Starting phenix.real_space_refine on Fri Aug 22 19:19:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gcr_29941/08_2025/8gcr_29941.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gcr_29941/08_2025/8gcr_29941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gcr_29941/08_2025/8gcr_29941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gcr_29941/08_2025/8gcr_29941.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gcr_29941/08_2025/8gcr_29941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gcr_29941/08_2025/8gcr_29941.map" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= -0.001 sd= 0.056 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 Zn 3 6.06 5 S 54 5.16 5 C 4579 2.51 5 N 1231 2.21 5 O 1339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7206 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1182 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 7, 'TRANS': 132} Chain: "B" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1410 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 13, 'TRANS': 162} Chain breaks: 4 Chain: "R" Number of atoms: 4611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 4611 Classifications: {'peptide': 561} Link IDs: {'PTRANS': 24, 'TRANS': 536} Chain breaks: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 249 SG CYS A 37 64.708 26.219 63.255 1.00 5.43 S ATOM 274 SG CYS A 40 67.479 23.688 63.215 1.00 5.90 S ATOM 530 SG CYS A 70 68.311 27.378 63.910 1.00 3.38 S ATOM 553 SG CYS A 73 67.268 26.278 60.456 1.00 3.65 S ATOM 872 SG CYS A 110 68.982 43.130 58.796 1.00 4.64 S ATOM 894 SG CYS A 113 68.695 41.086 61.859 1.00 4.82 S ATOM 1156 SG CYS A 143 70.435 44.608 61.803 1.00 13.10 S ATOM 1176 SG CYS A 146 72.128 41.503 60.364 1.00 16.93 S ATOM 1799 SG CYS B 176 48.262 60.708 90.861 1.00 44.70 S ATOM 2206 SG CYS B 238 47.112 60.028 87.041 1.00 35.67 S ATOM 2232 SG CYS B 242 50.705 59.535 88.387 1.00 39.55 S Time building chain proxies: 1.88, per 1000 atoms: 0.26 Number of scatterers: 7206 At special positions: 0 Unit cell: (91.3, 112.05, 102.09, 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) Zn 3 29.99 S 54 16.00 O 1339 8.00 N 1231 7.00 C 4579 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: 0.58 Conformation dependent library (CDL) restraints added in 351.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 500 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 40 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 73 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 37 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 70 " pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 110 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 113 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 146 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 143 " pdb=" ZN B 500 " pdb="ZN ZN B 500 " - pdb=" NE2 HIS B 179 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 242 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 176 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 238 " Number of angles added : 15 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 6 sheets defined 49.9% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 18 through 26 Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 70 through 85 Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 102 through 106 Processing helix chain 'A' and resid 118 through 128 Processing helix chain 'B' and resid 279 through 290 Processing helix chain 'R' and resid 129 through 143 removed outlier: 3.512A pdb=" N VAL R 133 " --> pdb=" O THR R 129 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG R 143 " --> pdb=" O LEU R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 157 Processing helix chain 'R' and resid 159 through 166 removed outlier: 3.967A pdb=" N LEU R 163 " --> pdb=" O SER R 159 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL R 164 " --> pdb=" O ALA R 160 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN R 165 " --> pdb=" O GLU R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 235 through 247 Processing helix chain 'R' and resid 249 through 264 Processing helix chain 'R' and resid 264 through 272 removed outlier: 3.989A pdb=" N ASP R 270 " --> pdb=" O ASN R 266 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR R 272 " --> pdb=" O GLU R 268 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 289 removed outlier: 3.869A pdb=" N LEU R 284 " --> pdb=" O PRO R 281 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE R 289 " --> pdb=" O LEU R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 297 Processing helix chain 'R' and resid 298 through 302 Processing helix chain 'R' and resid 304 through 315 removed outlier: 3.897A pdb=" N LYS R 315 " --> pdb=" O LYS R 311 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 330 removed outlier: 4.138A pdb=" N LYS R 330 " --> pdb=" O ARG R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 332 through 354 removed outlier: 3.745A pdb=" N PHE R 343 " --> pdb=" O MET R 339 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU R 346 " --> pdb=" O THR R 342 " (cutoff:3.500A) Processing helix chain 'R' and resid 361 through 364 removed outlier: 3.734A pdb=" N ASP R 364 " --> pdb=" O LEU R 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 361 through 364' Processing helix chain 'R' and resid 365 through 386 removed outlier: 4.348A pdb=" N MET R 377 " --> pdb=" O LYS R 373 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL R 378 " --> pdb=" O CYS R 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 414 removed outlier: 3.706A pdb=" N LEU R 409 " --> pdb=" O SER R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 445 through 450 removed outlier: 3.694A pdb=" N PHE R 449 " --> pdb=" O PHE R 446 " (cutoff:3.500A) Processing helix chain 'R' and resid 451 through 456 Processing helix chain 'R' and resid 459 through 469 removed outlier: 4.029A pdb=" N THR R 465 " --> pdb=" O ASP R 461 " (cutoff:3.500A) Processing helix chain 'R' and resid 480 through 484 removed outlier: 4.000A pdb=" N ILE R 483 " --> pdb=" O CYS R 480 " (cutoff:3.500A) Processing helix chain 'R' and resid 485 through 514 removed outlier: 3.582A pdb=" N MET R 501 " --> pdb=" O ASN R 497 " (cutoff:3.500A) Processing helix chain 'R' and resid 532 through 547 removed outlier: 4.176A pdb=" N VAL R 538 " --> pdb=" O ASP R 534 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG R 539 " --> pdb=" O ASP R 535 " (cutoff:3.500A) Processing helix chain 'R' and resid 548 through 551 removed outlier: 3.863A pdb=" N LEU R 551 " --> pdb=" O PRO R 548 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 548 through 551' Processing helix chain 'R' and resid 568 through 583 Processing helix chain 'R' and resid 608 through 625 Processing helix chain 'R' and resid 634 through 641 removed outlier: 3.663A pdb=" N TYR R 638 " --> pdb=" O PRO R 634 " (cutoff:3.500A) Processing helix chain 'R' and resid 647 through 649 No H-bonds generated for 'chain 'R' and resid 647 through 649' Processing helix chain 'R' and resid 650 through 655 removed outlier: 4.367A pdb=" N SER R 654 " --> pdb=" O ASP R 650 " (cutoff:3.500A) Processing helix chain 'R' and resid 655 through 667 removed outlier: 3.833A pdb=" N SER R 661 " --> pdb=" O VAL R 657 " (cutoff:3.500A) Processing helix chain 'R' and resid 709 through 723 removed outlier: 3.702A pdb=" N ASN R 715 " --> pdb=" O LYS R 711 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP R 719 " --> pdb=" O ASN R 715 " (cutoff:3.500A) Processing helix chain 'R' and resid 726 through 739 Processing helix chain 'R' and resid 745 through 750 Processing helix chain 'R' and resid 751 through 754 Processing helix chain 'R' and resid 755 through 760 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 removed outlier: 5.885A pdb=" N GLU A 36 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 91 removed outlier: 3.802A pdb=" N TYR A 88 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ARG A 109 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 110 through 113 Processing sheet with id=AA4, first strand: chain 'B' and resid 124 through 127 removed outlier: 3.519A pdb=" N ARG B 273 " --> pdb=" O MET B 133 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE B 251 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA B 161 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N HIS B 214 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 522 through 527 removed outlier: 3.706A pdb=" N GLU R 558 " --> pdb=" O LEU R 525 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 590 through 593 318 hydrogen bonds defined for protein. 879 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: 1.16 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1434 1.33 - 1.45: 1724 1.45 - 1.57: 4113 1.57 - 1.70: 0 1.70 - 1.82: 81 Bond restraints: 7352 Sorted by residual: bond pdb=" CB VAL A 69 " pdb=" CG2 VAL A 69 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.50e+00 bond pdb=" CG LEU R 629 " pdb=" CD1 LEU R 629 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.28e+00 bond pdb=" CD GLN R 576 " pdb=" OE1 GLN R 576 " ideal model delta sigma weight residual 1.231 1.204 0.027 1.90e-02 2.77e+03 2.09e+00 bond pdb=" CG GLN R 576 " pdb=" CD GLN R 576 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.88e+00 bond pdb=" CG ARG B 280 " pdb=" CD ARG B 280 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.76e+00 ... (remaining 7347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 9641 1.89 - 3.77: 233 3.77 - 5.66: 34 5.66 - 7.54: 13 7.54 - 9.43: 2 Bond angle restraints: 9923 Sorted by residual: angle pdb=" N GLN R 576 " pdb=" CA GLN R 576 " pdb=" CB GLN R 576 " ideal model delta sigma weight residual 110.28 117.63 -7.35 1.55e+00 4.16e-01 2.25e+01 angle pdb=" CA GLN R 576 " pdb=" CB GLN R 576 " pdb=" CG GLN R 576 " ideal model delta sigma weight residual 114.10 121.87 -7.77 2.00e+00 2.50e-01 1.51e+01 angle pdb=" C LEU R 428 " pdb=" N GLU R 429 " pdb=" CA GLU R 429 " ideal model delta sigma weight residual 121.54 128.76 -7.22 1.91e+00 2.74e-01 1.43e+01 angle pdb=" C TYR R 556 " pdb=" N VAL R 557 " pdb=" CA VAL R 557 " ideal model delta sigma weight residual 122.96 119.87 3.09 9.50e-01 1.11e+00 1.05e+01 angle pdb=" C PHE R 575 " pdb=" N GLN R 576 " pdb=" CA GLN R 576 " ideal model delta sigma weight residual 120.31 115.53 4.78 1.52e+00 4.33e-01 9.90e+00 ... (remaining 9918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 4011 17.86 - 35.72: 410 35.72 - 53.58: 64 53.58 - 71.44: 15 71.44 - 89.30: 6 Dihedral angle restraints: 4506 sinusoidal: 1912 harmonic: 2594 Sorted by residual: dihedral pdb=" CA PHE R 477 " pdb=" C PHE R 477 " pdb=" N MET R 478 " pdb=" CA MET R 478 " ideal model delta harmonic sigma weight residual 180.00 154.24 25.76 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA GLU R 429 " pdb=" C GLU R 429 " pdb=" N THR R 430 " pdb=" CA THR R 430 " ideal model delta harmonic sigma weight residual 180.00 160.03 19.97 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ASP R 650 " pdb=" C ASP R 650 " pdb=" N LEU R 651 " pdb=" CA LEU R 651 " ideal model delta harmonic sigma weight residual 180.00 161.32 18.68 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 4503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 618 0.036 - 0.071: 329 0.071 - 0.106: 94 0.106 - 0.142: 33 0.142 - 0.177: 7 Chirality restraints: 1081 Sorted by residual: chirality pdb=" CA GLU R 138 " pdb=" N GLU R 138 " pdb=" C GLU R 138 " pdb=" CB GLU R 138 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CB ILE A 34 " pdb=" CA ILE A 34 " pdb=" CG1 ILE A 34 " pdb=" CG2 ILE A 34 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA GLN R 576 " pdb=" N GLN R 576 " pdb=" C GLN R 576 " pdb=" CB GLN R 576 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.55e-01 ... (remaining 1078 not shown) Planarity restraints: 1286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 422 " 0.051 5.00e-02 4.00e+02 7.82e-02 9.79e+00 pdb=" N PRO R 423 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO R 423 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO R 423 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG R 751 " 0.036 5.00e-02 4.00e+02 5.42e-02 4.71e+00 pdb=" N PRO R 752 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO R 752 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 752 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 65 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.96e+00 pdb=" N PRO A 66 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " -0.027 5.00e-02 4.00e+02 ... (remaining 1283 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1212 2.76 - 3.30: 6819 3.30 - 3.83: 11685 3.83 - 4.37: 14193 4.37 - 4.90: 24539 Nonbonded interactions: 58448 Sorted by model distance: nonbonded pdb=" OH TYR R 668 " pdb=" OD2 ASP R 675 " model vdw 2.228 3.040 nonbonded pdb=" O PRO A 16 " pdb=" OH TYR A 61 " model vdw 2.239 3.040 nonbonded pdb=" OG1 THR R 430 " pdb=" OE1 GLU R 431 " model vdw 2.251 3.040 nonbonded pdb=" NZ LYS R 489 " pdb=" OE2 GLU R 754 " model vdw 2.278 3.120 nonbonded pdb=" OE1 GLU A 14 " pdb=" NZ LYS B 101 " model vdw 2.279 3.120 ... (remaining 58443 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: 5.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.240 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 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 0.074 7364 Z= 0.208 Angle : 0.771 9.427 9938 Z= 0.417 Chirality : 0.047 0.177 1081 Planarity : 0.006 0.078 1286 Dihedral : 14.738 89.297 2826 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.28), residues: 857 helix: -0.71 (0.26), residues: 379 sheet: -1.54 (0.52), residues: 98 loop : -1.02 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG B 280 TYR 0.025 0.002 TYR R 668 PHE 0.022 0.002 PHE R 730 TRP 0.009 0.002 TRP B 146 HIS 0.004 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 7352) covalent geometry : angle 0.75564 ( 9923) hydrogen bonds : bond 0.14147 ( 318) hydrogen bonds : angle 6.86640 ( 879) metal coordination : bond 0.02420 ( 12) metal coordination : angle 3.96493 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.308 Fit side-chains REVERT: R 473 ASN cc_start: 0.7210 (p0) cc_final: 0.6793 (p0) REVERT: R 665 LEU cc_start: 0.7674 (tp) cc_final: 0.7462 (tt) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.0790 time to fit residues: 13.0051 Evaluate side-chains 92 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0050 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS R 274 HIS ** R 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.180359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.161217 restraints weight = 10376.262| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 1.59 r_work: 0.3974 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3858 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7364 Z= 0.118 Angle : 0.562 11.094 9938 Z= 0.279 Chirality : 0.041 0.145 1081 Planarity : 0.005 0.059 1286 Dihedral : 4.555 21.879 976 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.62 % Allowed : 8.26 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.29), residues: 857 helix: 0.01 (0.27), residues: 383 sheet: -1.26 (0.53), residues: 98 loop : -0.70 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 280 TYR 0.012 0.001 TYR R 592 PHE 0.018 0.001 PHE R 730 TRP 0.006 0.001 TRP A 139 HIS 0.002 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7352) covalent geometry : angle 0.54029 ( 9923) hydrogen bonds : bond 0.03509 ( 318) hydrogen bonds : angle 5.16291 ( 879) metal coordination : bond 0.01510 ( 12) metal coordination : angle 3.99087 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.413 Fit side-chains REVERT: R 473 ASN cc_start: 0.7557 (p0) cc_final: 0.7147 (p0) outliers start: 5 outliers final: 4 residues processed: 103 average time/residue: 0.0798 time to fit residues: 11.5954 Evaluate side-chains 100 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 282 ASN Chi-restraints excluded: chain R residue 479 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 274 HIS ** R 723 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 = 0.4312 r_free = 0.4312 target = 0.178776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.160857 restraints weight = 10160.052| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 1.44 r_work: 0.3933 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7364 Z= 0.154 Angle : 0.563 11.280 9938 Z= 0.278 Chirality : 0.042 0.172 1081 Planarity : 0.004 0.049 1286 Dihedral : 4.487 20.989 976 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.48 % Allowed : 11.47 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.29), residues: 857 helix: 0.21 (0.27), residues: 382 sheet: -1.12 (0.55), residues: 98 loop : -0.63 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 280 TYR 0.011 0.001 TYR R 592 PHE 0.018 0.001 PHE R 730 TRP 0.007 0.001 TRP A 139 HIS 0.003 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 7352) covalent geometry : angle 0.54279 ( 9923) hydrogen bonds : bond 0.03496 ( 318) hydrogen bonds : angle 5.09084 ( 879) metal coordination : bond 0.01187 ( 12) metal coordination : angle 3.91697 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 473 ASN cc_start: 0.7610 (p0) cc_final: 0.7191 (p0) outliers start: 12 outliers final: 12 residues processed: 103 average time/residue: 0.0757 time to fit residues: 10.6298 Evaluate side-chains 106 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 274 HIS Chi-restraints excluded: chain R residue 282 ASN Chi-restraints excluded: chain R residue 479 THR Chi-restraints excluded: chain R residue 531 HIS Chi-restraints excluded: chain R residue 557 VAL Chi-restraints excluded: chain R residue 576 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 chunk 18 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 64 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 274 HIS ** R 723 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 = 0.4317 r_free = 0.4317 target = 0.181341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.161431 restraints weight = 10589.296| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 1.61 r_work: 0.3955 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7364 Z= 0.128 Angle : 0.531 9.210 9938 Z= 0.263 Chirality : 0.041 0.137 1081 Planarity : 0.004 0.045 1286 Dihedral : 4.359 20.909 976 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.97 % Allowed : 13.44 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.30), residues: 857 helix: 0.40 (0.27), residues: 382 sheet: -1.17 (0.54), residues: 101 loop : -0.53 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 280 TYR 0.012 0.001 TYR R 379 PHE 0.018 0.001 PHE R 730 TRP 0.007 0.001 TRP A 139 HIS 0.005 0.001 HIS R 274 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 7352) covalent geometry : angle 0.51527 ( 9923) hydrogen bonds : bond 0.03194 ( 318) hydrogen bonds : angle 4.92963 ( 879) metal coordination : bond 0.00931 ( 12) metal coordination : angle 3.35315 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.7497 (mtt) cc_final: 0.7281 (tpt) REVERT: B 130 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8012 (mt) REVERT: R 473 ASN cc_start: 0.7578 (p0) cc_final: 0.7181 (p0) REVERT: R 722 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7737 (pp) REVERT: R 748 TYR cc_start: 0.8665 (t80) cc_final: 0.8412 (t80) outliers start: 16 outliers final: 11 residues processed: 114 average time/residue: 0.0763 time to fit residues: 12.0739 Evaluate side-chains 105 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 282 ASN Chi-restraints excluded: chain R residue 479 THR Chi-restraints excluded: chain R residue 557 VAL Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 578 VAL Chi-restraints excluded: chain R residue 722 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 3 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 274 HIS ** R 723 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 = 0.4297 r_free = 0.4297 target = 0.177346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.157992 restraints weight = 10243.259| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 1.40 r_work: 0.3934 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3815 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7364 Z= 0.173 Angle : 0.583 14.336 9938 Z= 0.284 Chirality : 0.042 0.136 1081 Planarity : 0.004 0.044 1286 Dihedral : 4.454 21.489 976 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.59 % Allowed : 14.18 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.29), residues: 857 helix: 0.37 (0.27), residues: 382 sheet: -1.14 (0.54), residues: 101 loop : -0.54 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 280 TYR 0.020 0.002 TYR R 668 PHE 0.020 0.002 PHE R 730 TRP 0.007 0.001 TRP A 139 HIS 0.005 0.001 HIS R 274 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 7352) covalent geometry : angle 0.55501 ( 9923) hydrogen bonds : bond 0.03486 ( 318) hydrogen bonds : angle 5.03047 ( 879) metal coordination : bond 0.01096 ( 12) metal coordination : angle 4.61772 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 130 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8142 (mt) REVERT: R 473 ASN cc_start: 0.7451 (p0) cc_final: 0.7028 (p0) REVERT: R 722 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7768 (pp) outliers start: 21 outliers final: 18 residues processed: 115 average time/residue: 0.0664 time to fit residues: 10.6917 Evaluate side-chains 112 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 274 HIS Chi-restraints excluded: chain R residue 282 ASN Chi-restraints excluded: chain R residue 469 VAL Chi-restraints excluded: chain R residue 479 THR Chi-restraints excluded: chain R residue 513 LEU Chi-restraints excluded: chain R residue 531 HIS Chi-restraints excluded: chain R residue 557 VAL Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 578 VAL Chi-restraints excluded: chain R residue 722 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 12 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.0770 chunk 81 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 274 HIS ** R 723 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 = 0.4295 r_free = 0.4295 target = 0.179236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.158792 restraints weight = 10504.384| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 1.66 r_work: 0.3908 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3783 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7364 Z= 0.146 Angle : 0.559 12.157 9938 Z= 0.273 Chirality : 0.041 0.134 1081 Planarity : 0.004 0.050 1286 Dihedral : 4.387 22.416 976 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.59 % Allowed : 15.41 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.30), residues: 857 helix: 0.54 (0.28), residues: 375 sheet: -1.12 (0.54), residues: 101 loop : -0.50 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 280 TYR 0.023 0.001 TYR R 668 PHE 0.019 0.001 PHE R 730 TRP 0.008 0.001 TRP A 139 HIS 0.005 0.001 HIS R 274 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 7352) covalent geometry : angle 0.53657 ( 9923) hydrogen bonds : bond 0.03281 ( 318) hydrogen bonds : angle 4.92778 ( 879) metal coordination : bond 0.00990 ( 12) metal coordination : angle 4.04472 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 130 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8116 (mt) REVERT: R 473 ASN cc_start: 0.7570 (p0) cc_final: 0.7173 (p0) REVERT: R 676 MET cc_start: 0.6656 (ptp) cc_final: 0.6399 (ptp) REVERT: R 722 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7754 (pp) outliers start: 21 outliers final: 17 residues processed: 110 average time/residue: 0.0718 time to fit residues: 11.1851 Evaluate side-chains 114 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 274 HIS Chi-restraints excluded: chain R residue 282 ASN Chi-restraints excluded: chain R residue 469 VAL Chi-restraints excluded: chain R residue 479 THR Chi-restraints excluded: chain R residue 513 LEU Chi-restraints excluded: chain R residue 557 VAL Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 578 VAL Chi-restraints excluded: chain R residue 722 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 57 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 274 HIS ** R 723 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 = 0.4285 r_free = 0.4285 target = 0.177538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.158637 restraints weight = 10427.457| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 1.37 r_work: 0.3952 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3835 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7364 Z= 0.138 Angle : 0.550 10.949 9938 Z= 0.270 Chirality : 0.041 0.133 1081 Planarity : 0.004 0.056 1286 Dihedral : 4.324 21.447 976 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.84 % Allowed : 15.54 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.30), residues: 857 helix: 0.58 (0.28), residues: 376 sheet: -1.12 (0.54), residues: 101 loop : -0.48 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 280 TYR 0.023 0.001 TYR R 668 PHE 0.027 0.001 PHE R 648 TRP 0.007 0.001 TRP A 139 HIS 0.007 0.001 HIS R 274 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 7352) covalent geometry : angle 0.53079 ( 9923) hydrogen bonds : bond 0.03187 ( 318) hydrogen bonds : angle 4.87866 ( 879) metal coordination : bond 0.00906 ( 12) metal coordination : angle 3.76307 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 130 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8084 (mt) REVERT: R 473 ASN cc_start: 0.7390 (p0) cc_final: 0.6980 (p0) REVERT: R 676 MET cc_start: 0.6581 (ptp) cc_final: 0.6330 (ptp) outliers start: 23 outliers final: 17 residues processed: 117 average time/residue: 0.0696 time to fit residues: 11.8291 Evaluate side-chains 111 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 282 ASN Chi-restraints excluded: chain R residue 304 MET Chi-restraints excluded: chain R residue 469 VAL Chi-restraints excluded: chain R residue 479 THR Chi-restraints excluded: chain R residue 557 VAL Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 578 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 74 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.177166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.159087 restraints weight = 10321.422| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 1.49 r_work: 0.3923 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7364 Z= 0.168 Angle : 0.575 12.364 9938 Z= 0.283 Chirality : 0.042 0.144 1081 Planarity : 0.004 0.058 1286 Dihedral : 4.401 23.064 976 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.34 % Allowed : 16.40 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.30), residues: 857 helix: 0.54 (0.28), residues: 376 sheet: -1.10 (0.54), residues: 101 loop : -0.48 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 280 TYR 0.023 0.002 TYR R 668 PHE 0.020 0.002 PHE R 648 TRP 0.007 0.001 TRP A 139 HIS 0.003 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 7352) covalent geometry : angle 0.55261 ( 9923) hydrogen bonds : bond 0.03376 ( 318) hydrogen bonds : angle 4.93493 ( 879) metal coordination : bond 0.00975 ( 12) metal coordination : angle 4.10185 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 130 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8110 (mt) REVERT: R 473 ASN cc_start: 0.7588 (p0) cc_final: 0.7185 (p0) REVERT: R 676 MET cc_start: 0.6614 (ptp) cc_final: 0.6362 (ptp) outliers start: 19 outliers final: 17 residues processed: 111 average time/residue: 0.0729 time to fit residues: 11.1264 Evaluate side-chains 111 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 282 ASN Chi-restraints excluded: chain R residue 304 MET Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 469 VAL Chi-restraints excluded: chain R residue 479 THR Chi-restraints excluded: chain R residue 557 VAL Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 578 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 40 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 86 optimal weight: 0.0770 chunk 44 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.179860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.159640 restraints weight = 10499.225| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 1.67 r_work: 0.3929 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7364 Z= 0.132 Angle : 0.553 9.563 9938 Z= 0.274 Chirality : 0.041 0.167 1081 Planarity : 0.004 0.057 1286 Dihedral : 4.288 23.236 976 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.47 % Allowed : 16.40 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.30), residues: 857 helix: 0.67 (0.28), residues: 376 sheet: -1.07 (0.54), residues: 101 loop : -0.42 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 280 TYR 0.022 0.001 TYR R 668 PHE 0.018 0.001 PHE R 648 TRP 0.007 0.001 TRP A 139 HIS 0.002 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7352) covalent geometry : angle 0.53715 ( 9923) hydrogen bonds : bond 0.03116 ( 318) hydrogen bonds : angle 4.83167 ( 879) metal coordination : bond 0.00875 ( 12) metal coordination : angle 3.38226 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 130 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8084 (mt) REVERT: R 473 ASN cc_start: 0.7478 (p0) cc_final: 0.7075 (p0) REVERT: R 676 MET cc_start: 0.6589 (ptp) cc_final: 0.6176 (ptp) REVERT: R 682 ILE cc_start: 0.5992 (OUTLIER) cc_final: 0.5679 (pt) outliers start: 20 outliers final: 15 residues processed: 110 average time/residue: 0.0701 time to fit residues: 11.1409 Evaluate side-chains 106 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 469 VAL Chi-restraints excluded: chain R residue 479 THR Chi-restraints excluded: chain R residue 531 HIS Chi-restraints excluded: chain R residue 557 VAL Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 578 VAL Chi-restraints excluded: chain R residue 682 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 79 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 59 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.180288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.160670 restraints weight = 10079.856| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 1.59 r_work: 0.3908 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7364 Z= 0.166 Angle : 0.585 11.693 9938 Z= 0.288 Chirality : 0.042 0.151 1081 Planarity : 0.004 0.061 1286 Dihedral : 4.367 23.251 976 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.22 % Allowed : 16.65 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.30), residues: 857 helix: 0.58 (0.27), residues: 376 sheet: -1.12 (0.53), residues: 101 loop : -0.45 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 280 TYR 0.020 0.002 TYR R 379 PHE 0.029 0.002 PHE R 648 TRP 0.007 0.001 TRP A 139 HIS 0.003 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 7352) covalent geometry : angle 0.56518 ( 9923) hydrogen bonds : bond 0.03336 ( 318) hydrogen bonds : angle 4.90940 ( 879) metal coordination : bond 0.01005 ( 12) metal coordination : angle 3.94600 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 130 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8070 (mt) REVERT: R 473 ASN cc_start: 0.7354 (p0) cc_final: 0.6952 (p0) REVERT: R 676 MET cc_start: 0.6580 (ptp) cc_final: 0.6208 (ptp) REVERT: R 682 ILE cc_start: 0.6130 (OUTLIER) cc_final: 0.5807 (pt) outliers start: 18 outliers final: 14 residues processed: 108 average time/residue: 0.0673 time to fit residues: 10.1964 Evaluate side-chains 107 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 469 VAL Chi-restraints excluded: chain R residue 479 THR Chi-restraints excluded: chain R residue 557 VAL Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 578 VAL Chi-restraints excluded: chain R residue 682 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 54 optimal weight: 0.5980 chunk 63 optimal weight: 0.0070 chunk 41 optimal weight: 0.0470 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 22 optimal weight: 0.0980 overall best weight: 0.1896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.186286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.165384 restraints weight = 10372.466| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 1.65 r_work: 0.3981 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3854 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7364 Z= 0.102 Angle : 0.535 9.336 9938 Z= 0.266 Chirality : 0.040 0.141 1081 Planarity : 0.004 0.058 1286 Dihedral : 4.080 22.890 976 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.36 % Allowed : 17.63 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.30), residues: 857 helix: 0.80 (0.28), residues: 381 sheet: -1.03 (0.53), residues: 101 loop : -0.36 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 280 TYR 0.020 0.001 TYR R 379 PHE 0.024 0.001 PHE R 648 TRP 0.007 0.001 TRP A 139 HIS 0.001 0.000 HIS R 738 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 7352) covalent geometry : angle 0.52658 ( 9923) hydrogen bonds : bond 0.02787 ( 318) hydrogen bonds : angle 4.68309 ( 879) metal coordination : bond 0.00848 ( 12) metal coordination : angle 2.52633 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1731.32 seconds wall clock time: 30 minutes 25.54 seconds (1825.54 seconds total)