Starting phenix.real_space_refine on Thu Nov 14 19:45:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcr_29941/11_2024/8gcr_29941.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcr_29941/11_2024/8gcr_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcr_29941/11_2024/8gcr_29941.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcr_29941/11_2024/8gcr_29941.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcr_29941/11_2024/8gcr_29941.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcr_29941/11_2024/8gcr_29941.cif" } resolution = 3.38 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= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 5.14, per 1000 atoms: 0.71 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: 1.77 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.71 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: 2.22 Time building geometry restraints manager: 2.08 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: 3.620 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.920 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.030 ------------------------------------------------------------------------------- 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 0.052 7352 Z= 0.309 Angle : 0.756 9.427 9923 Z= 0.415 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 (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: -1.53 (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 TRP 0.009 0.002 TRP B 146 HIS 0.004 0.001 HIS B 115 PHE 0.022 0.002 PHE R 730 TYR 0.025 0.002 TYR R 668 ARG 0.029 0.001 ARG B 280 *********************** 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 : 0.948 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: 0.1766 time to fit residues: 28.6467 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 : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 68 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 0.2980 chunk 50 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7352 Z= 0.230 Angle : 0.566 7.239 9923 Z= 0.291 Chirality : 0.042 0.146 1081 Planarity : 0.005 0.058 1286 Dihedral : 4.689 21.960 976 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.99 % Allowed : 9.00 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.29), residues: 857 helix: -0.09 (0.27), residues: 383 sheet: -1.31 (0.53), residues: 98 loop : -0.72 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 139 HIS 0.003 0.001 HIS B 115 PHE 0.019 0.001 PHE R 730 TYR 0.014 0.001 TYR R 592 ARG 0.006 0.000 ARG B 280 *********************** 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: 8 poor density : 98 time to evaluate : 0.959 Fit side-chains REVERT: R 339 MET cc_start: 0.8631 (mtm) cc_final: 0.8180 (mtm) REVERT: R 473 ASN cc_start: 0.7117 (p0) cc_final: 0.6714 (p0) outliers start: 8 outliers final: 8 residues processed: 103 average time/residue: 0.1838 time to fit residues: 26.7005 Evaluate side-chains 100 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 269 SER Chi-restraints excluded: chain R residue 129 THR 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 557 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 78 optimal weight: 0.0000 chunk 26 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7352 Z= 0.242 Angle : 0.548 7.574 9923 Z= 0.280 Chirality : 0.042 0.141 1081 Planarity : 0.004 0.049 1286 Dihedral : 4.566 21.146 976 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.73 % Allowed : 11.96 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.29), residues: 857 helix: 0.17 (0.27), residues: 382 sheet: -1.32 (0.54), residues: 101 loop : -0.61 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 139 HIS 0.006 0.001 HIS R 274 PHE 0.019 0.002 PHE R 730 TYR 0.011 0.001 TYR R 592 ARG 0.007 0.000 ARG B 280 *********************** 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 112 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 130 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8084 (mt) REVERT: R 473 ASN cc_start: 0.7098 (p0) cc_final: 0.6704 (p0) REVERT: R 676 MET cc_start: 0.6212 (ptp) cc_final: 0.5956 (ptp) outliers start: 14 outliers final: 13 residues processed: 108 average time/residue: 0.2103 time to fit residues: 31.4947 Evaluate side-chains 107 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain R residue 578 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 0.0570 chunk 59 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 53 optimal weight: 0.0000 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.4302 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7352 Z= 0.185 Angle : 0.515 8.006 9923 Z= 0.262 Chirality : 0.040 0.135 1081 Planarity : 0.004 0.045 1286 Dihedral : 4.366 21.059 976 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.85 % Allowed : 13.32 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.29), residues: 857 helix: 0.41 (0.27), residues: 382 sheet: -1.23 (0.54), residues: 101 loop : -0.54 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 139 HIS 0.007 0.001 HIS R 274 PHE 0.017 0.001 PHE R 730 TYR 0.012 0.001 TYR R 379 ARG 0.009 0.000 ARG B 280 *********************** 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 115 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 473 ASN cc_start: 0.7058 (p0) cc_final: 0.6668 (p0) outliers start: 15 outliers final: 10 residues processed: 112 average time/residue: 0.1866 time to fit residues: 28.9734 Evaluate side-chains 105 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 34 ILE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 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 274 HIS ** R 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7352 Z= 0.260 Angle : 0.547 8.151 9923 Z= 0.279 Chirality : 0.043 0.210 1081 Planarity : 0.004 0.046 1286 Dihedral : 4.423 21.248 976 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.29), residues: 857 helix: 0.40 (0.27), residues: 382 sheet: -1.19 (0.54), residues: 101 loop : -0.56 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 139 HIS 0.007 0.001 HIS R 274 PHE 0.020 0.002 PHE R 730 TYR 0.021 0.002 TYR R 668 ARG 0.011 0.000 ARG B 280 *********************** 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 118 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 130 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8091 (mt) REVERT: R 473 ASN cc_start: 0.7006 (p0) cc_final: 0.6614 (p0) outliers start: 21 outliers final: 19 residues processed: 112 average time/residue: 0.1969 time to fit residues: 30.9643 Evaluate side-chains 113 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 304 MET 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 49 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7352 Z= 0.219 Angle : 0.529 8.472 9923 Z= 0.269 Chirality : 0.041 0.154 1081 Planarity : 0.004 0.052 1286 Dihedral : 4.359 21.615 976 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.71 % Allowed : 15.41 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.30), residues: 857 helix: 0.50 (0.27), residues: 382 sheet: -1.15 (0.54), residues: 101 loop : -0.49 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 139 HIS 0.004 0.001 HIS R 274 PHE 0.019 0.001 PHE R 730 TYR 0.023 0.001 TYR R 668 ARG 0.010 0.000 ARG B 280 *********************** 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 121 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 130 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8057 (mt) REVERT: R 473 ASN cc_start: 0.7031 (p0) cc_final: 0.6654 (p0) outliers start: 22 outliers final: 16 residues processed: 116 average time/residue: 0.1742 time to fit residues: 28.4147 Evaluate side-chains 113 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 557 VAL Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 578 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 50 optimal weight: 0.9980 chunk 25 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7352 Z= 0.242 Angle : 0.533 8.641 9923 Z= 0.272 Chirality : 0.042 0.137 1081 Planarity : 0.004 0.055 1286 Dihedral : 4.373 20.868 976 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.34 % Allowed : 16.15 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.30), residues: 857 helix: 0.53 (0.28), residues: 377 sheet: -1.11 (0.54), residues: 101 loop : -0.49 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 139 HIS 0.005 0.001 HIS R 274 PHE 0.019 0.001 PHE R 730 TYR 0.022 0.002 TYR R 668 ARG 0.012 0.000 ARG B 280 *********************** 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 116 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 130 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8050 (mt) REVERT: R 473 ASN cc_start: 0.6991 (p0) cc_final: 0.6608 (p0) outliers start: 19 outliers final: 17 residues processed: 112 average time/residue: 0.1746 time to fit residues: 27.7300 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 : 0.876 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 0.0370 chunk 53 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 65 optimal weight: 0.0170 chunk 76 optimal weight: 0.4980 chunk 80 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7352 Z= 0.181 Angle : 0.517 8.950 9923 Z= 0.263 Chirality : 0.040 0.142 1081 Planarity : 0.004 0.054 1286 Dihedral : 4.215 22.179 976 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.22 % Allowed : 16.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.30), residues: 857 helix: 0.67 (0.28), residues: 382 sheet: -1.10 (0.54), residues: 101 loop : -0.40 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 139 HIS 0.002 0.000 HIS B 115 PHE 0.027 0.001 PHE R 648 TYR 0.020 0.001 TYR R 668 ARG 0.013 0.000 ARG B 280 *********************** 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 118 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: B 130 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7964 (mt) REVERT: R 473 ASN cc_start: 0.7052 (p0) cc_final: 0.6694 (p0) REVERT: R 676 MET cc_start: 0.6093 (ptp) cc_final: 0.5774 (ptp) REVERT: R 682 ILE cc_start: 0.6194 (OUTLIER) cc_final: 0.5904 (pt) outliers start: 18 outliers final: 12 residues processed: 114 average time/residue: 0.1769 time to fit residues: 28.8438 Evaluate side-chains 106 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 34 ILE 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 R residue 129 THR Chi-restraints excluded: chain R residue 288 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 chunk 51 optimal weight: 0.0370 chunk 82 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 overall best weight: 0.4258 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7352 Z= 0.189 Angle : 0.524 9.110 9923 Z= 0.266 Chirality : 0.041 0.159 1081 Planarity : 0.004 0.056 1286 Dihedral : 4.166 21.942 976 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.10 % Allowed : 17.14 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.30), residues: 857 helix: 0.70 (0.28), residues: 382 sheet: -1.10 (0.54), residues: 101 loop : -0.37 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 139 HIS 0.002 0.000 HIS B 115 PHE 0.022 0.001 PHE R 648 TYR 0.019 0.001 TYR R 379 ARG 0.014 0.000 ARG B 280 *********************** 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 108 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: B 130 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8001 (mt) REVERT: R 473 ASN cc_start: 0.7010 (p0) cc_final: 0.6634 (p0) REVERT: R 676 MET cc_start: 0.6080 (ptp) cc_final: 0.5789 (ptp) REVERT: R 682 ILE cc_start: 0.6218 (OUTLIER) cc_final: 0.5925 (pt) outliers start: 17 outliers final: 14 residues processed: 105 average time/residue: 0.1772 time to fit residues: 26.4153 Evaluate side-chains 105 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 34 ILE 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 288 ILE 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 Chi-restraints excluded: chain R residue 739 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 0.0970 chunk 79 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 73 optimal weight: 0.4980 chunk 21 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7352 Z= 0.222 Angle : 0.541 9.001 9923 Z= 0.275 Chirality : 0.041 0.149 1081 Planarity : 0.004 0.057 1286 Dihedral : 4.216 22.260 976 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.10 % Allowed : 17.51 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.30), residues: 857 helix: 0.62 (0.27), residues: 382 sheet: -1.12 (0.54), residues: 101 loop : -0.40 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 139 HIS 0.003 0.000 HIS B 115 PHE 0.020 0.001 PHE R 648 TYR 0.023 0.001 TYR R 668 ARG 0.013 0.000 ARG B 280 ********************** 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 107 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: B 130 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8044 (mt) REVERT: R 473 ASN cc_start: 0.6999 (p0) cc_final: 0.6612 (p0) REVERT: R 676 MET cc_start: 0.6005 (ptp) cc_final: 0.5725 (ptp) REVERT: R 682 ILE cc_start: 0.6257 (OUTLIER) cc_final: 0.5961 (pt) outliers start: 17 outliers final: 15 residues processed: 104 average time/residue: 0.1656 time to fit residues: 24.8180 Evaluate side-chains 107 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 288 ILE 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 Chi-restraints excluded: chain R residue 739 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 5.9990 chunk 69 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 3 optimal weight: 0.0270 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 46 optimal weight: 0.1980 overall best weight: 0.3638 ------------------------------------------------------------------------------- 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 = 0.4284 r_free = 0.4284 target = 0.178409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.159144 restraints weight = 10202.560| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 1.37 r_work: 0.3956 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3839 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7352 Z= 0.175 Angle : 0.523 9.262 9923 Z= 0.266 Chirality : 0.041 0.143 1081 Planarity : 0.004 0.053 1286 Dihedral : 4.095 21.802 976 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.97 % Allowed : 18.13 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.30), residues: 857 helix: 0.73 (0.28), residues: 382 sheet: -1.05 (0.53), residues: 101 loop : -0.36 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 139 HIS 0.001 0.000 HIS B 115 PHE 0.018 0.001 PHE R 648 TYR 0.022 0.001 TYR R 668 ARG 0.013 0.000 ARG B 280 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1874.11 seconds wall clock time: 39 minutes 32.08 seconds (2372.08 seconds total)