Starting phenix.real_space_refine on Tue Mar 3 14:30:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n0b_24102/03_2026/7n0b_24102.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n0b_24102/03_2026/7n0b_24102.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 { model { file = "/net/cci-nas-00/data/ceres_data/7n0b_24102/03_2026/7n0b_24102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n0b_24102/03_2026/7n0b_24102.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n0b_24102/03_2026/7n0b_24102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n0b_24102/03_2026/7n0b_24102.map" } 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= 0.003 sd= 0.084 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 5 6.06 5 P 39 5.49 5 S 52 5.16 5 C 3589 2.51 5 N 995 2.21 5 O 1193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5875 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 955 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "B" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4089 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 26, 'TRANS': 485} Chain breaks: 1 Chain: "T" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 419 Classifications: {'RNA': 20} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 12} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 404 Classifications: {'RNA': 19} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 8} Link IDs: {'rna3p': 18} 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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' CA': 2, ' ZN': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 520 SG CYS A 74 36.388 29.677 93.960 1.00 45.58 S ATOM 546 SG CYS A 77 33.521 31.561 95.217 1.00 35.44 S ATOM 651 SG CYS A 90 33.777 28.393 95.952 1.00 53.66 S ATOM 854 SG CYS A 117 44.933 12.952 101.734 1.00 87.14 S ATOM 874 SG CYS A 120 45.542 13.925 105.225 1.00 89.83 S ATOM 935 SG CYS A 128 48.215 13.881 102.415 1.00 79.86 S ATOM 947 SG CYS A 130 47.587 11.036 103.195 1.00 83.52 S ATOM 2581 SG CYS B 207 37.217 26.751 62.636 1.00 32.38 S ATOM 2601 SG CYS B 210 38.310 26.605 59.183 1.00 42.28 S ATOM 2722 SG CYS B 226 35.594 28.831 60.379 1.00 33.72 S ATOM 3022 SG CYS B 261 27.187 61.749 57.555 1.00 44.79 S ATOM 3152 SG CYS B 279 30.047 59.367 59.050 1.00 18.04 S ATOM 4542 SG CYS B 452 42.808 40.337 10.665 1.00 95.65 S ATOM 4698 SG CYS B 484 41.023 39.224 13.041 1.00 96.43 S Time building chain proxies: 1.41, per 1000 atoms: 0.24 Number of scatterers: 5875 At special positions: 0 Unit cell: (69.42, 91.848, 129.228, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 Ca 2 19.99 S 52 16.00 P 39 15.00 O 1193 8.00 N 995 7.00 C 3589 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: 0.61 Conformation dependent library (CDL) restraints added in 193.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" NE2 HIS A 83 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 90 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 77 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 74 " pdb=" ZN A 202 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 120 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 130 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 128 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 117 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" ND1 HIS B 229 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 226 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 207 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 210 " pdb=" ZN B 604 " pdb="ZN ZN B 604 " - pdb=" NE2 HIS B 257 " pdb="ZN ZN B 604 " - pdb=" ND1 HIS B 264 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 261 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 279 " pdb=" ZN B 605 " pdb="ZN ZN B 605 " - pdb=" ND1 HIS B 487 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 484 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 452 " Number of angles added : 13 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1202 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 8 sheets defined 26.1% alpha, 12.0% beta 18 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 10 through 19 removed outlier: 3.876A pdb=" N PHE A 16 " --> pdb=" O THR A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 33 removed outlier: 3.586A pdb=" N ALA A 26 " --> pdb=" O ASP A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 80 Processing helix chain 'A' and resid 85 through 89 removed outlier: 4.219A pdb=" N PHE A 89 " --> pdb=" O PRO A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 107 through 114 removed outlier: 4.029A pdb=" N LYS A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.526A pdb=" N VAL B 29 " --> pdb=" O HIS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 245 through 248 removed outlier: 3.893A pdb=" N GLY B 248 " --> pdb=" O GLN B 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 245 through 248' Processing helix chain 'B' and resid 270 through 287 removed outlier: 3.863A pdb=" N MET B 276 " --> pdb=" O CYS B 272 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 281 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 325 removed outlier: 3.596A pdb=" N ASN B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 317 " --> pdb=" O GLN B 313 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS B 318 " --> pdb=" O HIS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 432 through 437 removed outlier: 3.934A pdb=" N VAL B 437 " --> pdb=" O SER B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 480 removed outlier: 3.725A pdb=" N GLY B 480 " --> pdb=" O ARG B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 505 removed outlier: 4.344A pdb=" N ASN B 489 " --> pdb=" O ARG B 485 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLU B 490 " --> pdb=" O HIS B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 523 removed outlier: 3.546A pdb=" N LEU B 519 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN B 521 " --> pdb=" O ASN B 518 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 69 Processing sheet with id=AA2, first strand: chain 'B' and resid 54 through 55 removed outlier: 4.256A pdb=" N TYR B 124 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 116 through 118 removed outlier: 5.648A pdb=" N CYS B 94 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 223 through 225 removed outlier: 3.712A pdb=" N THR B 223 " --> pdb=" O SER B 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 364 through 365 removed outlier: 3.721A pdb=" N LEU B 329 " --> pdb=" O GLU B 347 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS B 349 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 381 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 397 through 401 Processing sheet with id=AA7, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AA8, first strand: chain 'B' and resid 446 through 447 removed outlier: 6.220A pdb=" N TYR B 446 " --> pdb=" O ILE B 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 127 hydrogen bonds defined for protein. 336 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 41 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 0.98 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1589 1.33 - 1.46: 1648 1.46 - 1.58: 2720 1.58 - 1.70: 76 1.70 - 1.83: 68 Bond restraints: 6101 Sorted by residual: bond pdb=" N ARG B 212 " pdb=" CA ARG B 212 " ideal model delta sigma weight residual 1.453 1.494 -0.041 1.31e-02 5.83e+03 9.96e+00 bond pdb=" ND1 HIS B 487 " pdb=" CE1 HIS B 487 " ideal model delta sigma weight residual 1.321 1.352 -0.031 1.00e-02 1.00e+04 9.37e+00 bond pdb=" CG HIS B 487 " pdb=" ND1 HIS B 487 " ideal model delta sigma weight residual 1.378 1.409 -0.031 1.10e-02 8.26e+03 7.95e+00 bond pdb=" ND1 HIS B 264 " pdb=" CE1 HIS B 264 " ideal model delta sigma weight residual 1.321 1.349 -0.028 1.00e-02 1.00e+04 7.71e+00 bond pdb=" N VAL A 97 " pdb=" CA VAL A 97 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.35e-02 5.49e+03 7.71e+00 ... (remaining 6096 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 7952 2.17 - 4.33: 439 4.33 - 6.50: 61 6.50 - 8.66: 11 8.66 - 10.83: 7 Bond angle restraints: 8470 Sorted by residual: angle pdb=" N VAL A 13 " pdb=" CA VAL A 13 " pdb=" C VAL A 13 " ideal model delta sigma weight residual 112.96 102.13 10.83 1.00e+00 1.00e+00 1.17e+02 angle pdb=" N ASP B 273 " pdb=" CA ASP B 273 " pdb=" C ASP B 273 " ideal model delta sigma weight residual 113.12 102.64 10.48 1.25e+00 6.40e-01 7.04e+01 angle pdb=" N ALA B 187 " pdb=" CA ALA B 187 " pdb=" C ALA B 187 " ideal model delta sigma weight residual 111.07 118.72 -7.65 1.07e+00 8.73e-01 5.11e+01 angle pdb=" CB HIS B 487 " pdb=" CG HIS B 487 " pdb=" CD2 HIS B 487 " ideal model delta sigma weight residual 131.20 123.76 7.44 1.30e+00 5.92e-01 3.27e+01 angle pdb=" CA ALA B 187 " pdb=" C ALA B 187 " pdb=" O ALA B 187 " ideal model delta sigma weight residual 120.82 114.82 6.00 1.05e+00 9.07e-01 3.26e+01 ... (remaining 8465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.54: 3199 18.54 - 37.08: 278 37.08 - 55.61: 87 55.61 - 74.15: 44 74.15 - 92.69: 6 Dihedral angle restraints: 3614 sinusoidal: 1742 harmonic: 1872 Sorted by residual: dihedral pdb=" CA HIS B 268 " pdb=" C HIS B 268 " pdb=" N VAL B 269 " pdb=" CA VAL B 269 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA TYR B 237 " pdb=" C TYR B 237 " pdb=" N ASN B 238 " pdb=" CA ASN B 238 " ideal model delta harmonic sigma weight residual -180.00 -159.66 -20.34 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C PHE B 190 " pdb=" N PHE B 190 " pdb=" CA PHE B 190 " pdb=" CB PHE B 190 " ideal model delta harmonic sigma weight residual -122.60 -132.08 9.48 0 2.50e+00 1.60e-01 1.44e+01 ... (remaining 3611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 762 0.063 - 0.126: 158 0.126 - 0.190: 37 0.190 - 0.253: 5 0.253 - 0.316: 2 Chirality restraints: 964 Sorted by residual: chirality pdb=" CA LEU B 185 " pdb=" N LEU B 185 " pdb=" C LEU B 185 " pdb=" CB LEU B 185 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CB ILE B 231 " pdb=" CA ILE B 231 " pdb=" CG1 ILE B 231 " pdb=" CG2 ILE B 231 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CA PHE B 190 " pdb=" N PHE B 190 " pdb=" C PHE B 190 " pdb=" CB PHE B 190 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 961 not shown) Planarity restraints: 943 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 83 " 0.100 2.00e-02 2.50e+03 7.39e-02 8.19e+01 pdb=" CG HIS A 83 " -0.112 2.00e-02 2.50e+03 pdb=" ND1 HIS A 83 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 HIS A 83 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 HIS A 83 " 0.057 2.00e-02 2.50e+03 pdb=" NE2 HIS A 83 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 76 " -0.083 2.00e-02 2.50e+03 4.41e-02 3.89e+01 pdb=" CG TYR A 76 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 76 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR A 76 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR A 76 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 76 " 0.025 2.00e-02 2.50e+03 pdb=" CZ TYR A 76 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 76 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 271 " 0.024 2.00e-02 2.50e+03 4.75e-02 2.26e+01 pdb=" C SER B 271 " -0.082 2.00e-02 2.50e+03 pdb=" O SER B 271 " 0.031 2.00e-02 2.50e+03 pdb=" N CYS B 272 " 0.028 2.00e-02 2.50e+03 ... (remaining 940 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 42 2.52 - 3.11: 4151 3.11 - 3.71: 9418 3.71 - 4.30: 12840 4.30 - 4.90: 20212 Nonbonded interactions: 46663 Sorted by model distance: nonbonded pdb="CA CA B 601 " pdb=" O HOH D 101 " model vdw 1.921 2.510 nonbonded pdb=" OP1 C D 71 " pdb="CA CA B 601 " model vdw 1.925 2.510 nonbonded pdb=" OD2 ASP B 90 " pdb="CA CA B 601 " model vdw 2.013 2.510 nonbonded pdb=" OD2 ASP B 273 " pdb="CA CA B 601 " model vdw 2.123 2.510 nonbonded pdb=" OD1 ASP B 90 " pdb="CA CA B 602 " model vdw 2.197 2.510 ... (remaining 46658 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.650 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.040 Process input model: 8.210 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 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 : 0.013 0.482 6120 Z= 0.489 Angle : 1.212 25.170 8483 Z= 0.682 Chirality : 0.058 0.316 964 Planarity : 0.008 0.074 943 Dihedral : 16.966 92.688 2412 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.36 % Allowed : 7.58 % Favored : 92.06 % Cbeta Deviations : 0.17 % 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: -3.60 (0.27), residues: 637 helix: -3.30 (0.31), residues: 139 sheet: -2.38 (0.82), residues: 37 loop : -2.24 (0.25), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 163 TYR 0.083 0.003 TYR A 76 PHE 0.023 0.003 PHE A 110 TRP 0.024 0.003 TRP B 520 HIS 0.013 0.002 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00596 ( 6101) covalent geometry : angle 1.10353 ( 8470) hydrogen bonds : bond 0.19598 ( 168) hydrogen bonds : angle 8.15554 ( 418) metal coordination : bond 0.20815 ( 19) metal coordination : angle 12.84065 ( 13) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7419 (m-30) cc_final: 0.6871 (m-30) REVERT: A 98 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.6814 (mp10) REVERT: B 92 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7839 (mm-30) REVERT: B 195 MET cc_start: 0.8486 (mtt) cc_final: 0.8129 (mtt) REVERT: B 253 LEU cc_start: 0.7116 (tp) cc_final: 0.6789 (tp) REVERT: B 348 TRP cc_start: 0.6564 (t-100) cc_final: 0.6026 (t-100) REVERT: B 494 TYR cc_start: 0.8505 (t80) cc_final: 0.8234 (t80) REVERT: B 509 TRP cc_start: 0.8565 (m100) cc_final: 0.8321 (m100) outliers start: 2 outliers final: 0 residues processed: 141 average time/residue: 0.0856 time to fit residues: 15.2348 Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain B residue 92 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.0970 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 HIS B 228 HIS B 229 HIS B 314 HIS B 478 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.192569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.152622 restraints weight = 9445.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.150083 restraints weight = 9456.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.151926 restraints weight = 8145.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.152366 restraints weight = 5777.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.153174 restraints weight = 5461.774| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.726 6120 Z= 0.418 Angle : 0.636 8.831 8483 Z= 0.322 Chirality : 0.041 0.156 964 Planarity : 0.005 0.052 943 Dihedral : 16.567 95.640 1270 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.53 % Allowed : 15.34 % Favored : 82.13 % 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: -2.50 (0.30), residues: 637 helix: -2.04 (0.36), residues: 148 sheet: -2.07 (0.64), residues: 58 loop : -1.51 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 81 TYR 0.014 0.001 TYR B 447 PHE 0.016 0.002 PHE B 33 TRP 0.011 0.001 TRP B 348 HIS 0.005 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 6101) covalent geometry : angle 0.62687 ( 8470) hydrogen bonds : bond 0.04166 ( 168) hydrogen bonds : angle 5.28202 ( 418) metal coordination : bond 0.39630 ( 19) metal coordination : angle 2.80238 ( 13) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8407 (mtpp) cc_final: 0.8172 (ttmm) REVERT: B 72 MET cc_start: 0.8489 (mmm) cc_final: 0.7942 (mmm) REVERT: B 132 ASP cc_start: 0.7776 (t0) cc_final: 0.7420 (m-30) REVERT: B 241 MET cc_start: 0.6928 (ptp) cc_final: 0.6650 (mtm) REVERT: B 253 LEU cc_start: 0.7599 (tp) cc_final: 0.7302 (tp) REVERT: B 254 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6670 (tm-30) REVERT: B 445 PHE cc_start: 0.8249 (p90) cc_final: 0.7942 (p90) REVERT: B 494 TYR cc_start: 0.8873 (t80) cc_final: 0.8584 (t80) REVERT: B 509 TRP cc_start: 0.8796 (m100) cc_final: 0.8403 (m100) outliers start: 14 outliers final: 3 residues processed: 120 average time/residue: 0.0932 time to fit residues: 13.9851 Evaluate side-chains 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 341 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 40 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN ** B 330 HIS ** 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 = 0.4387 r_free = 0.4387 target = 0.195298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.154787 restraints weight = 9094.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.152089 restraints weight = 8823.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.153889 restraints weight = 8619.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.153972 restraints weight = 6155.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.154611 restraints weight = 6181.767| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.193 6120 Z= 0.165 Angle : 0.643 9.334 8483 Z= 0.323 Chirality : 0.041 0.134 964 Planarity : 0.004 0.048 943 Dihedral : 16.322 95.471 1264 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.25 % Allowed : 16.06 % Favored : 80.69 % 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: -2.20 (0.31), residues: 637 helix: -1.40 (0.40), residues: 146 sheet: -1.86 (0.62), residues: 60 loop : -1.47 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 78 TYR 0.028 0.002 TYR B 447 PHE 0.024 0.002 PHE B 133 TRP 0.007 0.001 TRP B 385 HIS 0.017 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 6101) covalent geometry : angle 0.61762 ( 8470) hydrogen bonds : bond 0.03819 ( 168) hydrogen bonds : angle 5.09036 ( 418) metal coordination : bond 0.04656 ( 19) metal coordination : angle 4.63735 ( 13) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 66 GLU cc_start: 0.6263 (tp30) cc_final: 0.5943 (tp30) REVERT: B 105 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7432 (mp) REVERT: B 253 LEU cc_start: 0.7415 (tp) cc_final: 0.7077 (tt) REVERT: B 276 MET cc_start: 0.7988 (mmm) cc_final: 0.6997 (mmm) REVERT: B 315 MET cc_start: 0.8004 (tmm) cc_final: 0.7704 (tmm) REVERT: B 494 TYR cc_start: 0.8818 (t80) cc_final: 0.8615 (t80) REVERT: B 509 TRP cc_start: 0.8756 (m100) cc_final: 0.8082 (m100) outliers start: 18 outliers final: 12 residues processed: 103 average time/residue: 0.0818 time to fit residues: 11.0289 Evaluate side-chains 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 466 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 7 optimal weight: 0.0040 chunk 46 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 52 optimal weight: 0.0980 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 GLN ** B 330 HIS ** 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 = 0.4418 r_free = 0.4418 target = 0.198187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.157698 restraints weight = 9243.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.156262 restraints weight = 7905.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.158046 restraints weight = 8682.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.158107 restraints weight = 5634.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.158699 restraints weight = 5607.103| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.182 6120 Z= 0.116 Angle : 0.575 8.184 8483 Z= 0.284 Chirality : 0.040 0.189 964 Planarity : 0.004 0.048 943 Dihedral : 16.083 95.144 1264 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.71 % Allowed : 19.31 % Favored : 77.98 % 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 (0.31), residues: 637 helix: -1.20 (0.41), residues: 150 sheet: -1.46 (0.63), residues: 58 loop : -1.32 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 78 TYR 0.011 0.001 TYR A 27 PHE 0.018 0.001 PHE B 133 TRP 0.011 0.001 TRP B 348 HIS 0.018 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 6101) covalent geometry : angle 0.55333 ( 8470) hydrogen bonds : bond 0.03204 ( 168) hydrogen bonds : angle 4.78830 ( 418) metal coordination : bond 0.04259 ( 19) metal coordination : angle 4.05006 ( 13) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8445 (mtpp) cc_final: 0.8164 (ttmm) REVERT: A 66 GLU cc_start: 0.6347 (tp30) cc_final: 0.5884 (tp30) REVERT: A 119 VAL cc_start: 0.9186 (m) cc_final: 0.8941 (p) REVERT: B 90 ASP cc_start: 0.6934 (t70) cc_final: 0.6670 (t0) REVERT: B 195 MET cc_start: 0.8244 (ttm) cc_final: 0.8033 (ttm) REVERT: B 241 MET cc_start: 0.6936 (ptp) cc_final: 0.6467 (mtm) REVERT: B 253 LEU cc_start: 0.7578 (tp) cc_final: 0.6930 (tt) REVERT: B 273 ASP cc_start: 0.7836 (t70) cc_final: 0.7194 (t0) REVERT: B 276 MET cc_start: 0.7900 (mmm) cc_final: 0.6728 (mmm) REVERT: B 315 MET cc_start: 0.8157 (tmm) cc_final: 0.7756 (tmm) REVERT: B 392 TYR cc_start: 0.7928 (m-80) cc_final: 0.7705 (m-80) REVERT: B 494 TYR cc_start: 0.8767 (t80) cc_final: 0.8502 (t80) REVERT: B 509 TRP cc_start: 0.8585 (m100) cc_final: 0.7862 (m100) outliers start: 15 outliers final: 11 residues processed: 110 average time/residue: 0.0874 time to fit residues: 12.3840 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 466 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 45 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 53 optimal weight: 0.0170 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 5 optimal weight: 0.0770 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 0.0060 chunk 14 optimal weight: 0.1980 overall best weight: 0.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 ASN ** B 330 HIS ** 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 = 0.4442 r_free = 0.4442 target = 0.201092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.161913 restraints weight = 9348.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.159685 restraints weight = 8535.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.161329 restraints weight = 9896.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.161579 restraints weight = 6158.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.162421 restraints weight = 5869.313| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.168 6120 Z= 0.105 Angle : 0.569 8.433 8483 Z= 0.281 Chirality : 0.039 0.136 964 Planarity : 0.004 0.054 943 Dihedral : 15.873 94.541 1264 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.07 % Allowed : 19.86 % Favored : 77.08 % 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: -1.73 (0.31), residues: 637 helix: -1.00 (0.41), residues: 149 sheet: -1.85 (0.63), residues: 56 loop : -1.12 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 78 TYR 0.008 0.001 TYR B 491 PHE 0.016 0.001 PHE B 133 TRP 0.016 0.001 TRP B 348 HIS 0.019 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 6101) covalent geometry : angle 0.54925 ( 8470) hydrogen bonds : bond 0.03006 ( 168) hydrogen bonds : angle 4.61158 ( 418) metal coordination : bond 0.03935 ( 19) metal coordination : angle 3.85311 ( 13) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8469 (mtpp) cc_final: 0.8215 (ttmm) REVERT: A 66 GLU cc_start: 0.6235 (tp30) cc_final: 0.5934 (tp30) REVERT: A 119 VAL cc_start: 0.9185 (m) cc_final: 0.8932 (p) REVERT: B 241 MET cc_start: 0.6673 (ptp) cc_final: 0.6315 (mtm) REVERT: B 273 ASP cc_start: 0.7792 (t70) cc_final: 0.7498 (t0) REVERT: B 276 MET cc_start: 0.7853 (mmm) cc_final: 0.6742 (mmm) REVERT: B 315 MET cc_start: 0.8240 (tmm) cc_final: 0.7746 (tmm) REVERT: B 509 TRP cc_start: 0.8474 (m100) cc_final: 0.7486 (m100) outliers start: 17 outliers final: 13 residues processed: 110 average time/residue: 0.0755 time to fit residues: 10.8842 Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 466 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 35 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 54 optimal weight: 0.0030 chunk 48 optimal weight: 0.0970 chunk 18 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.189312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.148630 restraints weight = 8721.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.147649 restraints weight = 9709.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.149645 restraints weight = 10032.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.149406 restraints weight = 7200.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.149850 restraints weight = 7210.041| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.164 6120 Z= 0.119 Angle : 0.573 8.593 8483 Z= 0.285 Chirality : 0.040 0.130 964 Planarity : 0.004 0.054 943 Dihedral : 15.805 94.247 1264 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.89 % Allowed : 21.12 % Favored : 75.99 % 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: -1.48 (0.32), residues: 637 helix: -0.80 (0.41), residues: 151 sheet: -1.59 (0.56), residues: 66 loop : -0.94 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 400 TYR 0.013 0.001 TYR A 27 PHE 0.012 0.001 PHE B 133 TRP 0.009 0.001 TRP B 348 HIS 0.018 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6101) covalent geometry : angle 0.55289 ( 8470) hydrogen bonds : bond 0.02987 ( 168) hydrogen bonds : angle 4.49242 ( 418) metal coordination : bond 0.03826 ( 19) metal coordination : angle 3.86011 ( 13) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8392 (mtpp) cc_final: 0.8077 (ttmm) REVERT: A 119 VAL cc_start: 0.9036 (m) cc_final: 0.8751 (p) REVERT: B 241 MET cc_start: 0.6800 (ptp) cc_final: 0.6483 (mtm) REVERT: B 258 ASP cc_start: 0.6492 (m-30) cc_final: 0.6272 (m-30) REVERT: B 273 ASP cc_start: 0.7722 (t70) cc_final: 0.7431 (t0) REVERT: B 276 MET cc_start: 0.7701 (mmm) cc_final: 0.6631 (mmm) REVERT: B 509 TRP cc_start: 0.8292 (m100) cc_final: 0.7432 (m100) REVERT: B 519 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7694 (pp) outliers start: 16 outliers final: 11 residues processed: 103 average time/residue: 0.0759 time to fit residues: 10.4911 Evaluate side-chains 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 519 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 10 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 29 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 14 optimal weight: 0.0050 chunk 20 optimal weight: 0.9980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.187809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.147851 restraints weight = 8947.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.145280 restraints weight = 10571.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.147222 restraints weight = 10597.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.147483 restraints weight = 7537.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.147659 restraints weight = 8438.301| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.162 6120 Z= 0.121 Angle : 0.581 8.811 8483 Z= 0.285 Chirality : 0.040 0.144 964 Planarity : 0.004 0.054 943 Dihedral : 15.776 93.907 1264 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.07 % Allowed : 21.30 % Favored : 75.63 % 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: -1.20 (0.33), residues: 637 helix: -0.32 (0.43), residues: 141 sheet: -1.33 (0.56), residues: 71 loop : -0.86 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 400 TYR 0.007 0.001 TYR B 491 PHE 0.012 0.001 PHE B 133 TRP 0.005 0.001 TRP B 247 HIS 0.018 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6101) covalent geometry : angle 0.56079 ( 8470) hydrogen bonds : bond 0.02999 ( 168) hydrogen bonds : angle 4.41118 ( 418) metal coordination : bond 0.03799 ( 19) metal coordination : angle 3.94097 ( 13) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8490 (mtpp) cc_final: 0.8198 (ttmm) REVERT: A 119 VAL cc_start: 0.9010 (m) cc_final: 0.8725 (p) REVERT: B 273 ASP cc_start: 0.7767 (t70) cc_final: 0.7520 (t0) REVERT: B 295 GLU cc_start: 0.7092 (tt0) cc_final: 0.6876 (mt-10) REVERT: B 509 TRP cc_start: 0.8305 (m100) cc_final: 0.7440 (m100) REVERT: B 519 LEU cc_start: 0.7892 (tt) cc_final: 0.7624 (pp) outliers start: 17 outliers final: 13 residues processed: 99 average time/residue: 0.0740 time to fit residues: 9.8441 Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 495 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 26 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 58 optimal weight: 0.3980 chunk 8 optimal weight: 0.0020 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.188000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.149310 restraints weight = 8840.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.145992 restraints weight = 11237.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.148390 restraints weight = 11261.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.148129 restraints weight = 7604.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.148391 restraints weight = 8504.239| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.161 6120 Z= 0.118 Angle : 0.585 8.759 8483 Z= 0.283 Chirality : 0.040 0.140 964 Planarity : 0.004 0.052 943 Dihedral : 15.738 93.639 1264 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.07 % Allowed : 22.92 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.33), residues: 637 helix: -0.22 (0.43), residues: 141 sheet: -1.18 (0.58), residues: 71 loop : -0.80 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 400 TYR 0.012 0.001 TYR A 27 PHE 0.012 0.001 PHE B 133 TRP 0.007 0.001 TRP B 247 HIS 0.018 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 6101) covalent geometry : angle 0.56459 ( 8470) hydrogen bonds : bond 0.02926 ( 168) hydrogen bonds : angle 4.49526 ( 418) metal coordination : bond 0.03769 ( 19) metal coordination : angle 3.91101 ( 13) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8517 (mtpp) cc_final: 0.8242 (ttmm) REVERT: A 119 VAL cc_start: 0.9037 (m) cc_final: 0.8765 (p) REVERT: B 273 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7528 (t0) REVERT: B 295 GLU cc_start: 0.7174 (tt0) cc_final: 0.6916 (mt-10) REVERT: B 509 TRP cc_start: 0.8312 (m100) cc_final: 0.7421 (m100) REVERT: B 519 LEU cc_start: 0.7799 (tt) cc_final: 0.7590 (pp) outliers start: 17 outliers final: 14 residues processed: 96 average time/residue: 0.0729 time to fit residues: 9.4146 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 495 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 65 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.186871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.147089 restraints weight = 8771.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.143685 restraints weight = 11024.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.145544 restraints weight = 11692.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.145927 restraints weight = 8219.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.146172 restraints weight = 8204.951| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 6120 Z= 0.135 Angle : 0.602 10.470 8483 Z= 0.294 Chirality : 0.040 0.188 964 Planarity : 0.003 0.026 943 Dihedral : 15.739 93.298 1264 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.07 % Allowed : 23.83 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.33), residues: 637 helix: -0.07 (0.43), residues: 140 sheet: -1.13 (0.58), residues: 71 loop : -0.76 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 400 TYR 0.010 0.001 TYR B 392 PHE 0.010 0.001 PHE B 133 TRP 0.007 0.001 TRP B 247 HIS 0.018 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6101) covalent geometry : angle 0.58215 ( 8470) hydrogen bonds : bond 0.03063 ( 168) hydrogen bonds : angle 4.54107 ( 418) metal coordination : bond 0.03764 ( 19) metal coordination : angle 3.97774 ( 13) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8554 (mtpp) cc_final: 0.8255 (ttmm) REVERT: A 119 VAL cc_start: 0.9051 (m) cc_final: 0.8776 (p) REVERT: B 509 TRP cc_start: 0.8381 (m100) cc_final: 0.7501 (m100) REVERT: B 519 LEU cc_start: 0.7863 (tt) cc_final: 0.7616 (pp) outliers start: 17 outliers final: 13 residues processed: 95 average time/residue: 0.0732 time to fit residues: 9.2403 Evaluate side-chains 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 495 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 32 optimal weight: 0.5980 chunk 66 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 26 optimal weight: 0.0670 chunk 4 optimal weight: 3.9990 overall best weight: 1.0920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 427 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.185886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.148091 restraints weight = 8853.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.145200 restraints weight = 11074.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.147007 restraints weight = 11051.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.147021 restraints weight = 7760.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.147220 restraints weight = 8619.641| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.158 6120 Z= 0.158 Angle : 0.628 10.509 8483 Z= 0.307 Chirality : 0.041 0.166 964 Planarity : 0.004 0.028 943 Dihedral : 15.775 93.286 1264 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.53 % Allowed : 23.83 % Favored : 73.65 % 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: -0.94 (0.33), residues: 637 helix: -0.00 (0.43), residues: 140 sheet: -1.05 (0.59), residues: 71 loop : -0.76 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 400 TYR 0.014 0.001 TYR A 30 PHE 0.015 0.002 PHE A 89 TRP 0.008 0.001 TRP B 247 HIS 0.018 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 6101) covalent geometry : angle 0.60871 ( 8470) hydrogen bonds : bond 0.03147 ( 168) hydrogen bonds : angle 4.55528 ( 418) metal coordination : bond 0.03764 ( 19) metal coordination : angle 4.03154 ( 13) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8589 (mtpp) cc_final: 0.8285 (ttmm) REVERT: A 119 VAL cc_start: 0.9012 (m) cc_final: 0.8727 (p) REVERT: B 509 TRP cc_start: 0.8402 (m100) cc_final: 0.7533 (m100) outliers start: 14 outliers final: 13 residues processed: 93 average time/residue: 0.0678 time to fit residues: 8.4682 Evaluate side-chains 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 495 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 25 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 64 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.187817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.149133 restraints weight = 8898.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.147053 restraints weight = 11268.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.148497 restraints weight = 11621.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.149234 restraints weight = 8495.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.149606 restraints weight = 7741.080| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 6120 Z= 0.131 Angle : 0.613 10.590 8483 Z= 0.304 Chirality : 0.040 0.158 964 Planarity : 0.004 0.031 943 Dihedral : 15.738 93.087 1264 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.53 % Allowed : 24.55 % Favored : 72.92 % 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: -0.81 (0.33), residues: 637 helix: 0.21 (0.43), residues: 141 sheet: -1.00 (0.60), residues: 66 loop : -0.70 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 400 TYR 0.010 0.001 TYR B 392 PHE 0.017 0.001 PHE A 68 TRP 0.005 0.001 TRP B 247 HIS 0.018 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 6101) covalent geometry : angle 0.59426 ( 8470) hydrogen bonds : bond 0.03052 ( 168) hydrogen bonds : angle 4.57501 ( 418) metal coordination : bond 0.03755 ( 19) metal coordination : angle 3.93123 ( 13) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1031.51 seconds wall clock time: 18 minutes 30.90 seconds (1110.90 seconds total)