Starting phenix.real_space_refine on Sat Dec 28 04:27:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xur_33477/12_2024/7xur_33477.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xur_33477/12_2024/7xur_33477.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xur_33477/12_2024/7xur_33477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xur_33477/12_2024/7xur_33477.map" model { file = "/net/cci-nas-00/data/ceres_data/7xur_33477/12_2024/7xur_33477.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xur_33477/12_2024/7xur_33477.cif" } resolution = 3.49 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= 0.048 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 48 5.49 5 S 37 5.16 5 C 4789 2.51 5 N 1358 2.21 5 O 1515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7749 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2575 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 296} Chain breaks: 3 Chain: "B" Number of atoms: 2970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2970 Classifications: {'peptide': 363} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 346} Chain breaks: 3 Chain: "C" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1218 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "X" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 491 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "Y" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 493 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3989 SG CYS B 221 47.978 59.465 63.902 1.00 45.55 S ATOM 4755 SG CYS B 317 47.149 63.072 65.218 1.00 41.15 S ATOM 5077 SG CYS B 354 42.014 56.574 39.587 1.00 56.99 S ATOM 5101 SG CYS B 357 42.759 54.951 36.094 1.00 61.59 S ATOM 5292 SG CYS B 380 45.586 56.425 38.451 1.00 57.93 S ATOM 5313 SG CYS B 383 43.384 58.310 36.240 1.00 60.97 S Time building chain proxies: 5.95, per 1000 atoms: 0.77 Number of scatterers: 7749 At special positions: 0 Unit cell: (76.396, 109.752, 119.436, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 37 16.00 P 48 15.00 O 1515 8.00 N 1358 7.00 C 4789 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" NE2 HIS B 313 " pdb="ZN ZN B1001 " - pdb=" NE2 HIS B 319 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 317 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 221 " pdb=" ZN B1002 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 383 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 380 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 357 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 354 " Number of angles added : 8 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1546 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 53.1% alpha, 6.0% beta 23 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 4.56 Creating SS restraints... Processing helix chain 'A' and resid 162 through 172 removed outlier: 3.786A pdb=" N ARG A 166 " --> pdb=" O ASN A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.753A pdb=" N LEU A 179 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 180 " --> pdb=" O GLU A 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 176 through 180' Processing helix chain 'A' and resid 185 through 200 Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.842A pdb=" N ASN A 246 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 removed outlier: 4.016A pdb=" N LEU A 253 " --> pdb=" O PRO A 249 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 254' Processing helix chain 'A' and resid 264 through 270 Processing helix chain 'A' and resid 278 through 288 removed outlier: 3.955A pdb=" N GLN A 285 " --> pdb=" O ARG A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 313 removed outlier: 3.767A pdb=" N GLU A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 324 Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.583A pdb=" N CYS A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 364 removed outlier: 3.922A pdb=" N ASP A 354 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 379 removed outlier: 3.834A pdb=" N ILE A 375 " --> pdb=" O PRO A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 394 Processing helix chain 'A' and resid 405 through 420 Processing helix chain 'A' and resid 423 through 431 removed outlier: 4.289A pdb=" N GLU A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 431 " --> pdb=" O ILE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 446 Processing helix chain 'A' and resid 457 through 472 removed outlier: 3.518A pdb=" N GLU A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 487 through 502 removed outlier: 3.728A pdb=" N LEU A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 56 Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 78 through 90 Processing helix chain 'B' and resid 93 through 104 Processing helix chain 'B' and resid 127 through 142 Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 271 through 278 Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 380 through 388 removed outlier: 3.976A pdb=" N ARG B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 removed outlier: 3.764A pdb=" N PHE B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 20 removed outlier: 4.069A pdb=" N ASP C 10 " --> pdb=" O GLY C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 36 removed outlier: 3.530A pdb=" N THR C 30 " --> pdb=" O PHE C 26 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU C 31 " --> pdb=" O GLU C 27 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 41 Processing helix chain 'C' and resid 47 through 67 removed outlier: 3.514A pdb=" N LEU C 67 " --> pdb=" O TRP C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 89 removed outlier: 3.902A pdb=" N ARG C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL C 76 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY C 77 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 117 removed outlier: 3.793A pdb=" N ALA C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 132 removed outlier: 3.799A pdb=" N ALA C 123 " --> pdb=" O HIS C 119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 324 through 328 removed outlier: 3.608A pdb=" N SER B 183 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE B 326 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE B 181 " --> pdb=" O ILE B 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 289 through 292 removed outlier: 3.737A pdb=" N LEU B 310 " --> pdb=" O TYR B 253 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS B 317 " --> pdb=" O HIS B 313 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 377 through 379 Processing sheet with id=AA4, first strand: chain 'C' and resid 97 through 99 281 hydrogen bonds defined for protein. 798 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 2.60 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2109 1.33 - 1.45: 1741 1.45 - 1.57: 4032 1.57 - 1.69: 94 1.69 - 1.81: 54 Bond restraints: 8030 Sorted by residual: bond pdb=" C4' DG Y 56 " pdb=" O4' DG Y 56 " ideal model delta sigma weight residual 1.450 1.430 0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" C1' DG X -67 " pdb=" N9 DG X -67 " ideal model delta sigma weight residual 1.460 1.440 0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" CA VAL B 356 " pdb=" CB VAL B 356 " ideal model delta sigma weight residual 1.545 1.536 0.009 9.10e-03 1.21e+04 9.44e-01 bond pdb=" C PRO C 68 " pdb=" N PRO C 69 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.94e-01 bond pdb=" CG LEU B 207 " pdb=" CD1 LEU B 207 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.14e-01 ... (remaining 8025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 10644 1.75 - 3.50: 330 3.50 - 5.25: 43 5.25 - 7.00: 9 7.00 - 8.75: 2 Bond angle restraints: 11028 Sorted by residual: angle pdb=" N PRO C 68 " pdb=" CA PRO C 68 " pdb=" C PRO C 68 " ideal model delta sigma weight residual 110.70 115.46 -4.76 1.22e+00 6.72e-01 1.52e+01 angle pdb=" C LYS B 199 " pdb=" N PRO B 200 " pdb=" CA PRO B 200 " ideal model delta sigma weight residual 119.84 123.76 -3.92 1.25e+00 6.40e-01 9.81e+00 angle pdb=" CA PRO C 93 " pdb=" C PRO C 93 " pdb=" O PRO C 93 " ideal model delta sigma weight residual 123.07 119.40 3.67 1.38e+00 5.25e-01 7.07e+00 angle pdb=" CA PRO C 68 " pdb=" C PRO C 68 " pdb=" N PRO C 69 " ideal model delta sigma weight residual 117.93 121.09 -3.16 1.20e+00 6.94e-01 6.93e+00 angle pdb=" CA LYS B 199 " pdb=" C LYS B 199 " pdb=" N PRO B 200 " ideal model delta sigma weight residual 118.83 116.55 2.28 8.70e-01 1.32e+00 6.87e+00 ... (remaining 11023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 3825 17.61 - 35.21: 594 35.21 - 52.81: 206 52.81 - 70.42: 58 70.42 - 88.02: 14 Dihedral angle restraints: 4697 sinusoidal: 2314 harmonic: 2383 Sorted by residual: dihedral pdb=" CA TRP B 277 " pdb=" C TRP B 277 " pdb=" N SER B 278 " pdb=" CA SER B 278 " ideal model delta harmonic sigma weight residual 180.00 -157.98 -22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA SER A 287 " pdb=" C SER A 287 " pdb=" N GLU A 288 " pdb=" CA GLU A 288 " ideal model delta harmonic sigma weight residual 180.00 158.52 21.48 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA HIS C 119 " pdb=" C HIS C 119 " pdb=" N PHE C 120 " pdb=" CA PHE C 120 " ideal model delta harmonic sigma weight residual -180.00 -158.55 -21.45 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 4694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 995 0.061 - 0.122: 153 0.122 - 0.183: 6 0.183 - 0.244: 0 0.244 - 0.305: 1 Chirality restraints: 1155 Sorted by residual: chirality pdb=" CB VAL A 376 " pdb=" CA VAL A 376 " pdb=" CG1 VAL A 376 " pdb=" CG2 VAL A 376 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA PRO B 35 " pdb=" N PRO B 35 " pdb=" C PRO B 35 " pdb=" CB PRO B 35 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CG LEU A 387 " pdb=" CB LEU A 387 " pdb=" CD1 LEU A 387 " pdb=" CD2 LEU A 387 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1152 not shown) Planarity restraints: 1250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 117 " 0.045 5.00e-02 4.00e+02 6.79e-02 7.37e+00 pdb=" N PRO B 118 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 118 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 118 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 307 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO B 308 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 308 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 308 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 67 " -0.028 5.00e-02 4.00e+02 4.23e-02 2.87e+00 pdb=" N PRO C 68 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 68 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 68 " -0.023 5.00e-02 4.00e+02 ... (remaining 1247 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 932 2.75 - 3.28: 7331 3.28 - 3.82: 12430 3.82 - 4.36: 14458 4.36 - 4.90: 24478 Nonbonded interactions: 59629 Sorted by model distance: nonbonded pdb=" OD1 ASN B 185 " pdb=" OG1 THR B 203 " model vdw 2.207 3.040 nonbonded pdb=" NE2 GLN A 490 " pdb=" OP2 DT X -65 " model vdw 2.241 3.120 nonbonded pdb=" OD1 ASN B 170 " pdb=" N SER B 171 " model vdw 2.246 3.120 nonbonded pdb=" OG1 THR B 125 " pdb=" OD1 ASP B 126 " model vdw 2.273 3.040 nonbonded pdb=" NE1 TRP A 456 " pdb=" OE1 GLN A 490 " model vdw 2.275 3.120 ... (remaining 59624 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.990 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: 0.000 Extract box with map and model: 0.780 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 27.380 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:3.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 0.035 8030 Z= 0.288 Angle : 0.722 8.747 11028 Z= 0.417 Chirality : 0.042 0.305 1155 Planarity : 0.004 0.068 1250 Dihedral : 19.356 88.023 3151 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -2.26 (0.28), residues: 796 helix: -0.31 (0.27), residues: 362 sheet: -1.45 (0.93), residues: 32 loop : -2.74 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 317 HIS 0.005 0.001 HIS B 331 PHE 0.011 0.002 PHE C 72 TYR 0.017 0.002 TYR A 389 ARG 0.004 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.919 Fit side-chains REVERT: A 299 ARG cc_start: 0.7718 (tpp-160) cc_final: 0.6992 (tpt170) REVERT: B 119 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6233 (pm20) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.2563 time to fit residues: 23.0291 Evaluate side-chains 55 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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: 6.9990 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 HIS B 152 GLN B 198 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8030 Z= 0.220 Angle : 0.644 9.411 11028 Z= 0.355 Chirality : 0.042 0.223 1155 Planarity : 0.005 0.065 1250 Dihedral : 20.665 89.806 1434 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.28 % Allowed : 6.93 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.28), residues: 796 helix: -0.04 (0.27), residues: 361 sheet: -1.49 (0.91), residues: 32 loop : -2.57 (0.27), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 317 HIS 0.021 0.002 HIS A 340 PHE 0.014 0.001 PHE B 251 TYR 0.017 0.002 TYR A 389 ARG 0.005 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.925 Fit side-chains REVERT: A 299 ARG cc_start: 0.7663 (tpp-160) cc_final: 0.6969 (tpt170) REVERT: B 119 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6197 (pm20) outliers start: 2 outliers final: 2 residues processed: 65 average time/residue: 0.2414 time to fit residues: 21.1679 Evaluate side-chains 59 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 335 LEU 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: 1.9990 chunk 63 optimal weight: 2.9990 chunk 51 optimal weight: 0.0030 chunk 21 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 68 optimal weight: 0.0870 chunk 75 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 overall best weight: 0.5168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN A 312 HIS B 198 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8030 Z= 0.171 Angle : 0.563 8.564 11028 Z= 0.312 Chirality : 0.038 0.178 1155 Planarity : 0.004 0.063 1250 Dihedral : 20.206 89.343 1434 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.55 % Allowed : 10.25 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.28), residues: 796 helix: 0.21 (0.27), residues: 366 sheet: -2.14 (0.74), residues: 46 loop : -2.38 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 317 HIS 0.004 0.001 HIS B 331 PHE 0.013 0.001 PHE B 47 TYR 0.016 0.001 TYR A 389 ARG 0.003 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.909 Fit side-chains REVERT: A 299 ARG cc_start: 0.7541 (tpp-160) cc_final: 0.6947 (tpt170) REVERT: A 356 MET cc_start: 0.7329 (tpt) cc_final: 0.7007 (ttm) REVERT: A 501 LYS cc_start: 0.4828 (mttp) cc_final: 0.4611 (mttp) REVERT: B 119 GLU cc_start: 0.7476 (mm-30) cc_final: 0.6228 (pm20) outliers start: 4 outliers final: 1 residues processed: 73 average time/residue: 0.2891 time to fit residues: 27.8879 Evaluate side-chains 63 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 LEU 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: 0.2980 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 51 optimal weight: 0.0170 chunk 76 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN A 286 ASN B 299 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8030 Z= 0.170 Angle : 0.541 8.308 11028 Z= 0.300 Chirality : 0.038 0.168 1155 Planarity : 0.004 0.062 1250 Dihedral : 20.139 89.633 1434 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.55 % Allowed : 11.77 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.28), residues: 796 helix: 0.38 (0.27), residues: 368 sheet: -2.04 (0.74), residues: 46 loop : -2.26 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 317 HIS 0.003 0.001 HIS B 331 PHE 0.014 0.001 PHE A 283 TYR 0.014 0.001 TYR A 389 ARG 0.008 0.000 ARG C 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.893 Fit side-chains REVERT: A 299 ARG cc_start: 0.7445 (tpp-160) cc_final: 0.6910 (tpt170) REVERT: B 119 GLU cc_start: 0.7404 (mm-30) cc_final: 0.6231 (pm20) outliers start: 4 outliers final: 2 residues processed: 72 average time/residue: 0.2565 time to fit residues: 24.7489 Evaluate side-chains 65 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain B residue 335 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8030 Z= 0.191 Angle : 0.552 8.124 11028 Z= 0.305 Chirality : 0.039 0.160 1155 Planarity : 0.004 0.075 1250 Dihedral : 20.080 87.494 1434 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.40 % Favored : 94.47 % Rotamer: Outliers : 0.97 % Allowed : 13.57 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.29), residues: 796 helix: 0.41 (0.27), residues: 369 sheet: -2.00 (0.76), residues: 46 loop : -2.19 (0.28), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 317 HIS 0.002 0.001 HIS A 312 PHE 0.014 0.001 PHE A 283 TYR 0.014 0.001 TYR A 389 ARG 0.002 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.883 Fit side-chains REVERT: A 299 ARG cc_start: 0.7426 (tpp-160) cc_final: 0.6881 (tpt170) REVERT: B 119 GLU cc_start: 0.7444 (mm-30) cc_final: 0.6250 (pm20) outliers start: 7 outliers final: 3 residues processed: 68 average time/residue: 0.2496 time to fit residues: 22.6267 Evaluate side-chains 63 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain B residue 335 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 37 optimal weight: 0.0170 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8030 Z= 0.165 Angle : 0.535 7.726 11028 Z= 0.295 Chirality : 0.038 0.149 1155 Planarity : 0.004 0.060 1250 Dihedral : 19.985 84.323 1434 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.83 % Allowed : 14.68 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.29), residues: 796 helix: 0.50 (0.27), residues: 369 sheet: -1.95 (0.75), residues: 46 loop : -2.11 (0.28), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 317 HIS 0.003 0.001 HIS A 340 PHE 0.016 0.001 PHE A 283 TYR 0.013 0.001 TYR A 389 ARG 0.008 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.885 Fit side-chains REVERT: A 299 ARG cc_start: 0.7372 (tpp-160) cc_final: 0.6880 (tpt170) REVERT: B 119 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6225 (pm20) outliers start: 6 outliers final: 1 residues processed: 71 average time/residue: 0.2364 time to fit residues: 22.3441 Evaluate side-chains 62 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LYS 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: 0.8980 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 37 optimal weight: 0.0870 chunk 32 optimal weight: 0.7980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8030 Z= 0.172 Angle : 0.536 7.367 11028 Z= 0.296 Chirality : 0.038 0.148 1155 Planarity : 0.004 0.077 1250 Dihedral : 19.939 79.487 1434 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.28 % Allowed : 15.93 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.29), residues: 796 helix: 0.52 (0.27), residues: 370 sheet: -1.98 (0.75), residues: 46 loop : -2.05 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 317 HIS 0.003 0.001 HIS A 340 PHE 0.019 0.001 PHE A 283 TYR 0.013 0.001 TYR A 389 ARG 0.004 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 1.000 Fit side-chains REVERT: A 299 ARG cc_start: 0.7329 (tpp-160) cc_final: 0.6827 (tpt170) REVERT: B 119 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6168 (pm20) outliers start: 2 outliers final: 1 residues processed: 63 average time/residue: 0.2659 time to fit residues: 22.1954 Evaluate side-chains 63 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 15 optimal weight: 0.0030 chunk 51 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8030 Z= 0.163 Angle : 0.526 7.009 11028 Z= 0.290 Chirality : 0.037 0.144 1155 Planarity : 0.004 0.078 1250 Dihedral : 19.856 72.450 1434 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.97 % Allowed : 15.51 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.29), residues: 796 helix: 0.63 (0.27), residues: 370 sheet: -1.93 (0.76), residues: 46 loop : -2.02 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 317 HIS 0.003 0.001 HIS A 340 PHE 0.016 0.001 PHE A 283 TYR 0.012 0.001 TYR A 389 ARG 0.003 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.796 Fit side-chains REVERT: A 299 ARG cc_start: 0.7283 (tpp-160) cc_final: 0.6929 (tpt170) REVERT: B 119 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6168 (pm20) outliers start: 7 outliers final: 4 residues processed: 71 average time/residue: 0.2279 time to fit residues: 21.8790 Evaluate side-chains 65 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain B residue 51 TRP Chi-restraints excluded: chain B residue 285 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.0050 chunk 77 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 68 optimal weight: 0.0370 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 overall best weight: 0.5272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8030 Z= 0.158 Angle : 0.524 7.443 11028 Z= 0.290 Chirality : 0.037 0.144 1155 Planarity : 0.004 0.079 1250 Dihedral : 19.770 67.589 1434 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.55 % Allowed : 16.76 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.29), residues: 796 helix: 0.68 (0.27), residues: 371 sheet: -1.93 (0.75), residues: 46 loop : -1.98 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 317 HIS 0.002 0.001 HIS A 340 PHE 0.010 0.001 PHE B 251 TYR 0.012 0.001 TYR A 443 ARG 0.002 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 299 ARG cc_start: 0.7334 (tpp-160) cc_final: 0.6978 (tpt170) REVERT: A 499 MET cc_start: 0.7158 (ptt) cc_final: 0.6786 (mmp) REVERT: B 119 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6156 (pm20) REVERT: C 12 GLU cc_start: 0.5775 (mm-30) cc_final: 0.5572 (mm-30) outliers start: 4 outliers final: 4 residues processed: 72 average time/residue: 0.2228 time to fit residues: 21.7874 Evaluate side-chains 67 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain B residue 51 TRP Chi-restraints excluded: chain B residue 285 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.0470 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 51 optimal weight: 0.0980 chunk 40 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8030 Z= 0.150 Angle : 0.522 7.572 11028 Z= 0.288 Chirality : 0.037 0.144 1155 Planarity : 0.004 0.080 1250 Dihedral : 19.703 65.971 1434 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.42 % Allowed : 17.45 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.29), residues: 796 helix: 0.68 (0.27), residues: 373 sheet: -1.87 (0.75), residues: 46 loop : -1.95 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 317 HIS 0.002 0.000 HIS A 340 PHE 0.011 0.001 PHE A 449 TYR 0.012 0.001 TYR A 389 ARG 0.003 0.000 ARG B 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.972 Fit side-chains REVERT: A 299 ARG cc_start: 0.7316 (tpp-160) cc_final: 0.6987 (tpt170) REVERT: A 499 MET cc_start: 0.7270 (ptt) cc_final: 0.6826 (mmp) REVERT: B 119 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6176 (pm20) outliers start: 3 outliers final: 3 residues processed: 67 average time/residue: 0.2410 time to fit residues: 21.9059 Evaluate side-chains 65 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain B residue 51 TRP Chi-restraints excluded: chain B residue 285 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.115534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.102168 restraints weight = 17493.130| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.17 r_work: 0.3514 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8030 Z= 0.193 Angle : 0.555 7.475 11028 Z= 0.303 Chirality : 0.039 0.248 1155 Planarity : 0.005 0.080 1250 Dihedral : 19.839 67.963 1434 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.55 % Allowed : 17.45 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.29), residues: 796 helix: 0.63 (0.27), residues: 371 sheet: -2.01 (0.74), residues: 46 loop : -1.96 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 317 HIS 0.002 0.001 HIS A 340 PHE 0.011 0.001 PHE B 251 TYR 0.012 0.001 TYR A 443 ARG 0.003 0.000 ARG B 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1802.58 seconds wall clock time: 34 minutes 16.88 seconds (2056.88 seconds total)