Starting phenix.real_space_refine on Fri Dec 27 17:12:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n0b_24102/12_2024/7n0b_24102.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n0b_24102/12_2024/7n0b_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7n0b_24102/12_2024/7n0b_24102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n0b_24102/12_2024/7n0b_24102.map" model { file = "/net/cci-nas-00/data/ceres_data/7n0b_24102/12_2024/7n0b_24102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n0b_24102/12_2024/7n0b_24102.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 4.41, per 1000 atoms: 0.75 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: 1.56 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 2.15 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: 2.05 Time building geometry restraints manager: 1.88 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: 0.570 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 23.070 Find NCS groups from input model: 0.060 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.870 ------------------------------------------------------------------------------- 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 : 0.006 0.044 6101 Z= 0.392 Angle : 1.104 10.826 8470 Z= 0.674 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.024 0.003 TRP B 520 HIS 0.013 0.002 HIS B 229 PHE 0.023 0.003 PHE A 110 TYR 0.083 0.003 TYR A 76 ARG 0.005 0.001 ARG B 163 *********************** 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 : 0.606 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: 0.7448 (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: 0.6790 (tp) REVERT: B 348 TRP cc_start: 0.6563 (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: 0.2246 time to fit residues: 39.7293 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 : 0.588 ------------------------------------------------------------------------------- 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 56 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 28 optimal weight: 0.4980 chunk 17 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 0.2980 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6101 Z= 0.226 Angle : 0.636 8.757 8470 Z= 0.327 Chirality : 0.042 0.178 964 Planarity : 0.005 0.052 943 Dihedral : 16.624 95.593 1270 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.89 % Allowed : 14.62 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.30), residues: 637 helix: -2.01 (0.37), residues: 148 sheet: -2.10 (0.64), residues: 58 loop : -1.53 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 348 HIS 0.005 0.001 HIS B 330 PHE 0.016 0.002 PHE B 33 TYR 0.014 0.001 TYR B 447 ARG 0.003 0.000 ARG B 81 *********************** 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 124 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8079 (mtpp) cc_final: 0.7850 (ttmm) REVERT: B 105 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7351 (mp) REVERT: B 241 MET cc_start: 0.6968 (ptp) cc_final: 0.6702 (mtm) REVERT: B 253 LEU cc_start: 0.7341 (tp) cc_final: 0.7132 (tp) REVERT: B 254 GLN cc_start: 0.6893 (OUTLIER) cc_final: 0.6517 (tm-30) REVERT: B 315 MET cc_start: 0.7690 (tmm) cc_final: 0.7477 (tmm) REVERT: B 445 PHE cc_start: 0.7857 (p90) cc_final: 0.7655 (p90) outliers start: 16 outliers final: 4 residues processed: 119 average time/residue: 0.2138 time to fit residues: 32.0201 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 CYS Chi-restraints excluded: chain B residue 105 LEU 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 33 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 6101 Z= 0.408 Angle : 0.703 6.503 8470 Z= 0.367 Chirality : 0.044 0.153 964 Planarity : 0.005 0.055 943 Dihedral : 16.509 95.691 1264 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.79 % Allowed : 16.97 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.31), residues: 637 helix: -1.36 (0.41), residues: 143 sheet: -2.02 (0.54), residues: 70 loop : -1.40 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 509 HIS 0.016 0.002 HIS B 229 PHE 0.022 0.003 PHE B 377 TYR 0.027 0.002 TYR B 447 ARG 0.004 0.001 ARG A 78 *********************** 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 114 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.6546 (mtp) cc_final: 0.6220 (mtt) REVERT: B 72 MET cc_start: 0.8825 (mmm) cc_final: 0.8570 (mtp) REVERT: B 315 MET cc_start: 0.7775 (tmm) cc_final: 0.7373 (tmm) outliers start: 21 outliers final: 13 residues processed: 110 average time/residue: 0.1914 time to fit residues: 27.2734 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 : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 39 CYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 VAL 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 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 31 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN B 67 ASN B 82 HIS ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6101 Z= 0.225 Angle : 0.615 7.947 8470 Z= 0.316 Chirality : 0.041 0.196 964 Planarity : 0.004 0.044 943 Dihedral : 16.295 95.621 1264 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.43 % Allowed : 19.86 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.31), residues: 637 helix: -1.13 (0.41), residues: 145 sheet: -1.78 (0.62), residues: 60 loop : -1.33 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 348 HIS 0.018 0.001 HIS B 229 PHE 0.021 0.002 PHE B 436 TYR 0.015 0.001 TYR B 447 ARG 0.004 0.000 ARG A 78 *********************** 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: 19 poor density : 96 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 VAL cc_start: 0.9120 (m) cc_final: 0.8800 (p) REVERT: B 253 LEU cc_start: 0.7461 (tp) cc_final: 0.7157 (tt) REVERT: B 392 TYR cc_start: 0.7676 (m-80) cc_final: 0.7451 (m-80) outliers start: 19 outliers final: 15 residues processed: 110 average time/residue: 0.1735 time to fit residues: 25.1727 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 : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 58 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 0.0070 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6101 Z= 0.182 Angle : 0.594 8.865 8470 Z= 0.302 Chirality : 0.040 0.150 964 Planarity : 0.004 0.044 943 Dihedral : 16.091 95.450 1264 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.25 % Allowed : 21.84 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.31), residues: 637 helix: -1.18 (0.40), residues: 154 sheet: -1.67 (0.57), residues: 59 loop : -1.17 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 509 HIS 0.018 0.001 HIS B 229 PHE 0.022 0.002 PHE B 436 TYR 0.020 0.001 TYR B 447 ARG 0.004 0.000 ARG A 78 *********************** 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 114 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8734 (t) cc_final: 0.8477 (p) REVERT: A 119 VAL cc_start: 0.9098 (m) cc_final: 0.8766 (p) REVERT: B 392 TYR cc_start: 0.7573 (m-80) cc_final: 0.7367 (m-80) outliers start: 18 outliers final: 12 residues processed: 109 average time/residue: 0.1838 time to fit residues: 26.0889 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 : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 95 HIS 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 466 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 53 optimal weight: 0.0870 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 47 optimal weight: 10.0000 overall best weight: 0.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6101 Z= 0.203 Angle : 0.602 8.738 8470 Z= 0.307 Chirality : 0.040 0.131 964 Planarity : 0.004 0.046 943 Dihedral : 15.998 95.220 1264 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.61 % Allowed : 22.02 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.32), residues: 637 helix: -0.78 (0.42), residues: 148 sheet: -1.90 (0.51), residues: 72 loop : -0.93 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 509 HIS 0.018 0.001 HIS B 229 PHE 0.024 0.002 PHE B 436 TYR 0.009 0.001 TYR B 447 ARG 0.005 0.000 ARG B 400 *********************** 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: 20 poor density : 88 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8734 (t) cc_final: 0.8473 (p) REVERT: A 119 VAL cc_start: 0.9091 (m) cc_final: 0.8759 (p) REVERT: B 241 MET cc_start: 0.6952 (ptp) cc_final: 0.6523 (mtm) outliers start: 20 outliers final: 15 residues processed: 103 average time/residue: 0.1602 time to fit residues: 22.3357 Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 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 366 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 495 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 0.0070 chunk 64 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 8.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6101 Z= 0.181 Angle : 0.595 6.830 8470 Z= 0.304 Chirality : 0.040 0.130 964 Planarity : 0.004 0.047 943 Dihedral : 15.930 94.796 1264 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.89 % Allowed : 23.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.32), residues: 637 helix: -0.65 (0.43), residues: 148 sheet: -1.86 (0.50), residues: 72 loop : -0.84 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 509 HIS 0.018 0.001 HIS B 229 PHE 0.020 0.002 PHE B 436 TYR 0.011 0.001 TYR B 392 ARG 0.004 0.000 ARG B 400 *********************** 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 111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8706 (t) cc_final: 0.8493 (p) REVERT: A 68 PHE cc_start: 0.7958 (m-80) cc_final: 0.7723 (m-80) REVERT: A 119 VAL cc_start: 0.9100 (m) cc_final: 0.8772 (p) outliers start: 16 outliers final: 15 residues processed: 107 average time/residue: 0.1593 time to fit residues: 22.9004 Evaluate side-chains 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 95 HIS 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 366 LEU Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 466 VAL 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 43 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 0.0030 chunk 61 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 36 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 47 optimal weight: 0.0270 overall best weight: 0.4048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 6101 Z= 0.166 Angle : 0.592 10.293 8470 Z= 0.300 Chirality : 0.040 0.134 964 Planarity : 0.004 0.049 943 Dihedral : 15.816 94.061 1264 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.25 % Allowed : 23.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.33), residues: 637 helix: -0.24 (0.44), residues: 142 sheet: -1.75 (0.51), residues: 79 loop : -0.71 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 509 HIS 0.019 0.001 HIS B 229 PHE 0.013 0.001 PHE B 133 TYR 0.007 0.001 TYR B 491 ARG 0.006 0.000 ARG B 400 *********************** 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 108 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 VAL cc_start: 0.9083 (m) cc_final: 0.8766 (p) REVERT: B 95 HIS cc_start: 0.8410 (OUTLIER) cc_final: 0.8197 (m-70) REVERT: B 241 MET cc_start: 0.6957 (ptp) cc_final: 0.6496 (mtm) outliers start: 18 outliers final: 14 residues processed: 103 average time/residue: 0.1629 time to fit residues: 22.4708 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 B residue 35 THR Chi-restraints excluded: chain B residue 95 HIS 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 366 LEU Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 466 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 61 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6101 Z= 0.236 Angle : 0.605 9.711 8470 Z= 0.308 Chirality : 0.041 0.135 964 Planarity : 0.004 0.050 943 Dihedral : 15.855 94.210 1264 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.89 % Allowed : 24.73 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.33), residues: 637 helix: -0.16 (0.44), residues: 142 sheet: -1.59 (0.53), residues: 81 loop : -0.69 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 509 HIS 0.018 0.001 HIS B 229 PHE 0.020 0.002 PHE B 133 TYR 0.013 0.001 TYR A 96 ARG 0.005 0.000 ARG B 400 *********************** 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 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 119 VAL cc_start: 0.9097 (m) cc_final: 0.8770 (p) outliers start: 16 outliers final: 13 residues processed: 93 average time/residue: 0.1665 time to fit residues: 21.1686 Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 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 444 PHE Chi-restraints excluded: chain B residue 466 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 14 optimal weight: 0.0470 chunk 22 optimal weight: 4.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6101 Z= 0.206 Angle : 0.601 10.185 8470 Z= 0.306 Chirality : 0.040 0.136 964 Planarity : 0.004 0.050 943 Dihedral : 15.830 94.060 1264 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.35 % Allowed : 24.91 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.33), residues: 637 helix: -0.04 (0.44), residues: 142 sheet: -1.69 (0.52), residues: 80 loop : -0.69 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 509 HIS 0.018 0.001 HIS B 229 PHE 0.017 0.002 PHE B 133 TYR 0.010 0.001 TYR B 392 ARG 0.005 0.000 ARG B 400 ********************** 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 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 119 VAL cc_start: 0.9091 (m) cc_final: 0.8765 (p) outliers start: 13 outliers final: 13 residues processed: 92 average time/residue: 0.1695 time to fit residues: 21.0672 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 : 0.674 ------------------------------------------------------------------------------- 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 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 444 PHE Chi-restraints excluded: chain B residue 466 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 46 optimal weight: 0.5980 chunk 3 optimal weight: 0.0040 chunk 38 optimal weight: 0.0770 chunk 60 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.9354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4411 r_free = 0.4411 target = 0.201900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.154577 restraints weight = 8999.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.152988 restraints weight = 7935.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.154384 restraints weight = 7350.883| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6101 Z= 0.216 Angle : 0.609 10.084 8470 Z= 0.311 Chirality : 0.041 0.177 964 Planarity : 0.004 0.050 943 Dihedral : 15.808 93.853 1264 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.89 % Allowed : 24.73 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.34), residues: 637 helix: 0.05 (0.44), residues: 142 sheet: -1.71 (0.51), residues: 80 loop : -0.63 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 509 HIS 0.018 0.001 HIS B 229 PHE 0.022 0.002 PHE B 326 TYR 0.020 0.001 TYR A 96 ARG 0.005 0.001 ARG B 400 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1481.17 seconds wall clock time: 28 minutes 12.74 seconds (1692.74 seconds total)