-chains 65 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 512 ASN Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 271 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 48 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 ASN ** B 108 GLN ** 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 = 0.3628 r_free = 0.3628 target = 0.069815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.050340 restraints weight = 63154.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.051740 restraints weight = 32772.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.052519 restraints weight = 22203.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.052913 restraints weight = 17851.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.053168 restraints weight = 16057.901| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12030 Z= 0.171 Angle : 0.616 11.968 16878 Z= 0.316 Chirality : 0.038 0.203 1944 Planarity : 0.004 0.040 1620 Dihedral : 15.160 168.040 2858 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 2.00 % Allowed : 21.27 % Favored : 76.73 % 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: -0.92 (0.27), residues: 1037 helix: 1.23 (0.24), residues: 464 sheet: -1.77 (0.44), residues: 142 loop : -2.33 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 438 TYR 0.041 0.002 TYR A 140 PHE 0.014 0.002 PHE A 190 TRP 0.018 0.002 TRP A 443 HIS 0.005 0.001 HIS B 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (12021) covalent geometry : angle 0.61556 / 0.32 (16875) hydrogen bonds : bond 0.04779 / 3.29 ( 479) hydrogen bonds : angle 4.26599 / 3.05 ( 1281) metal coordination : bond 0.01241 / 0.60 ( 9) metal coordination : angle 1.76006 / 1.41 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 TYR cc_start: 0.6878 (OUTLIER) cc_final: 0.6217 (m-10) REVERT: A 121 TYR cc_start: 0.8886 (t80) cc_final: 0.8336 (t80) REVERT: A 510 ASP cc_start: 0.8535 (m-30) cc_final: 0.8243 (m-30) outliers start: 18 outliers final: 14 residues processed: 67 average time/residue: 0.0871 time to fit residues: 8.7764 Evaluate side-chains 64 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 512 ASN Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 271 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 78 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 57 optimal weight: 0.0370 chunk 89 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 overall best weight: 1.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.070485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.050889 restraints weight = 63093.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.052281 restraints weight = 32825.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.053085 restraints weight = 22287.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.053520 restraints weight = 17933.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.053775 restraints weight = 15987.684| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12030 Z= 0.143 Angle : 0.606 13.135 16878 Z= 0.310 Chirality : 0.038 0.207 1944 Planarity : 0.004 0.040 1620 Dihedral : 15.100 168.657 2858 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 2.45 % Allowed : 21.16 % Favored : 76.39 % 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: -0.85 (0.27), residues: 1037 helix: 1.28 (0.24), residues: 464 sheet: -1.66 (0.45), residues: 137 loop : -2.30 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 440 TYR 0.038 0.002 TYR A 140 PHE 0.016 0.001 PHE A 214 TRP 0.023 0.002 TRP A 443 HIS 0.005 0.001 HIS B 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (12021) covalent geometry : angle 0.60601 / 0.31 (16875) hydrogen bonds : bond 0.04593 / 3.15 ( 479) hydrogen bonds : angle 4.21851 / 3.01 ( 1281) metal coordination : bond 0.00923 / 0.44 ( 9) metal coordination : angle 1.47068 / 1.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 TYR cc_start: 0.6755 (OUTLIER) cc_final: 0.6067 (m-10) REVERT: A 121 TYR cc_start: 0.8887 (t80) cc_final: 0.8328 (t80) REVERT: A 354 PHE cc_start: 0.8646 (t80) cc_final: 0.7681 (t80) REVERT: A 358 MET cc_start: 0.7736 (mtm) cc_final: 0.7260 (ptp) REVERT: A 485 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7204 (t80) REVERT: A 510 ASP cc_start: 0.8478 (m-30) cc_final: 0.8228 (m-30) outliers start: 22 outliers final: 17 residues processed: 75 average time/residue: 0.0968 time to fit residues: 10.6956 Evaluate side-chains 68 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 512 ASN Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 271 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 16 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 29 optimal weight: 0.0050 chunk 46 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 ASN A 210 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 ASN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.069682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.050518 restraints weight = 63540.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.051902 restraints weight = 32748.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.052720 restraints weight = 22160.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.053178 restraints weight = 17693.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.053379 restraints weight = 15645.523| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12030 Z= 0.177 Angle : 0.629 13.675 16878 Z= 0.322 Chirality : 0.039 0.208 1944 Planarity : 0.004 0.052 1620 Dihedral : 15.144 168.340 2858 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 2.45 % Allowed : 21.16 % Favored : 76.39 % 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: -0.97 (0.27), residues: 1037 helix: 1.14 (0.24), residues: 464 sheet: -1.83 (0.43), residues: 143 loop : -2.27 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 361 TYR 0.039 0.002 TYR A 140 PHE 0.015 0.002 PHE A 190 TRP 0.016 0.002 TRP A 443 HIS 0.005 0.001 HIS B 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (12021) covalent geometry : angle 0.62844 / 0.32 (16875) hydrogen bonds : bond 0.04784 / 3.30 ( 479) hydrogen bonds : angle 4.31589 / 3.08 ( 1281) metal coordination : bond 0.01206 / 0.58 ( 9) metal coordination : angle 1.72659 / 1.38 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 TYR cc_start: 0.6864 (OUTLIER) cc_final: 0.6105 (m-10) REVERT: A 121 TYR cc_start: 0.8891 (t80) cc_final: 0.8364 (t80) REVERT: A 358 MET cc_start: 0.8001 (mtm) cc_final: 0.7190 (ptp) REVERT: A 485 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7175 (t80) REVERT: A 510 ASP cc_start: 0.8484 (m-30) cc_final: 0.8240 (m-30) outliers start: 22 outliers final: 18 residues processed: 70 average time/residue: 0.0870 time to fit residues: 9.2791 Evaluate side-chains 70 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 512 ASN Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 369 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 58 optimal weight: 20.0000 chunk 84 optimal weight: 0.0050 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.069821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.050720 restraints weight = 63131.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.051919 restraints weight = 33770.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.052749 restraints weight = 22468.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.053260 restraints weight = 17904.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.053476 restraints weight = 15726.265| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 12030 Z= 0.198 Angle : 0.925 59.199 16878 Z= 0.537 Chirality : 0.043 0.685 1944 Planarity : 0.006 0.161 1620 Dihedral : 15.147 168.400 2858 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 2.34 % Allowed : 21.38 % Favored : 76.28 % Cbeta Deviations : 0.20 % 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: -0.98 (0.27), residues: 1037 helix: 1.12 (0.24), residues: 464 sheet: -1.83 (0.43), residues: 143 loop : -2.27 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 361 TYR 0.036 0.002 TYR A 140 PHE 0.015 0.002 PHE A 214 TRP 0.014 0.002 TRP A 443 HIS 0.004 0.001 HIS B 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.20 (12021) covalent geometry : angle 0.92458 / 0.54 (16875) hydrogen bonds : bond 0.04795 / 3.30 ( 479) hydrogen bonds : angle 4.31250 / 3.07 ( 1281) metal coordination : bond 0.01199 / 0.57 ( 9) metal coordination : angle 1.72458 / 1.36 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1733.28 seconds wall clock time: 31 minutes 0.39 seconds (1860.39 seconds total)