Starting phenix.real_space_refine on Mon Mar 11 03:47:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn4_33310/03_2024/7xn4_33310_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn4_33310/03_2024/7xn4_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_33310/03_2024/7xn4_33310.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn4_33310/03_2024/7xn4_33310.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn4_33310/03_2024/7xn4_33310_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn4_33310/03_2024/7xn4_33310_updated.pdb" } resolution = 3.35 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= 0.000 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-dev-5265/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: 4.72, per 1000 atoms: 0.69 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: 2.79 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: 1.23 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: 1.59 Time building geometry restraints manager: 2.95 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: 3659 16.17 - 32.34: 401 32.34 - 48.50: 123 48.50 - 64.67: 22 64.67 - 80.84: 8 Dihedral angle restraints: 4213 sinusoidal: 1731 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 4210 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: 2.540 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: 10.040 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 22.190 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.730 ------------------------------------------------------------------------------- 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 : 15.383 80.840 2611 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 % Allowed : 0.70 % Favored : 98.60 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 214 HIS 0.005 0.001 HIS B 202 PHE 0.020 0.001 PHE B 233 TYR 0.022 0.001 TYR A 37 ARG 0.006 0.000 ARG C 79 *********************** 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 : 0.927 Fit side-chains REVERT: A 102 ASP cc_start: 0.7355 (m-30) cc_final: 0.7034 (m-30) REVERT: A 135 ASP cc_start: 0.6982 (p0) cc_final: 0.6333 (t70) REVERT: C 107 ASP cc_start: 0.7442 (t70) cc_final: 0.7105 (t0) REVERT: D 85 ILE cc_start: 0.8045 (pt) cc_final: 0.7838 (mt) REVERT: D 130 ILE cc_start: 0.5948 (mm) cc_final: 0.5373 (tp) outliers start: 5 outliers final: 0 residues processed: 152 average time/residue: 0.2270 time to fit residues: 45.0902 Evaluate side-chains 125 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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: 0.7995 moved from start: 0.1283 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= 0.253 Angle : 0.616 13.209 9430 Z= 0.314 Chirality : 0.043 0.180 1009 Planarity : 0.005 0.049 1218 Dihedral : 7.780 51.075 988 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 0.56 % Allowed : 10.63 % Favored : 88.81 % 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: -2.67 (0.28), residues: 837 helix: -1.30 (0.27), residues: 312 sheet: -2.92 (0.44), residues: 127 loop : -1.64 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 214 HIS 0.017 0.001 HIS A 121 PHE 0.013 0.001 PHE B 78 TYR 0.015 0.001 TYR D 99 ARG 0.006 0.000 ARG C 75 *********************** 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 137 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 133 time to evaluate : 0.862 Fit side-chains REVERT: A 102 ASP cc_start: 0.7491 (m-30) cc_final: 0.7085 (m-30) REVERT: A 135 ASP cc_start: 0.7071 (p0) cc_final: 0.6540 (t70) REVERT: B 302 TYR cc_start: 0.6595 (OUTLIER) cc_final: 0.5787 (t80) REVERT: B 448 MET cc_start: 0.8078 (mtt) cc_final: 0.7803 (mtt) REVERT: C 240 ASN cc_start: 0.8481 (t0) cc_final: 0.8279 (t0) REVERT: D 85 ILE cc_start: 0.8101 (pt) cc_final: 0.7878 (mt) outliers start: 4 outliers final: 1 residues processed: 134 average time/residue: 0.1833 time to fit residues: 32.8944 Evaluate side-chains 126 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 302 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.8033 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7002 Z= 0.302 Angle : 0.602 9.361 9430 Z= 0.312 Chirality : 0.043 0.165 1009 Planarity : 0.005 0.050 1218 Dihedral : 7.173 58.618 988 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 1.96 % Allowed : 13.01 % Favored : 85.03 % 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: -2.83 (0.28), residues: 837 helix: -1.30 (0.27), residues: 331 sheet: -2.98 (0.43), residues: 127 loop : -1.87 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 214 HIS 0.006 0.001 HIS B 202 PHE 0.016 0.001 PHE B 78 TYR 0.011 0.001 TYR B 225 ARG 0.003 0.000 ARG C 79 *********************** 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 141 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 0.851 Fit side-chains REVERT: A 102 ASP cc_start: 0.7488 (m-30) cc_final: 0.7101 (m-30) REVERT: A 135 ASP cc_start: 0.7106 (p0) cc_final: 0.6721 (t70) REVERT: B 302 TYR cc_start: 0.6541 (OUTLIER) cc_final: 0.5720 (t80) REVERT: D 85 ILE cc_start: 0.8088 (pt) cc_final: 0.7861 (mt) outliers start: 14 outliers final: 10 residues processed: 135 average time/residue: 0.1862 time to fit residues: 33.7794 Evaluate side-chains 134 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 449 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 0.0170 chunk 76 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.8018 ------------------------------------------------------------------------------- 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: 0.7997 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7002 Z= 0.208 Angle : 0.577 16.320 9430 Z= 0.292 Chirality : 0.041 0.155 1009 Planarity : 0.004 0.050 1218 Dihedral : 6.906 59.037 988 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.44 % Favored : 90.44 % Rotamer: Outliers : 2.10 % Allowed : 15.24 % Favored : 82.66 % 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: -1.07 (0.28), residues: 326 sheet: -2.88 (0.43), residues: 127 loop : -1.79 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 214 HIS 0.005 0.001 HIS B 202 PHE 0.014 0.001 PHE B 299 TYR 0.009 0.001 TYR B 225 ARG 0.002 0.000 ARG C 79 *********************** 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 145 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 0.763 Fit side-chains REVERT: A 102 ASP cc_start: 0.7530 (m-30) cc_final: 0.7135 (m-30) REVERT: A 135 ASP cc_start: 0.7136 (p0) cc_final: 0.6800 (t70) REVERT: B 122 ARG cc_start: 0.8037 (mmp80) cc_final: 0.7700 (mmp80) REVERT: B 302 TYR cc_start: 0.6386 (OUTLIER) cc_final: 0.5732 (t80) REVERT: B 308 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7620 (ptt) REVERT: D 85 ILE cc_start: 0.8074 (pt) cc_final: 0.7859 (mt) outliers start: 15 outliers final: 11 residues processed: 136 average time/residue: 0.1823 time to fit residues: 33.8924 Evaluate side-chains 136 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain C residue 97 VAL 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: 3.9990 chunk 1 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 0.0470 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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: 0.7959 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7002 Z= 0.165 Angle : 0.540 14.018 9430 Z= 0.275 Chirality : 0.040 0.154 1009 Planarity : 0.004 0.050 1218 Dihedral : 6.562 56.783 988 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.96 % Favored : 90.92 % Rotamer: Outliers : 2.10 % Allowed : 16.78 % Favored : 81.12 % 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: -2.44 (0.29), residues: 837 helix: -0.88 (0.28), residues: 328 sheet: -2.70 (0.44), residues: 127 loop : -1.78 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 214 HIS 0.007 0.001 HIS A 121 PHE 0.013 0.001 PHE B 233 TYR 0.008 0.001 TYR B 225 ARG 0.002 0.000 ARG C 79 *********************** 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 148 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 0.791 Fit side-chains REVERT: A 102 ASP cc_start: 0.7567 (m-30) cc_final: 0.7174 (m-30) REVERT: A 135 ASP cc_start: 0.7054 (p0) cc_final: 0.6775 (t70) REVERT: B 122 ARG cc_start: 0.7910 (mmp80) cc_final: 0.7667 (mmp80) REVERT: B 302 TYR cc_start: 0.6385 (OUTLIER) cc_final: 0.5690 (t80) REVERT: B 308 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7495 (ptt) REVERT: B 336 ASP cc_start: 0.7913 (t0) cc_final: 0.7620 (t0) REVERT: B 448 MET cc_start: 0.7887 (mtt) cc_final: 0.7647 (mtt) outliers start: 15 outliers final: 10 residues processed: 139 average time/residue: 0.2018 time to fit residues: 37.9011 Evaluate side-chains 139 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 449 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 0.0050 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- 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: 0.8014 moved from start: 0.1854 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= 0.262 Angle : 0.592 14.563 9430 Z= 0.301 Chirality : 0.042 0.187 1009 Planarity : 0.004 0.050 1218 Dihedral : 6.799 56.144 988 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.44 % Favored : 90.44 % Rotamer: Outliers : 2.10 % Allowed : 16.50 % Favored : 81.40 % 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: -2.51 (0.29), residues: 837 helix: -0.93 (0.28), residues: 328 sheet: -2.76 (0.44), residues: 127 loop : -1.83 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 261 HIS 0.006 0.001 HIS B 202 PHE 0.016 0.001 PHE B 233 TYR 0.010 0.001 TYR B 225 ARG 0.002 0.000 ARG B 260 *********************** 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 144 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 0.859 Fit side-chains REVERT: A 102 ASP cc_start: 0.7544 (m-30) cc_final: 0.7155 (m-30) REVERT: B 302 TYR cc_start: 0.6399 (OUTLIER) cc_final: 0.5684 (t80) REVERT: B 308 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7660 (ptt) REVERT: B 336 ASP cc_start: 0.7940 (t0) cc_final: 0.7654 (t0) REVERT: B 448 MET cc_start: 0.8139 (mtt) cc_final: 0.7902 (mtt) REVERT: C 157 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8876 (mt) outliers start: 15 outliers final: 11 residues processed: 136 average time/residue: 0.2300 time to fit residues: 42.8309 Evaluate side-chains 140 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 157 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 0.0070 chunk 46 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- 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** A 261 GLN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1902 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 : 0.569 15.510 9430 Z= 0.287 Chirality : 0.041 0.173 1009 Planarity : 0.004 0.050 1218 Dihedral : 6.608 54.159 988 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 2.80 % Allowed : 16.92 % Favored : 80.28 % 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: -2.43 (0.29), residues: 837 helix: -0.84 (0.29), residues: 327 sheet: -2.65 (0.44), residues: 127 loop : -1.82 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 261 HIS 0.004 0.001 HIS B 202 PHE 0.014 0.001 PHE B 233 TYR 0.009 0.001 TYR B 225 ARG 0.002 0.000 ARG B 122 *********************** 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 150 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 0.715 Fit side-chains REVERT: A 102 ASP cc_start: 0.7559 (m-30) cc_final: 0.7174 (m-30) REVERT: B 71 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7781 (mtp) REVERT: B 302 TYR cc_start: 0.6344 (OUTLIER) cc_final: 0.5528 (t80) REVERT: B 308 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7632 (ptt) REVERT: B 336 ASP cc_start: 0.7914 (t0) cc_final: 0.7633 (t0) REVERT: B 448 MET cc_start: 0.8058 (mtt) cc_final: 0.7855 (mtt) REVERT: C 161 GLN cc_start: 0.7710 (tt0) cc_final: 0.7445 (tt0) outliers start: 20 outliers final: 14 residues processed: 137 average time/residue: 0.1881 time to fit residues: 34.8210 Evaluate side-chains 143 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 110 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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** A 261 GLN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1945 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= 0.265 Angle : 0.591 15.798 9430 Z= 0.299 Chirality : 0.042 0.206 1009 Planarity : 0.004 0.049 1218 Dihedral : 6.757 53.656 988 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 2.94 % Allowed : 17.48 % Favored : 79.58 % 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: -0.86 (0.29), residues: 324 sheet: -2.74 (0.44), residues: 127 loop : -1.80 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 261 HIS 0.006 0.001 HIS A 121 PHE 0.018 0.001 PHE A 128 TYR 0.010 0.001 TYR B 225 ARG 0.003 0.000 ARG B 122 *********************** 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 148 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: A 102 ASP cc_start: 0.7538 (m-30) cc_final: 0.7149 (m-30) REVERT: B 71 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7858 (mtp) REVERT: B 302 TYR cc_start: 0.6337 (OUTLIER) cc_final: 0.5501 (t80) REVERT: B 308 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7682 (ptt) REVERT: B 336 ASP cc_start: 0.7923 (t0) cc_final: 0.7649 (t0) REVERT: B 448 MET cc_start: 0.8166 (mtt) cc_final: 0.7952 (mtt) REVERT: C 157 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8879 (mt) REVERT: C 161 GLN cc_start: 0.7770 (tt0) cc_final: 0.7514 (tt0) REVERT: D 123 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7556 (tm-30) outliers start: 21 outliers final: 15 residues processed: 138 average time/residue: 0.1864 time to fit residues: 34.5422 Evaluate side-chains 142 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain D residue 110 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** A 261 GLN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1964 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= 0.195 Angle : 0.580 16.310 9430 Z= 0.289 Chirality : 0.041 0.191 1009 Planarity : 0.004 0.050 1218 Dihedral : 6.547 51.420 988 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.32 % Favored : 90.56 % Rotamer: Outliers : 2.94 % Allowed : 17.62 % Favored : 79.44 % 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: -2.32 (0.29), residues: 837 helix: -0.79 (0.29), residues: 325 sheet: -2.62 (0.44), residues: 127 loop : -1.71 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 261 HIS 0.006 0.001 HIS A 121 PHE 0.010 0.001 PHE B 78 TYR 0.009 0.001 TYR B 225 ARG 0.002 0.000 ARG A 207 *********************** 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 150 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 129 time to evaluate : 0.889 Fit side-chains REVERT: A 102 ASP cc_start: 0.7562 (m-30) cc_final: 0.7208 (m-30) REVERT: B 71 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7856 (mtp) REVERT: B 302 TYR cc_start: 0.6269 (OUTLIER) cc_final: 0.5471 (t80) REVERT: B 308 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7655 (ptt) REVERT: B 336 ASP cc_start: 0.7912 (t0) cc_final: 0.7643 (t0) REVERT: B 448 MET cc_start: 0.8082 (mtt) cc_final: 0.7868 (mtt) REVERT: C 157 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8858 (mt) REVERT: C 161 GLN cc_start: 0.7764 (tt0) cc_final: 0.7485 (tt0) REVERT: D 123 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7487 (tm-30) outliers start: 21 outliers final: 14 residues processed: 138 average time/residue: 0.1862 time to fit residues: 34.9634 Evaluate side-chains 143 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain D residue 110 THR 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: 2.9990 chunk 83 optimal weight: 0.0970 chunk 77 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 70 optimal weight: 0.0270 chunk 20 optimal weight: 1.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- 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** A 261 GLN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2028 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= 0.202 Angle : 0.593 16.638 9430 Z= 0.295 Chirality : 0.041 0.208 1009 Planarity : 0.004 0.049 1218 Dihedral : 6.453 54.333 988 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.56 % Favored : 90.32 % Rotamer: Outliers : 3.22 % Allowed : 17.62 % Favored : 79.16 % 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: -2.28 (0.29), residues: 837 helix: -0.76 (0.29), residues: 324 sheet: -2.60 (0.44), residues: 127 loop : -1.67 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 206 HIS 0.004 0.001 HIS B 327 PHE 0.017 0.001 PHE A 128 TYR 0.008 0.001 TYR B 225 ARG 0.002 0.000 ARG A 207 ********************** 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 147 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 0.926 Fit side-chains REVERT: A 102 ASP cc_start: 0.7564 (m-30) cc_final: 0.7216 (m-30) REVERT: A 128 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7753 (m-80) REVERT: B 71 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7861 (mtp) REVERT: B 302 TYR cc_start: 0.6247 (OUTLIER) cc_final: 0.5439 (t80) REVERT: B 308 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7669 (ptt) REVERT: B 336 ASP cc_start: 0.7894 (t0) cc_final: 0.7684 (t0) REVERT: C 157 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8852 (mt) REVERT: C 161 GLN cc_start: 0.7804 (tt0) cc_final: 0.7533 (tt0) REVERT: D 123 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7544 (tm-30) outliers start: 23 outliers final: 16 residues processed: 135 average time/residue: 0.1693 time to fit residues: 31.5165 Evaluate side-chains 145 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain D residue 110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** A 261 GLN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.138535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.110389 restraints weight = 11475.289| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.71 r_work: 0.3340 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2025 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= 0.225 Angle : 0.607 16.648 9430 Z= 0.300 Chirality : 0.042 0.200 1009 Planarity : 0.004 0.051 1218 Dihedral : 6.463 54.429 988 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 2.94 % Allowed : 17.76 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.77 (0.28), residues: 324 sheet: -2.61 (0.44), residues: 127 loop : -1.69 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 261 HIS 0.008 0.001 HIS A 234 PHE 0.019 0.001 PHE A 128 TYR 0.009 0.001 TYR B 225 ARG 0.002 0.000 ARG B 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1876.46 seconds wall clock time: 34 minutes 51.46 seconds (2091.46 seconds total)