Starting phenix.real_space_refine on Tue Mar 11 14:30:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n0b_24102/03_2025/7n0b_24102.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n0b_24102/03_2025/7n0b_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_24102/03_2025/7n0b_24102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n0b_24102/03_2025/7n0b_24102.map" model { file = "/net/cci-nas-00/data/ceres_data/7n0b_24102/03_2025/7n0b_24102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n0b_24102/03_2025/7n0b_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-5624/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: 4.28, per 1000 atoms: 0.73 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: 1.54 Conformation dependent library (CDL) restraints added in 764.9 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: 2.04 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: 1.87 Time building geometry restraints manager: 1.81 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: 0.400 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: 0.060 Process input model: 20.590 Find NCS groups from input model: 0.050 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.220 ------------------------------------------------------------------------------- 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 : 0.937 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: 0.2149 time to fit residues: 37.9580 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 : 0.606 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.204089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.157405 restraints weight = 9173.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.153308 restraints weight = 7031.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.155658 restraints weight = 7022.420| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 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 : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8395 (mtpp) cc_final: 0.8141 (ttmm) REVERT: A 40 ASN cc_start: 0.8288 (t0) cc_final: 0.8058 (t0) REVERT: B 105 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7079 (mp) REVERT: B 132 ASP cc_start: 0.7700 (t0) cc_final: 0.7370 (m-30) REVERT: B 241 MET cc_start: 0.6953 (ptp) cc_final: 0.6746 (mtm) REVERT: B 253 LEU cc_start: 0.7642 (tp) cc_final: 0.7357 (tp) REVERT: B 254 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.6636 (tm-30) REVERT: B 445 PHE cc_start: 0.8469 (p90) cc_final: 0.8161 (p90) REVERT: B 447 TYR cc_start: 0.7357 (t80) cc_final: 0.7138 (t80) REVERT: B 509 TRP cc_start: 0.8923 (m100) cc_final: 0.8565 (m100) REVERT: B 514 PHE cc_start: 0.7430 (t80) cc_final: 0.7125 (t80) outliers start: 16 outliers final: 4 residues processed: 119 average time/residue: 0.2167 time to fit residues: 32.5711 Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 25 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.194804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.155407 restraints weight = 9209.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.154321 restraints weight = 8962.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.155711 restraints weight = 8195.161| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6101 Z= 0.255 Angle : 0.624 9.225 8470 Z= 0.320 Chirality : 0.041 0.135 964 Planarity : 0.004 0.046 943 Dihedral : 16.373 95.495 1264 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.07 % Allowed : 16.25 % 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 (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: -2.12 (0.31), residues: 637 helix: -1.40 (0.40), residues: 146 sheet: -1.76 (0.64), residues: 58 loop : -1.40 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 385 HIS 0.015 0.001 HIS B 229 PHE 0.024 0.002 PHE B 377 TYR 0.020 0.002 TYR B 351 ARG 0.005 0.000 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 108 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.6520 (mtt) cc_final: 0.6247 (mtt) REVERT: B 72 MET cc_start: 0.8625 (mmm) cc_final: 0.8339 (mtp) REVERT: B 132 ASP cc_start: 0.7926 (t0) cc_final: 0.7688 (m-30) REVERT: B 253 LEU cc_start: 0.7406 (tp) cc_final: 0.7076 (tt) REVERT: B 315 MET cc_start: 0.8085 (tmm) cc_final: 0.7760 (tmm) outliers start: 17 outliers final: 12 residues processed: 104 average time/residue: 0.1875 time to fit residues: 25.2998 Evaluate side-chains 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 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 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 37 optimal weight: 0.5980 chunk 45 optimal weight: 9.9990 chunk 2 optimal weight: 0.0670 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 48 optimal weight: 0.0270 chunk 36 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.4428 r_free = 0.4428 target = 0.204707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.156044 restraints weight = 9434.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.155648 restraints weight = 6821.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.157046 restraints weight = 6847.087| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6101 Z= 0.162 Angle : 0.581 8.017 8470 Z= 0.293 Chirality : 0.040 0.189 964 Planarity : 0.004 0.045 943 Dihedral : 16.166 95.285 1264 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.71 % Allowed : 19.68 % Favored : 77.62 % 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: -1.95 (0.31), residues: 637 helix: -1.14 (0.41), residues: 148 sheet: -1.64 (0.62), residues: 60 loop : -1.33 (0.29), residues: 429 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 0.012 0.001 PHE B 133 TYR 0.013 0.001 TYR A 27 ARG 0.004 0.000 ARG B 400 *********************** 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 117 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8430 (mtpp) cc_final: 0.8136 (ttmm) REVERT: A 66 GLU cc_start: 0.6376 (tp30) cc_final: 0.6106 (tp30) REVERT: A 119 VAL cc_start: 0.9245 (m) cc_final: 0.9002 (p) REVERT: B 132 ASP cc_start: 0.8020 (t0) cc_final: 0.7689 (m-30) REVERT: B 195 MET cc_start: 0.8093 (ttm) cc_final: 0.7777 (ttm) REVERT: B 241 MET cc_start: 0.6841 (ptp) cc_final: 0.6401 (mtm) REVERT: B 253 LEU cc_start: 0.7553 (tp) cc_final: 0.7136 (tt) REVERT: B 447 TYR cc_start: 0.7535 (t80) cc_final: 0.7270 (t80) outliers start: 15 outliers final: 11 residues processed: 112 average time/residue: 0.1740 time to fit residues: 25.6205 Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 218 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 59 optimal weight: 20.0000 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.0470 chunk 55 optimal weight: 4.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- 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 = 0.4405 r_free = 0.4405 target = 0.197401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.157841 restraints weight = 9125.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.156546 restraints weight = 9455.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.157736 restraints weight = 9356.708| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6101 Z= 0.180 Angle : 0.567 8.020 8470 Z= 0.290 Chirality : 0.040 0.137 964 Planarity : 0.004 0.046 943 Dihedral : 16.013 95.099 1264 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.89 % Allowed : 19.86 % Favored : 77.26 % 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: -1.74 (0.31), residues: 637 helix: -0.98 (0.41), residues: 147 sheet: -1.51 (0.57), residues: 65 loop : -1.18 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 509 HIS 0.018 0.001 HIS B 229 PHE 0.023 0.002 PHE B 514 TYR 0.007 0.001 TYR B 491 ARG 0.005 0.000 ARG B 400 *********************** 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 108 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8762 (t) cc_final: 0.8444 (p) REVERT: A 66 GLU cc_start: 0.6237 (tp30) cc_final: 0.5931 (tp30) REVERT: A 119 VAL cc_start: 0.9216 (m) cc_final: 0.8950 (p) REVERT: B 195 MET cc_start: 0.7993 (ttm) cc_final: 0.7507 (ttm) REVERT: B 241 MET cc_start: 0.6841 (ptp) cc_final: 0.6494 (mtm) REVERT: B 253 LEU cc_start: 0.7614 (tp) cc_final: 0.7352 (tt) REVERT: B 311 LYS cc_start: 0.8376 (ptpt) cc_final: 0.8125 (ptpp) REVERT: B 392 TYR cc_start: 0.7911 (m-80) cc_final: 0.7657 (m-80) outliers start: 16 outliers final: 12 residues processed: 104 average time/residue: 0.1734 time to fit residues: 24.0478 Evaluate side-chains 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 329 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 66 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 47 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 13 optimal weight: 0.0970 chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 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 = 0.4408 r_free = 0.4408 target = 0.197712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.157308 restraints weight = 9048.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.154995 restraints weight = 8979.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.156843 restraints weight = 9755.539| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6101 Z= 0.180 Angle : 0.566 9.204 8470 Z= 0.287 Chirality : 0.040 0.161 964 Planarity : 0.004 0.052 943 Dihedral : 15.908 94.710 1264 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.07 % Allowed : 20.22 % 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: -1.54 (0.32), residues: 637 helix: -0.77 (0.41), residues: 148 sheet: -1.76 (0.53), residues: 72 loop : -0.96 (0.30), residues: 417 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 0.028 0.002 PHE B 436 TYR 0.011 0.001 TYR A 27 ARG 0.003 0.000 ARG A 78 *********************** 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 107 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8596 (mtpp) cc_final: 0.8306 (ttmm) REVERT: A 42 VAL cc_start: 0.8717 (t) cc_final: 0.8502 (p) REVERT: A 66 GLU cc_start: 0.6307 (tp30) cc_final: 0.6005 (tp30) REVERT: A 119 VAL cc_start: 0.9227 (m) cc_final: 0.8970 (p) REVERT: B 188 HIS cc_start: 0.8006 (OUTLIER) cc_final: 0.7703 (t70) REVERT: B 195 MET cc_start: 0.7930 (ttm) cc_final: 0.7383 (ttm) REVERT: B 241 MET cc_start: 0.6709 (ptp) cc_final: 0.6386 (mtm) REVERT: B 253 LEU cc_start: 0.7410 (tp) cc_final: 0.7095 (tt) REVERT: B 392 TYR cc_start: 0.7928 (m-80) cc_final: 0.7700 (m-80) outliers start: 17 outliers final: 12 residues processed: 103 average time/residue: 0.1591 time to fit residues: 21.8445 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 169 MET Chi-restraints excluded: chain B residue 188 HIS 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 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 5 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 53 optimal weight: 0.0980 chunk 65 optimal weight: 10.0000 chunk 13 optimal weight: 0.1980 chunk 61 optimal weight: 0.9980 chunk 40 optimal weight: 0.0470 chunk 33 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 0.3678 ------------------------------------------------------------------------------- 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 = 0.4431 r_free = 0.4431 target = 0.200133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.159983 restraints weight = 9250.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.158061 restraints weight = 8626.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.160143 restraints weight = 7832.643| |-----------------------------------------------------------------------------| r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6101 Z= 0.154 Angle : 0.551 7.638 8470 Z= 0.280 Chirality : 0.040 0.147 964 Planarity : 0.004 0.054 943 Dihedral : 15.799 93.969 1264 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.71 % Allowed : 21.30 % 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 (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: -1.25 (0.32), residues: 637 helix: -0.25 (0.43), residues: 142 sheet: -1.74 (0.51), residues: 79 loop : -0.83 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 509 HIS 0.019 0.001 HIS B 229 PHE 0.021 0.002 PHE B 436 TYR 0.007 0.001 TYR B 420 ARG 0.005 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 112 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8442 (mtpp) cc_final: 0.8166 (ttmm) REVERT: A 119 VAL cc_start: 0.9069 (m) cc_final: 0.8787 (p) REVERT: B 195 MET cc_start: 0.8179 (ttm) cc_final: 0.7788 (ttm) REVERT: B 241 MET cc_start: 0.6626 (ptp) cc_final: 0.6276 (mtm) REVERT: B 253 LEU cc_start: 0.7426 (tp) cc_final: 0.7200 (tt) outliers start: 15 outliers final: 11 residues processed: 108 average time/residue: 0.1627 time to fit residues: 23.8490 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 : 0.566 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 61 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 0.0000 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 = 0.4423 r_free = 0.4423 target = 0.199101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.160258 restraints weight = 9106.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.156898 restraints weight = 10493.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.158551 restraints weight = 10578.273| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.4459 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= 0.171 Angle : 0.578 7.222 8470 Z= 0.295 Chirality : 0.040 0.150 964 Planarity : 0.004 0.052 943 Dihedral : 15.759 93.715 1264 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.89 % Allowed : 22.56 % Favored : 74.55 % 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: -1.00 (0.33), residues: 637 helix: 0.04 (0.43), residues: 142 sheet: -1.58 (0.52), residues: 77 loop : -0.71 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 509 HIS 0.018 0.001 HIS B 229 PHE 0.021 0.002 PHE B 436 TYR 0.012 0.001 TYR A 27 ARG 0.005 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 109 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8622 (mtpp) cc_final: 0.8326 (ttmm) REVERT: A 119 VAL cc_start: 0.9148 (m) cc_final: 0.8894 (p) REVERT: B 188 HIS cc_start: 0.7879 (OUTLIER) cc_final: 0.7657 (t70) REVERT: B 253 LEU cc_start: 0.7498 (tp) cc_final: 0.7228 (tt) outliers start: 16 outliers final: 12 residues processed: 104 average time/residue: 0.1582 time to fit residues: 22.2450 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 : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 64 ASP 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 188 HIS 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 23 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 0.0370 chunk 59 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 = 0.4172 r_free = 0.4172 target = 0.184542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.147889 restraints weight = 8836.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.145225 restraints weight = 11967.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.146865 restraints weight = 10851.410| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6101 Z= 0.190 Angle : 0.589 10.224 8470 Z= 0.296 Chirality : 0.041 0.188 964 Planarity : 0.004 0.028 943 Dihedral : 15.749 93.507 1264 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.71 % Allowed : 24.73 % Favored : 72.56 % 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: -0.96 (0.33), residues: 637 helix: 0.10 (0.43), residues: 142 sheet: -1.61 (0.53), residues: 77 loop : -0.68 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 509 HIS 0.018 0.001 HIS B 229 PHE 0.020 0.002 PHE B 436 TYR 0.008 0.001 TYR B 420 ARG 0.006 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: 15 poor density : 83 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8564 (mtpp) cc_final: 0.8240 (ttmm) REVERT: A 119 VAL cc_start: 0.8930 (m) cc_final: 0.8639 (p) REVERT: B 253 LEU cc_start: 0.7344 (tp) cc_final: 0.7117 (tt) outliers start: 15 outliers final: 14 residues processed: 94 average time/residue: 0.1860 time to fit residues: 23.2085 Evaluate side-chains 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS 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 341 VAL 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 23 optimal weight: 0.9980 chunk 42 optimal weight: 0.0050 chunk 46 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- 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 = 0.4429 r_free = 0.4429 target = 0.204016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.156707 restraints weight = 9273.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.155561 restraints weight = 7959.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.157072 restraints weight = 7282.283| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6101 Z= 0.217 Angle : 0.602 10.320 8470 Z= 0.303 Chirality : 0.041 0.169 964 Planarity : 0.004 0.030 943 Dihedral : 15.758 93.262 1264 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.71 % Allowed : 24.19 % 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: -0.92 (0.33), residues: 637 helix: 0.21 (0.43), residues: 142 sheet: -1.62 (0.53), residues: 78 loop : -0.67 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 509 HIS 0.018 0.001 HIS B 229 PHE 0.018 0.002 PHE B 436 TYR 0.009 0.001 TYR B 420 ARG 0.005 0.001 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 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8642 (mtpp) cc_final: 0.8315 (ttmm) REVERT: A 119 VAL cc_start: 0.9132 (m) cc_final: 0.8862 (p) REVERT: B 188 HIS cc_start: 0.7939 (OUTLIER) cc_final: 0.7686 (t70) REVERT: B 241 MET cc_start: 0.6846 (ptp) cc_final: 0.6599 (mtm) REVERT: B 253 LEU cc_start: 0.7362 (tp) cc_final: 0.7093 (tt) REVERT: B 302 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7072 (mm-30) outliers start: 15 outliers final: 14 residues processed: 93 average time/residue: 0.1798 time to fit residues: 22.3011 Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS 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 188 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 57 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 66 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 58 optimal weight: 0.2980 chunk 40 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 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 = 0.4410 r_free = 0.4410 target = 0.202256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.154985 restraints weight = 9237.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.152032 restraints weight = 8299.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.153263 restraints weight = 9281.732| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6101 Z= 0.253 Angle : 0.621 10.307 8470 Z= 0.314 Chirality : 0.041 0.173 964 Planarity : 0.004 0.033 943 Dihedral : 15.818 93.332 1264 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.89 % Allowed : 24.55 % Favored : 72.56 % 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: -0.90 (0.33), residues: 637 helix: 0.32 (0.43), residues: 142 sheet: -1.69 (0.53), residues: 78 loop : -0.68 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 509 HIS 0.018 0.001 HIS B 229 PHE 0.018 0.002 PHE B 133 TYR 0.010 0.001 TYR B 420 ARG 0.006 0.000 ARG B 400 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1960.80 seconds wall clock time: 34 minutes 40.41 seconds (2080.41 seconds total)