Starting phenix.real_space_refine on Sat Nov 16 11:09:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0u_17338/11_2024/8p0u_17338.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0u_17338/11_2024/8p0u_17338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0u_17338/11_2024/8p0u_17338.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0u_17338/11_2024/8p0u_17338.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0u_17338/11_2024/8p0u_17338.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0u_17338/11_2024/8p0u_17338.cif" } resolution = 2.92 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 6853 2.51 5 N 1891 2.21 5 O 2086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10912 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 5015 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 31, 'TRANS': 589} Chain: "B" Number of atoms: 4676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4676 Classifications: {'peptide': 587} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 555} Chain breaks: 2 Chain: "C" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 833 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 6, 'TRANS': 95} Chain breaks: 2 Chain: "R" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 123 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 3} Chain: "V" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 264 Classifications: {'RNA': 12} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 7, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 8} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.26, per 1000 atoms: 0.67 Number of scatterers: 10912 At special positions: 0 Unit cell: (101.721, 121.569, 100.894, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 18 15.00 Mg 1 11.99 O 2086 8.00 N 1891 7.00 C 6853 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: 3.21 Conformation dependent library (CDL) restraints added in 1.6 seconds 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2486 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 13 sheets defined 49.9% alpha, 11.4% beta 2 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 3.98 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 removed outlier: 3.970A pdb=" N THR A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 25 Processing helix chain 'A' and resid 27 through 47 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 134 through 155 Processing helix chain 'A' and resid 157 through 166 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 246 through 257 removed outlier: 3.563A pdb=" N GLN A 257 " --> pdb=" O TRP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 273 through 286 removed outlier: 3.690A pdb=" N LEU A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 280 " --> pdb=" O CYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 305 through 316 Processing helix chain 'A' and resid 335 through 345 removed outlier: 3.878A pdb=" N GLU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG A 345 " --> pdb=" O MET A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 4.481A pdb=" N ARG A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 400 Processing helix chain 'A' and resid 485 through 492 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 498 through 517 Processing helix chain 'A' and resid 540 through 557 Processing helix chain 'A' and resid 559 through 581 removed outlier: 4.578A pdb=" N ARG A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 599 removed outlier: 3.652A pdb=" N LYS A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 617 removed outlier: 3.524A pdb=" N MET A 617 " --> pdb=" O GLY A 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 5 Processing helix chain 'B' and resid 13 through 20 removed outlier: 3.974A pdb=" N GLU B 17 " --> pdb=" O THR B 14 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR B 20 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 49 Proline residue: B 44 - end of helix removed outlier: 4.653A pdb=" N TYR B 49 " --> pdb=" O TYR B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 80 through 95 Processing helix chain 'B' and resid 95 through 109 Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'B' and resid 114 through 121 removed outlier: 3.603A pdb=" N GLU B 117 " --> pdb=" O LYS B 114 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY B 121 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 Processing helix chain 'B' and resid 157 through 169 Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 250 through 266 Processing helix chain 'B' and resid 276 through 287 removed outlier: 4.378A pdb=" N LYS B 280 " --> pdb=" O GLY B 276 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 284 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.727A pdb=" N CYS B 308 " --> pdb=" O PHE B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 325 removed outlier: 3.506A pdb=" N MET B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 344 Proline residue: B 338 - end of helix Processing helix chain 'B' and resid 373 through 378 removed outlier: 4.420A pdb=" N ARG B 378 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 407 removed outlier: 3.717A pdb=" N SER B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 451 Processing helix chain 'B' and resid 455 through 459 Processing helix chain 'B' and resid 496 through 514 Processing helix chain 'B' and resid 518 through 537 removed outlier: 3.591A pdb=" N TYR B 537 " --> pdb=" O TYR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 552 Processing helix chain 'B' and resid 568 through 572 removed outlier: 4.297A pdb=" N MET B 572 " --> pdb=" O PHE B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 583 Processing helix chain 'B' and resid 587 through 595 Processing helix chain 'C' and resid 57 through 69 removed outlier: 5.175A pdb=" N VAL C 64 " --> pdb=" O GLN C 60 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TYR C 65 " --> pdb=" O MET C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 114 removed outlier: 4.281A pdb=" N ASP C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 142 removed outlier: 4.681A pdb=" N ALA C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLU C 132 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 731 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 59 Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 211 Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 242 removed outlier: 7.061A pdb=" N TRP A 426 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 475 " --> pdb=" O MET A 451 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL A 464 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 242 removed outlier: 5.256A pdb=" N PHE A 425 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR A 416 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 427 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA7, first strand: chain 'A' and resid 526 through 527 Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 126 removed outlier: 3.704A pdb=" N ARG B 131 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 173 through 178 Processing sheet with id=AB1, first strand: chain 'B' and resid 242 through 245 removed outlier: 4.667A pdb=" N THR B 228 " --> pdb=" O ASP B 348 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS B 345 " --> pdb=" O CYS B 387 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N CYS B 387 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 467 through 470 Processing sheet with id=AB3, first strand: chain 'C' and resid 73 through 75 Processing sheet with id=AB4, first strand: chain 'C' and resid 84 through 85 527 hydrogen bonds defined for protein. 1422 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 5 hydrogen bonds 10 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 4.01 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3323 1.33 - 1.45: 1649 1.45 - 1.57: 6079 1.57 - 1.69: 34 1.69 - 1.81: 104 Bond restraints: 11189 Sorted by residual: bond pdb=" N SER B 625 " pdb=" CA SER B 625 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.27e-02 6.20e+03 6.71e+00 bond pdb=" N TYR B 624 " pdb=" CA TYR B 624 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.14e-02 7.69e+03 6.47e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N ASP B 623 " pdb=" CA ASP B 623 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.28e+00 bond pdb=" CA SER B 625 " pdb=" CB SER B 625 " ideal model delta sigma weight residual 1.529 1.506 0.022 1.66e-02 3.63e+03 1.79e+00 ... (remaining 11184 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.88: 14538 0.88 - 1.76: 534 1.76 - 2.64: 85 2.64 - 3.52: 61 3.52 - 4.40: 23 Bond angle restraints: 15241 Sorted by residual: angle pdb=" C ASN A 524 " pdb=" CA ASN A 524 " pdb=" CB ASN A 524 " ideal model delta sigma weight residual 111.01 115.41 -4.40 1.38e+00 5.25e-01 1.02e+01 angle pdb=" CA SER B 625 " pdb=" C SER B 625 " pdb=" O SER B 625 " ideal model delta sigma weight residual 121.56 118.16 3.40 1.09e+00 8.42e-01 9.73e+00 angle pdb=" CA ASN A 524 " pdb=" CB ASN A 524 " pdb=" CG ASN A 524 " ideal model delta sigma weight residual 112.60 115.48 -2.88 1.00e+00 1.00e+00 8.29e+00 angle pdb=" C TYR B 624 " pdb=" N SER B 625 " pdb=" CA SER B 625 " ideal model delta sigma weight residual 120.94 124.58 -3.64 1.57e+00 4.06e-01 5.38e+00 angle pdb=" N ILE A 494 " pdb=" CA ILE A 494 " pdb=" C ILE A 494 " ideal model delta sigma weight residual 113.00 110.04 2.96 1.30e+00 5.92e-01 5.18e+00 ... (remaining 15236 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.88: 6045 20.88 - 41.75: 552 41.75 - 62.63: 161 62.63 - 83.51: 35 83.51 - 104.38: 8 Dihedral angle restraints: 6801 sinusoidal: 2968 harmonic: 3833 Sorted by residual: dihedral pdb=" CG ARG B 122 " pdb=" CD ARG B 122 " pdb=" NE ARG B 122 " pdb=" CZ ARG B 122 " ideal model delta sinusoidal sigma weight residual 90.00 41.35 48.65 2 1.50e+01 4.44e-03 1.20e+01 dihedral pdb=" CA ASP B 348 " pdb=" CB ASP B 348 " pdb=" CG ASP B 348 " pdb=" OD1 ASP B 348 " ideal model delta sinusoidal sigma weight residual -30.00 -88.53 58.53 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP B 575 " pdb=" CB ASP B 575 " pdb=" CG ASP B 575 " pdb=" OD1 ASP B 575 " ideal model delta sinusoidal sigma weight residual -30.00 -87.34 57.34 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 6798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1146 0.030 - 0.059: 399 0.059 - 0.089: 80 0.089 - 0.118: 71 0.118 - 0.148: 13 Chirality restraints: 1709 Sorted by residual: chirality pdb=" CA ASN A 524 " pdb=" N ASN A 524 " pdb=" C ASN A 524 " pdb=" CB ASN A 524 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA ILE B 385 " pdb=" N ILE B 385 " pdb=" C ILE B 385 " pdb=" CB ILE B 385 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ILE A 192 " pdb=" N ILE A 192 " pdb=" C ILE A 192 " pdb=" CB ILE A 192 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 1706 not shown) Planarity restraints: 1886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 122 " 0.209 9.50e-02 1.11e+02 9.41e-02 5.98e+00 pdb=" NE ARG B 122 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 122 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 122 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 122 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 524 " 0.008 2.00e-02 2.50e+03 1.49e-02 2.21e+00 pdb=" C ASN A 524 " -0.026 2.00e-02 2.50e+03 pdb=" O ASN A 524 " 0.010 2.00e-02 2.50e+03 pdb=" N PRO A 525 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 39 " 0.008 2.00e-02 2.50e+03 8.34e-03 1.39e+00 pdb=" CG TYR A 39 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR A 39 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 39 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 39 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 39 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 39 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 39 " 0.000 2.00e-02 2.50e+03 ... (remaining 1883 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 70 2.50 - 3.10: 7831 3.10 - 3.70: 16986 3.70 - 4.30: 25470 4.30 - 4.90: 42315 Nonbonded interactions: 92672 Sorted by model distance: nonbonded pdb=" OD1 ASP B 423 " pdb="MG MG B 801 " model vdw 1.895 2.170 nonbonded pdb=" OG1 THR A 178 " pdb=" OE1 GLU B 170 " model vdw 2.066 3.040 nonbonded pdb=" OG1 THR A 158 " pdb=" OE1 GLU B 100 " model vdw 2.086 3.040 nonbonded pdb=" O ASN A 524 " pdb=" OD1 ASN A 524 " model vdw 2.118 3.040 nonbonded pdb=" OG SER A 268 " pdb=" OP1 G V 2 " model vdw 2.130 3.040 ... (remaining 92667 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: 4.970 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: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.720 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 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 : 0.002 0.033 11189 Z= 0.154 Angle : 0.455 4.404 15241 Z= 0.239 Chirality : 0.037 0.148 1709 Planarity : 0.003 0.094 1886 Dihedral : 17.808 104.385 4315 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.47 % Favored : 97.45 % Rotamer: Outliers : 3.00 % Allowed : 19.18 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.72 (0.24), residues: 1296 helix: 1.99 (0.22), residues: 589 sheet: -0.85 (0.40), residues: 143 loop : -0.78 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 336 HIS 0.003 0.001 HIS B 129 PHE 0.009 0.001 PHE A 144 TYR 0.020 0.001 TYR A 39 ARG 0.013 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 1.305 Fit side-chains REVERT: C 726 ILE cc_start: 0.8134 (mt) cc_final: 0.7766 (tp) REVERT: C 728 SER cc_start: 0.8154 (t) cc_final: 0.7864 (p) outliers start: 35 outliers final: 24 residues processed: 151 average time/residue: 1.3807 time to fit residues: 224.1230 Evaluate side-chains 108 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain C residue 114 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 0.0010 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 524 ASN A 535 GLN A 603 ASN B 129 HIS B 227 ASN B 397 ASN B 429 ASN B 453 ASN B 531 HIS B 582 HIS C 60 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11189 Z= 0.213 Angle : 0.540 7.776 15241 Z= 0.276 Chirality : 0.039 0.141 1709 Planarity : 0.004 0.035 1886 Dihedral : 11.054 105.485 1718 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.01 % Favored : 97.92 % Rotamer: Outliers : 3.25 % Allowed : 21.32 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.74 (0.24), residues: 1296 helix: 1.93 (0.22), residues: 589 sheet: -0.97 (0.39), residues: 143 loop : -0.64 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 13 HIS 0.006 0.001 HIS B 291 PHE 0.010 0.001 PHE B 145 TYR 0.013 0.001 TYR A 39 ARG 0.008 0.001 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 87 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8694 (tmt90) REVERT: C 133 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.6987 (t70) REVERT: C 137 GLN cc_start: 0.7602 (mp10) cc_final: 0.7344 (mp10) REVERT: C 726 ILE cc_start: 0.8272 (mt) cc_final: 0.7849 (tp) outliers start: 38 outliers final: 10 residues processed: 118 average time/residue: 1.3859 time to fit residues: 177.1112 Evaluate side-chains 90 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 133 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 128 optimal weight: 0.2980 chunk 106 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 95 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 GLN C 126 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11189 Z= 0.169 Angle : 0.503 8.713 15241 Z= 0.251 Chirality : 0.039 0.138 1709 Planarity : 0.003 0.033 1886 Dihedral : 10.762 104.952 1700 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.08 % Favored : 97.84 % Rotamer: Outliers : 3.00 % Allowed : 21.49 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.85 (0.24), residues: 1296 helix: 1.98 (0.22), residues: 593 sheet: -0.89 (0.39), residues: 143 loop : -0.56 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 13 HIS 0.007 0.001 HIS B 291 PHE 0.011 0.001 PHE B 145 TYR 0.016 0.001 TYR B 22 ARG 0.006 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 86 time to evaluate : 1.304 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8315 (tmt90) REVERT: C 726 ILE cc_start: 0.8191 (mt) cc_final: 0.7785 (tp) outliers start: 35 outliers final: 10 residues processed: 113 average time/residue: 1.4543 time to fit residues: 177.2523 Evaluate side-chains 89 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain C residue 129 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 126 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN B 227 ASN B 531 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11189 Z= 0.273 Angle : 0.536 9.820 15241 Z= 0.266 Chirality : 0.040 0.140 1709 Planarity : 0.004 0.039 1886 Dihedral : 10.730 104.112 1696 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.16 % Favored : 97.76 % Rotamer: Outliers : 2.74 % Allowed : 21.92 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.89 (0.24), residues: 1296 helix: 1.94 (0.22), residues: 598 sheet: -0.80 (0.39), residues: 143 loop : -0.47 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 13 HIS 0.006 0.001 HIS B 291 PHE 0.013 0.001 PHE B 145 TYR 0.014 0.001 TYR B 533 ARG 0.005 0.000 ARG C 138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 81 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8524 (tmt90) REVERT: C 92 ASP cc_start: 0.6691 (OUTLIER) cc_final: 0.5771 (p0) REVERT: C 726 ILE cc_start: 0.8313 (mt) cc_final: 0.7823 (tp) outliers start: 32 outliers final: 14 residues processed: 106 average time/residue: 1.3457 time to fit residues: 154.3094 Evaluate side-chains 92 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 129 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 11189 Z= 0.380 Angle : 0.569 9.950 15241 Z= 0.284 Chirality : 0.042 0.179 1709 Planarity : 0.004 0.044 1886 Dihedral : 10.750 103.492 1696 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.24 % Favored : 97.69 % Rotamer: Outliers : 2.31 % Allowed : 22.77 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.80 (0.24), residues: 1296 helix: 1.76 (0.22), residues: 600 sheet: -0.81 (0.39), residues: 143 loop : -0.42 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 230 HIS 0.006 0.001 HIS B 291 PHE 0.014 0.001 PHE B 145 TYR 0.015 0.001 TYR B 533 ARG 0.004 0.000 ARG C 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 726 ILE cc_start: 0.8342 (mt) cc_final: 0.7812 (tp) outliers start: 27 outliers final: 14 residues processed: 100 average time/residue: 0.9914 time to fit residues: 106.9658 Evaluate side-chains 88 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain C residue 104 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 10 optimal weight: 0.0870 chunk 41 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 GLN A 535 GLN B 531 HIS C 119 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11189 Z= 0.174 Angle : 0.502 11.029 15241 Z= 0.251 Chirality : 0.039 0.188 1709 Planarity : 0.003 0.038 1886 Dihedral : 10.670 104.540 1696 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.93 % Favored : 97.99 % Rotamer: Outliers : 2.48 % Allowed : 22.00 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.92 (0.24), residues: 1296 helix: 1.90 (0.22), residues: 599 sheet: -0.79 (0.40), residues: 143 loop : -0.38 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.007 0.001 HIS B 291 PHE 0.011 0.001 PHE B 145 TYR 0.012 0.001 TYR B 533 ARG 0.003 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: C 92 ASP cc_start: 0.6689 (OUTLIER) cc_final: 0.5953 (p0) REVERT: C 133 ASP cc_start: 0.7703 (t0) cc_final: 0.7394 (t0) REVERT: C 726 ILE cc_start: 0.8348 (mt) cc_final: 0.7845 (tp) outliers start: 29 outliers final: 15 residues processed: 105 average time/residue: 1.3481 time to fit residues: 153.4569 Evaluate side-chains 91 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain C residue 92 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 126 optimal weight: 0.0010 chunk 79 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 GLN A 535 GLN A 604 ASN B 227 ASN B 531 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11189 Z= 0.184 Angle : 0.507 12.863 15241 Z= 0.251 Chirality : 0.039 0.199 1709 Planarity : 0.003 0.037 1886 Dihedral : 10.642 104.283 1696 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.23 % Allowed : 22.43 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.98 (0.24), residues: 1296 helix: 1.93 (0.21), residues: 599 sheet: -0.74 (0.40), residues: 143 loop : -0.34 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.006 0.001 HIS B 291 PHE 0.012 0.001 PHE B 145 TYR 0.012 0.001 TYR B 533 ARG 0.007 0.000 ARG C 138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 1.349 Fit side-chains revert: symmetry clash REVERT: B 248 MET cc_start: 0.8333 (tpp) cc_final: 0.8128 (mmt) REVERT: C 92 ASP cc_start: 0.6802 (OUTLIER) cc_final: 0.6309 (p0) REVERT: C 133 ASP cc_start: 0.7683 (t0) cc_final: 0.7432 (t0) outliers start: 26 outliers final: 15 residues processed: 99 average time/residue: 1.3793 time to fit residues: 147.6686 Evaluate side-chains 89 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 0.1980 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 99 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 535 GLN B 531 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11189 Z= 0.182 Angle : 0.525 12.895 15241 Z= 0.259 Chirality : 0.039 0.197 1709 Planarity : 0.003 0.038 1886 Dihedral : 10.614 103.961 1696 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.97 % Allowed : 23.20 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.24), residues: 1296 helix: 1.96 (0.22), residues: 599 sheet: -0.67 (0.40), residues: 143 loop : -0.29 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 144 HIS 0.007 0.001 HIS B 291 PHE 0.012 0.001 PHE B 145 TYR 0.012 0.001 TYR B 533 ARG 0.006 0.000 ARG C 138 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 1.350 Fit side-chains revert: symmetry clash REVERT: C 133 ASP cc_start: 0.7721 (t0) cc_final: 0.7407 (t0) outliers start: 23 outliers final: 15 residues processed: 98 average time/residue: 1.3561 time to fit residues: 143.8571 Evaluate side-chains 87 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain C residue 76 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 36 optimal weight: 0.0870 chunk 106 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11189 Z= 0.187 Angle : 0.529 13.130 15241 Z= 0.264 Chirality : 0.039 0.201 1709 Planarity : 0.003 0.038 1886 Dihedral : 10.586 103.563 1696 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.88 % Allowed : 23.12 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.05 (0.24), residues: 1296 helix: 1.91 (0.22), residues: 600 sheet: -0.62 (0.40), residues: 143 loop : -0.24 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 144 HIS 0.007 0.001 HIS B 291 PHE 0.012 0.001 PHE B 145 TYR 0.011 0.001 TYR B 533 ARG 0.007 0.000 ARG C 138 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 1.366 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 96 average time/residue: 1.4334 time to fit residues: 148.8688 Evaluate side-chains 90 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain C residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 0.0370 chunk 59 optimal weight: 0.9990 chunk 86 optimal weight: 0.0870 chunk 130 optimal weight: 10.0000 chunk 120 optimal weight: 0.2980 chunk 103 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 80 optimal weight: 0.4980 chunk 63 optimal weight: 0.0980 chunk 82 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.2036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11189 Z= 0.137 Angle : 0.535 13.425 15241 Z= 0.262 Chirality : 0.038 0.197 1709 Planarity : 0.003 0.039 1886 Dihedral : 10.513 103.250 1696 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.37 % Allowed : 23.37 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.12 (0.24), residues: 1296 helix: 1.98 (0.22), residues: 600 sheet: -0.60 (0.40), residues: 143 loop : -0.21 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 13 HIS 0.007 0.001 HIS B 291 PHE 0.011 0.001 PHE B 145 TYR 0.011 0.001 TYR B 533 ARG 0.010 0.000 ARG A 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 94 average time/residue: 1.3946 time to fit residues: 142.1863 Evaluate side-chains 91 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain C residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 9.9990 chunk 95 optimal weight: 0.0870 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 GLN A 573 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.060040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.042338 restraints weight = 38056.618| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.72 r_work: 0.2694 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11189 Z= 0.214 Angle : 0.541 13.307 15241 Z= 0.267 Chirality : 0.039 0.214 1709 Planarity : 0.004 0.052 1886 Dihedral : 10.442 102.713 1694 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.37 % Allowed : 23.54 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.18 (0.24), residues: 1296 helix: 2.00 (0.22), residues: 599 sheet: -0.52 (0.40), residues: 143 loop : -0.15 (0.29), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.006 0.001 HIS B 291 PHE 0.012 0.001 PHE B 145 TYR 0.012 0.001 TYR B 533 ARG 0.007 0.000 ARG A 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3538.90 seconds wall clock time: 68 minutes 52.33 seconds (4132.33 seconds total)