Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 10:52:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn4_33310/04_2023/7xn4_33310_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn4_33310/04_2023/7xn4_33310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn4_33310/04_2023/7xn4_33310.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn4_33310/04_2023/7xn4_33310.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn4_33310/04_2023/7xn4_33310_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn4_33310/04_2023/7xn4_33310_updated.pdb" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 38 5.16 5 C 4335 2.51 5 N 1209 2.21 5 O 1275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 231": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "D GLU 87": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 6859 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1706 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 6, 'TRANS': 203} Chain breaks: 2 Chain: "B" Number of atoms: 3256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3256 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain: "C" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1387 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain breaks: 5 Chain: "D" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 466 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.08, per 1000 atoms: 0.59 Number of scatterers: 6859 At special positions: 0 Unit cell: (110.302, 95.988, 74.096, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 2 15.00 O 1275 8.00 N 1209 7.00 C 4335 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 - 3.50 Amino acid : False - 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: 2.40 Conformation dependent library (CDL) restraints added in 1.1 seconds 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1602 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 8 sheets defined 36.1% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 68 through 81 removed outlier: 3.791A pdb=" N LEU A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 4.267A pdb=" N VAL A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 143 removed outlier: 3.576A pdb=" N THR A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N PHE A 143 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 226 removed outlier: 4.298A pdb=" N GLN A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.962A pdb=" N ARG A 238 " --> pdb=" O HIS A 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 73 removed outlier: 3.668A pdb=" N ILE B 55 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU B 59 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 63 " --> pdb=" O ARG B 60 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN B 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 67 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE B 72 " --> pdb=" O GLY B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 80 No H-bonds generated for 'chain 'B' and resid 77 through 80' Processing helix chain 'B' and resid 94 through 113 removed outlier: 3.729A pdb=" N LEU B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 128 removed outlier: 3.997A pdb=" N LYS B 125 " --> pdb=" O ARG B 122 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLU B 126 " --> pdb=" O GLY B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 219 through 223 removed outlier: 3.635A pdb=" N ARG B 222 " --> pdb=" O PRO B 219 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N HIS B 223 " --> pdb=" O ALA B 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 219 through 223' Processing helix chain 'B' and resid 245 through 248 No H-bonds generated for 'chain 'B' and resid 245 through 248' Processing helix chain 'B' and resid 279 through 292 removed outlier: 3.894A pdb=" N VAL B 283 " --> pdb=" O MET B 279 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA B 284 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 301 No H-bonds generated for 'chain 'B' and resid 298 through 301' Processing helix chain 'B' and resid 315 through 321 removed outlier: 3.521A pdb=" N SER B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 352 Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 366 through 377 Processing helix chain 'B' and resid 382 through 391 removed outlier: 3.524A pdb=" N GLY B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN B 391 " --> pdb=" O HIS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 400 No H-bonds generated for 'chain 'B' and resid 398 through 400' Processing helix chain 'B' and resid 410 through 414 Processing helix chain 'B' and resid 421 through 430 removed outlier: 4.243A pdb=" N ARG B 430 " --> pdb=" O GLN B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 454 Processing helix chain 'B' and resid 458 through 467 removed outlier: 3.648A pdb=" N ALA B 463 " --> pdb=" O GLU B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 80 Processing helix chain 'C' and resid 97 through 105 removed outlier: 3.549A pdb=" N VAL C 103 " --> pdb=" O LEU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 137 through 143 removed outlier: 3.509A pdb=" N ASN C 141 " --> pdb=" O LYS C 137 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N PHE C 142 " --> pdb=" O LYS C 138 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE C 143 " --> pdb=" O ILE C 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 137 through 143' Processing helix chain 'C' and resid 214 through 226 Processing helix chain 'C' and resid 232 through 245 removed outlier: 3.520A pdb=" N ALA C 244 " --> pdb=" O ASN C 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 105 through 111 removed outlier: 3.747A pdb=" N ASN D 111 " --> pdb=" O HIS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 126 removed outlier: 4.066A pdb=" N GLU D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 141 removed outlier: 4.040A pdb=" N GLU D 140 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE D 141 " --> pdb=" O TYR D 138 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 84 through 89 removed outlier: 6.872A pdb=" N VAL A 115 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ILE A 50 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL A 117 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU A 157 " --> pdb=" O CYS A 116 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N LEU A 118 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE A 159 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 126 through 128 Processing sheet with id= C, first strand: chain 'B' and resid 134 through 136 Processing sheet with id= D, first strand: chain 'B' and resid 150 through 152 Processing sheet with id= E, first strand: chain 'B' and resid 182 through 184 Processing sheet with id= F, first strand: chain 'B' and resid 211 through 213 Processing sheet with id= G, first strand: chain 'C' and resid 84 through 88 removed outlier: 3.929A pdb=" N ARG C 86 " --> pdb=" O CYS C 47 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL C 115 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE C 50 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL C 117 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 194 through 197 removed outlier: 3.644A pdb=" N TYR C 197 " --> pdb=" O CYS C 264 " (cutoff:3.500A) 177 hydrogen bonds defined for protein. 453 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.48 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1144 1.29 - 1.42: 1886 1.42 - 1.55: 3903 1.55 - 1.68: 5 1.68 - 1.81: 64 Bond restraints: 7002 Sorted by residual: bond pdb=" CA ASN B 355 " pdb=" C ASN B 355 " ideal model delta sigma weight residual 1.526 1.438 0.087 1.08e-02 8.57e+03 6.53e+01 bond pdb=" CA LYS B 454 " pdb=" C LYS B 454 " ideal model delta sigma weight residual 1.524 1.443 0.081 1.26e-02 6.30e+03 4.09e+01 bond pdb=" C ASN B 443 " pdb=" O ASN B 443 " ideal model delta sigma weight residual 1.235 1.162 0.073 1.26e-02 6.30e+03 3.37e+01 bond pdb=" C VAL B 442 " pdb=" N ASN B 443 " ideal model delta sigma weight residual 1.332 1.253 0.079 1.40e-02 5.10e+03 3.21e+01 bond pdb=" N GLU A 272 " pdb=" CA GLU A 272 " ideal model delta sigma weight residual 1.454 1.389 0.065 1.16e-02 7.43e+03 3.14e+01 ... (remaining 6997 not shown) Histogram of bond angle deviations from ideal: 99.62 - 107.17: 195 107.17 - 114.73: 4039 114.73 - 122.28: 4122 122.28 - 129.83: 1027 129.83 - 137.38: 47 Bond angle restraints: 9430 Sorted by residual: angle pdb=" N GLU D 123 " pdb=" CA GLU D 123 " pdb=" C GLU D 123 " ideal model delta sigma weight residual 112.23 104.22 8.01 1.26e+00 6.30e-01 4.04e+01 angle pdb=" O VAL B 442 " pdb=" C VAL B 442 " pdb=" N ASN B 443 " ideal model delta sigma weight residual 123.03 117.08 5.95 1.05e+00 9.07e-01 3.21e+01 angle pdb=" C ASN B 355 " pdb=" CA ASN B 355 " pdb=" CB ASN B 355 " ideal model delta sigma weight residual 111.23 103.22 8.01 1.42e+00 4.96e-01 3.18e+01 angle pdb=" O1A NAD B1001 " pdb=" PA NAD B1001 " pdb=" O2A NAD B1001 " ideal model delta sigma weight residual 122.64 105.74 16.90 3.00e+00 1.11e-01 3.17e+01 angle pdb=" N LEU A 230 " pdb=" CA LEU A 230 " pdb=" C LEU A 230 " ideal model delta sigma weight residual 111.81 119.28 -7.47 1.54e+00 4.22e-01 2.35e+01 ... (remaining 9425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 3639 16.17 - 32.34: 393 32.34 - 48.50: 111 48.50 - 64.67: 15 64.67 - 80.84: 5 Dihedral angle restraints: 4163 sinusoidal: 1681 harmonic: 2482 Sorted by residual: dihedral pdb=" C ASN B 355 " pdb=" N ASN B 355 " pdb=" CA ASN B 355 " pdb=" CB ASN B 355 " ideal model delta harmonic sigma weight residual -122.60 -108.59 -14.01 0 2.50e+00 1.60e-01 3.14e+01 dihedral pdb=" CA PRO B 329 " pdb=" C PRO B 329 " pdb=" N ARG B 330 " pdb=" CA ARG B 330 " ideal model delta harmonic sigma weight residual -180.00 -157.54 -22.46 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA GLN B 253 " pdb=" C GLN B 253 " pdb=" N MET B 254 " pdb=" CA MET B 254 " ideal model delta harmonic sigma weight residual 180.00 157.64 22.36 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 4160 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 896 0.065 - 0.131: 99 0.131 - 0.196: 10 0.196 - 0.261: 2 0.261 - 0.326: 2 Chirality restraints: 1009 Sorted by residual: chirality pdb=" CA ASN B 443 " pdb=" N ASN B 443 " pdb=" C ASN B 443 " pdb=" CB ASN B 443 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" C2B NAD B1001 " pdb=" C1B NAD B1001 " pdb=" C3B NAD B1001 " pdb=" O2B NAD B1001 " both_signs ideal model delta sigma weight residual False -2.53 -2.84 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA GLN B 66 " pdb=" N GLN B 66 " pdb=" C GLN B 66 " pdb=" CB GLN B 66 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1006 not shown) Planarity restraints: 1218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 442 " 0.025 2.00e-02 2.50e+03 4.77e-02 2.28e+01 pdb=" C VAL B 442 " -0.083 2.00e-02 2.50e+03 pdb=" O VAL B 442 " 0.029 2.00e-02 2.50e+03 pdb=" N ASN B 443 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 126 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ARG D 126 " -0.064 2.00e-02 2.50e+03 pdb=" O ARG D 126 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU D 127 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 122 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.77e+00 pdb=" C ASP D 122 " -0.051 2.00e-02 2.50e+03 pdb=" O ASP D 122 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU D 123 " 0.017 2.00e-02 2.50e+03 ... (remaining 1215 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1147 2.76 - 3.29: 6518 3.29 - 3.83: 10607 3.83 - 4.36: 13373 4.36 - 4.90: 22643 Nonbonded interactions: 54288 Sorted by model distance: nonbonded pdb=" NE2 GLN B 253 " pdb=" O LYS B 295 " model vdw 2.223 2.520 nonbonded pdb=" O2B NAD B1001 " pdb=" O3B NAD B1001 " model vdw 2.261 2.432 nonbonded pdb=" O GLY B 171 " pdb=" N LEU B 175 " model vdw 2.275 2.520 nonbonded pdb=" OD1 ASN D 97 " pdb=" N GLY D 98 " model vdw 2.279 2.520 nonbonded pdb=" OG SER B 429 " pdb=" ND1 HIS B 467 " model vdw 2.296 2.520 ... (remaining 54283 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 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: 10.240 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 20.110 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.102 7002 Z= 0.352 Angle : 0.795 16.897 9430 Z= 0.404 Chirality : 0.047 0.326 1009 Planarity : 0.005 0.068 1218 Dihedral : 14.679 80.840 2561 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.12 % 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: -2.93 (0.28), residues: 837 helix: -1.71 (0.26), residues: 305 sheet: -2.94 (0.48), residues: 115 loop : -1.72 (0.31), residues: 417 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 150 time to evaluate : 0.858 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 152 average time/residue: 0.2181 time to fit residues: 43.1033 Evaluate side-chains 124 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.829 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS C 161 GLN D 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 7002 Z= 0.252 Angle : 0.609 13.492 9430 Z= 0.313 Chirality : 0.043 0.179 1009 Planarity : 0.005 0.049 1218 Dihedral : 5.551 47.180 938 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.65 (0.29), residues: 837 helix: -1.29 (0.27), residues: 312 sheet: -2.91 (0.44), residues: 127 loop : -1.61 (0.33), residues: 398 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 0.878 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 136 average time/residue: 0.1862 time to fit residues: 34.0169 Evaluate side-chains 127 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 0.812 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0625 time to fit residues: 1.3544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 51 optimal weight: 0.0010 chunk 21 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 61 optimal weight: 0.7980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 7002 Z= 0.174 Angle : 0.544 12.605 9430 Z= 0.279 Chirality : 0.041 0.168 1009 Planarity : 0.004 0.050 1218 Dihedral : 5.263 47.326 938 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer Outliers : 1.68 % 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: -2.61 (0.29), residues: 837 helix: -1.11 (0.27), residues: 333 sheet: -2.81 (0.44), residues: 127 loop : -1.78 (0.33), residues: 377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 0.812 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 140 average time/residue: 0.1784 time to fit residues: 34.0769 Evaluate side-chains 135 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 0.763 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0720 time to fit residues: 2.0382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 81 optimal weight: 0.0570 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 7002 Z= 0.194 Angle : 0.564 14.509 9430 Z= 0.287 Chirality : 0.041 0.174 1009 Planarity : 0.004 0.049 1218 Dihedral : 5.218 47.247 938 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.45 (0.29), residues: 837 helix: -0.94 (0.28), residues: 329 sheet: -2.74 (0.44), residues: 127 loop : -1.73 (0.33), residues: 381 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 133 time to evaluate : 0.922 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 135 average time/residue: 0.1838 time to fit residues: 33.7250 Evaluate side-chains 132 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 0.830 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0734 time to fit residues: 1.5112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 0.0060 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 7002 Z= 0.313 Angle : 0.608 12.748 9430 Z= 0.315 Chirality : 0.043 0.158 1009 Planarity : 0.004 0.051 1218 Dihedral : 5.559 48.684 938 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.56 % Favored : 90.32 % Rotamer Outliers : 1.68 % 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: -2.68 (0.28), residues: 837 helix: -1.15 (0.27), residues: 334 sheet: -2.88 (0.44), residues: 127 loop : -1.83 (0.32), residues: 376 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 0.868 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 134 average time/residue: 0.1923 time to fit residues: 34.8683 Evaluate side-chains 133 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 0.777 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0768 time to fit residues: 1.9070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7002 Z= 0.197 Angle : 0.563 14.153 9430 Z= 0.287 Chirality : 0.041 0.167 1009 Planarity : 0.004 0.049 1218 Dihedral : 5.332 47.757 938 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.60 % Favored : 91.28 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.40 (0.29), residues: 837 helix: -0.86 (0.29), residues: 324 sheet: -2.71 (0.44), residues: 127 loop : -1.73 (0.32), residues: 386 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 135 time to evaluate : 0.765 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 136 average time/residue: 0.1877 time to fit residues: 34.3983 Evaluate side-chains 133 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 0.828 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0738 time to fit residues: 1.7698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 7002 Z= 0.238 Angle : 0.587 13.973 9430 Z= 0.299 Chirality : 0.042 0.213 1009 Planarity : 0.004 0.050 1218 Dihedral : 5.368 47.661 938 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer Outliers : 0.56 % 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: -2.39 (0.29), residues: 837 helix: -0.84 (0.29), residues: 324 sheet: -2.75 (0.44), residues: 127 loop : -1.72 (0.32), residues: 386 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 0.785 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 130 average time/residue: 0.1876 time to fit residues: 32.8799 Evaluate side-chains 130 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 0.790 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0683 time to fit residues: 1.6946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.9980 chunk 24 optimal weight: 0.0980 chunk 15 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS C 161 GLN D 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7002 Z= 0.199 Angle : 0.566 15.096 9430 Z= 0.287 Chirality : 0.041 0.175 1009 Planarity : 0.004 0.049 1218 Dihedral : 5.252 47.286 938 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer Outliers : 0.28 % 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: -2.31 (0.29), residues: 837 helix: -0.78 (0.29), residues: 325 sheet: -2.63 (0.45), residues: 127 loop : -1.70 (0.32), residues: 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 0.864 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 129 average time/residue: 0.1947 time to fit residues: 33.7948 Evaluate side-chains 127 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 0.812 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0655 time to fit residues: 1.2376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 0.0050 chunk 59 optimal weight: 0.0020 chunk 23 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 107 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7002 Z= 0.163 Angle : 0.563 18.053 9430 Z= 0.282 Chirality : 0.040 0.172 1009 Planarity : 0.004 0.050 1218 Dihedral : 4.987 46.151 938 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.21 (0.29), residues: 837 helix: -0.65 (0.29), residues: 330 sheet: -2.57 (0.45), residues: 126 loop : -1.70 (0.33), residues: 381 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 134 time to evaluate : 0.765 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 138 average time/residue: 0.1820 time to fit residues: 34.3701 Evaluate side-chains 131 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 0.810 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0657 time to fit residues: 1.3819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 0.0060 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN D 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 7002 Z= 0.208 Angle : 0.594 17.794 9430 Z= 0.298 Chirality : 0.042 0.176 1009 Planarity : 0.004 0.049 1218 Dihedral : 5.130 46.750 938 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer Outliers : 0.42 % 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: -2.21 (0.29), residues: 837 helix: -0.67 (0.29), residues: 329 sheet: -2.51 (0.45), residues: 127 loop : -1.70 (0.33), residues: 381 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 124 time to evaluate : 0.826 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 125 average time/residue: 0.1776 time to fit residues: 30.7703 Evaluate side-chains 124 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 0.873 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0714 time to fit residues: 1.3662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.0170 chunk 9 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 107 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.138073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.109983 restraints weight = 11446.076| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.68 r_work: 0.3342 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 7002 Z= 0.236 Angle : 0.607 17.622 9430 Z= 0.307 Chirality : 0.042 0.178 1009 Planarity : 0.004 0.051 1218 Dihedral : 5.268 47.193 938 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer Outliers : 0.42 % 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: -2.30 (0.29), residues: 837 helix: -0.73 (0.28), residues: 329 sheet: -2.67 (0.44), residues: 126 loop : -1.74 (0.32), residues: 382 =============================================================================== Job complete usr+sys time: 1749.82 seconds wall clock time: 32 minutes 11.11 seconds (1931.11 seconds total)