Starting phenix.real_space_refine on Mon Jul 28 08:55:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6f07_4163/07_2025/6f07_4163.cif Found real_map, /net/cci-nas-00/data/ceres_data/6f07_4163/07_2025/6f07_4163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6f07_4163/07_2025/6f07_4163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6f07_4163/07_2025/6f07_4163.map" model { file = "/net/cci-nas-00/data/ceres_data/6f07_4163/07_2025/6f07_4163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6f07_4163/07_2025/6f07_4163.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 2 6.06 5 S 54 5.16 5 C 6551 2.51 5 N 1670 2.21 5 O 1872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10149 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4249 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 16, 'TRANS': 493} Chain breaks: 2 Chain: "B" Number of atoms: 4746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4746 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1152 Classifications: {'peptide': 142} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 132} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4346 SG CYS B 14 22.504 74.855 65.425 1.00228.19 S ATOM 4425 SG CYS B 24 25.564 72.810 64.715 1.00223.95 S ATOM 4346 SG CYS B 14 22.504 74.855 65.425 1.00228.19 S ATOM 4473 SG CYS B 30 25.268 77.024 64.816 1.00203.85 S ATOM 4491 SG CYS B 33 22.225 78.973 63.646 1.00205.77 S ATOM 4564 SG CYS B 42 22.697 77.660 67.746 1.00216.67 S Time building chain proxies: 6.46, per 1000 atoms: 0.64 Number of scatterers: 10149 At special positions: 0 Unit cell: (119.658, 112.112, 120.736, 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 2 29.99 S 54 16.00 O 1872 8.00 N 1670 7.00 C 6551 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 215 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.13 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 14 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 24 " pdb=" ZN B 702 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 33 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 42 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 14 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 30 " Number of angles added : 6 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2386 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 2 sheets defined 73.4% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 57 through 73 removed outlier: 3.613A pdb=" N GLN A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 107 through 122 Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.877A pdb=" N TYR A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 146 removed outlier: 4.095A pdb=" N ARG A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 173 Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 185 through 192 Processing helix chain 'A' and resid 203 through 223 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 242 through 243 No H-bonds generated for 'chain 'A' and resid 242 through 243' Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.542A pdb=" N ASP A 248 " --> pdb=" O PHE A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 266 Processing helix chain 'A' and resid 279 through 302 removed outlier: 3.529A pdb=" N SER A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 357 Processing helix chain 'A' and resid 366 through 386 Processing helix chain 'A' and resid 393 through 422 Processing helix chain 'A' and resid 426 through 444 Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 451 through 455 Processing helix chain 'A' and resid 456 through 477 removed outlier: 4.079A pdb=" N MET A 460 " --> pdb=" O HIS A 456 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE A 476 " --> pdb=" O PHE A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 494 removed outlier: 3.819A pdb=" N ALA A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 496 No H-bonds generated for 'chain 'A' and resid 495 through 496' Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 523 removed outlier: 3.640A pdb=" N LEU A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TRP A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 552 removed outlier: 3.758A pdb=" N LYS A 539 " --> pdb=" O HIS A 535 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 563 removed outlier: 3.859A pdb=" N GLY A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 601 Processing helix chain 'A' and resid 603 through 607 removed outlier: 3.524A pdb=" N LEU A 607 " --> pdb=" O SER A 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 20 removed outlier: 3.509A pdb=" N ARG B 20 " --> pdb=" O VAL B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 37 Processing helix chain 'B' and resid 38 through 44 removed outlier: 3.732A pdb=" N CYS B 42 " --> pdb=" O GLN B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 72 removed outlier: 3.682A pdb=" N LEU B 61 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.813A pdb=" N TYR B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 105 Processing helix chain 'B' and resid 107 through 122 Processing helix chain 'B' and resid 122 through 127 removed outlier: 3.887A pdb=" N TYR B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 146 removed outlier: 4.055A pdb=" N LEU B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG B 139 " --> pdb=" O GLU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 173 Processing helix chain 'B' and resid 175 through 183 Processing helix chain 'B' and resid 185 through 192 removed outlier: 3.723A pdb=" N HIS B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 202 Processing helix chain 'B' and resid 203 through 223 removed outlier: 3.531A pdb=" N VAL B 207 " --> pdb=" O GLY B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 228 removed outlier: 3.696A pdb=" N HIS B 228 " --> pdb=" O PHE B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 241 removed outlier: 4.437A pdb=" N VAL B 234 " --> pdb=" O ASP B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 249 removed outlier: 4.015A pdb=" N GLU B 249 " --> pdb=" O PHE B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 266 Processing helix chain 'B' and resid 279 through 302 Processing helix chain 'B' and resid 341 through 357 removed outlier: 3.791A pdb=" N ILE B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 386 removed outlier: 3.751A pdb=" N LEU B 370 " --> pdb=" O PRO B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 422 Processing helix chain 'B' and resid 426 through 444 Processing helix chain 'B' and resid 451 through 455 Processing helix chain 'B' and resid 456 through 477 removed outlier: 3.973A pdb=" N MET B 460 " --> pdb=" O HIS B 456 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE B 476 " --> pdb=" O PHE B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 494 Processing helix chain 'B' and resid 495 through 496 No H-bonds generated for 'chain 'B' and resid 495 through 496' Processing helix chain 'B' and resid 497 through 499 No H-bonds generated for 'chain 'B' and resid 497 through 499' Processing helix chain 'B' and resid 500 through 523 removed outlier: 3.546A pdb=" N LEU B 504 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP B 505 " --> pdb=" O GLY B 501 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 519 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 552 removed outlier: 3.663A pdb=" N LYS B 539 " --> pdb=" O HIS B 535 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LYS B 546 " --> pdb=" O GLN B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 563 removed outlier: 3.948A pdb=" N GLY B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 601 Processing helix chain 'B' and resid 602 through 606 removed outlier: 3.937A pdb=" N ASP B 605 " --> pdb=" O ASN B 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 83 through 97 Processing helix chain 'D' and resid 107 through 112 Processing helix chain 'D' and resid 117 through 124 Processing helix chain 'D' and resid 127 through 142 Processing helix chain 'D' and resid 143 through 159 Processing helix chain 'D' and resid 177 through 187 removed outlier: 3.608A pdb=" N ALA D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU D 187 " --> pdb=" O ALA D 183 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 527 through 528 removed outlier: 4.126A pdb=" N TYR A 534 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 15 through 18 removed outlier: 6.459A pdb=" N VAL D 7 " --> pdb=" O MET D 77 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1755 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: 2.91 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3061 1.34 - 1.46: 2009 1.46 - 1.58: 5223 1.58 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 10378 Sorted by residual: bond pdb=" CA ASN B 543 " pdb=" C ASN B 543 " ideal model delta sigma weight residual 1.522 1.502 0.020 1.20e-02 6.94e+03 2.77e+00 bond pdb=" C SER B 363 " pdb=" N LYS B 364 " ideal model delta sigma weight residual 1.331 1.310 0.021 1.36e-02 5.41e+03 2.32e+00 bond pdb=" N ASN B 543 " pdb=" CA ASN B 543 " ideal model delta sigma weight residual 1.460 1.443 0.017 1.14e-02 7.69e+03 2.29e+00 bond pdb=" C LEU A 58 " pdb=" N PRO A 59 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.20e-02 6.94e+03 2.20e+00 bond pdb=" CA LEU A 58 " pdb=" C LEU A 58 " ideal model delta sigma weight residual 1.521 1.538 -0.017 1.14e-02 7.69e+03 2.18e+00 ... (remaining 10373 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 13741 2.73 - 5.46: 261 5.46 - 8.19: 31 8.19 - 10.92: 4 10.92 - 13.66: 1 Bond angle restraints: 14038 Sorted by residual: angle pdb=" N ASN B 543 " pdb=" CA ASN B 543 " pdb=" C ASN B 543 " ideal model delta sigma weight residual 114.62 100.96 13.66 1.14e+00 7.69e-01 1.43e+02 angle pdb=" N VAL A 185 " pdb=" CA VAL A 185 " pdb=" C VAL A 185 " ideal model delta sigma weight residual 113.53 107.58 5.95 9.80e-01 1.04e+00 3.68e+01 angle pdb=" N THR B 6 " pdb=" CA THR B 6 " pdb=" C THR B 6 " ideal model delta sigma weight residual 108.76 116.77 -8.01 1.58e+00 4.01e-01 2.57e+01 angle pdb=" N GLU A 338 " pdb=" CA GLU A 338 " pdb=" C GLU A 338 " ideal model delta sigma weight residual 114.56 108.84 5.72 1.27e+00 6.20e-01 2.03e+01 angle pdb=" C VAL B 185 " pdb=" N TYR B 186 " pdb=" CA TYR B 186 " ideal model delta sigma weight residual 120.09 125.49 -5.40 1.25e+00 6.40e-01 1.87e+01 ... (remaining 14033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 5875 15.42 - 30.84: 300 30.84 - 46.27: 62 46.27 - 61.69: 7 61.69 - 77.11: 8 Dihedral angle restraints: 6252 sinusoidal: 2588 harmonic: 3664 Sorted by residual: dihedral pdb=" CA LEU B 312 " pdb=" C LEU B 312 " pdb=" N HIS B 313 " pdb=" CA HIS B 313 " ideal model delta harmonic sigma weight residual 180.00 142.37 37.63 0 5.00e+00 4.00e-02 5.66e+01 dihedral pdb=" CA LEU B 8 " pdb=" C LEU B 8 " pdb=" N LYS B 9 " pdb=" CA LYS B 9 " ideal model delta harmonic sigma weight residual -180.00 -149.13 -30.87 0 5.00e+00 4.00e-02 3.81e+01 dihedral pdb=" CA MET B 27 " pdb=" C MET B 27 " pdb=" N ILE B 28 " pdb=" CA ILE B 28 " ideal model delta harmonic sigma weight residual 180.00 -153.17 -26.83 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 6249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 993 0.046 - 0.092: 431 0.092 - 0.138: 115 0.138 - 0.184: 14 0.184 - 0.230: 3 Chirality restraints: 1556 Sorted by residual: chirality pdb=" CA ASN B 543 " pdb=" N ASN B 543 " pdb=" C ASN B 543 " pdb=" CB ASN B 543 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB ILE B 28 " pdb=" CA ILE B 28 " pdb=" CG1 ILE B 28 " pdb=" CG2 ILE B 28 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL B 459 " pdb=" CA VAL B 459 " pdb=" CG1 VAL B 459 " pdb=" CG2 VAL B 459 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1553 not shown) Planarity restraints: 1769 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 245 " 0.053 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO A 246 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 246 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 246 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 245 " -0.047 5.00e-02 4.00e+02 7.05e-02 7.96e+00 pdb=" N PRO B 246 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 246 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 246 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 508 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C VAL B 508 " 0.044 2.00e-02 2.50e+03 pdb=" O VAL B 508 " -0.017 2.00e-02 2.50e+03 pdb=" N TYR B 509 " -0.015 2.00e-02 2.50e+03 ... (remaining 1766 not shown) Histogram of nonbonded interaction distances: 0.71 - 1.55: 9 1.55 - 2.38: 39 2.38 - 3.22: 9695 3.22 - 4.06: 24077 4.06 - 4.90: 43465 Warning: very small nonbonded interaction distances. Nonbonded interactions: 77285 Sorted by model distance: nonbonded pdb=" CB HIS B 12 " pdb=" CG PHE D 176 " model vdw 0.707 3.660 nonbonded pdb=" CG HIS B 12 " pdb=" CG PHE D 176 " model vdw 0.866 3.480 nonbonded pdb=" CB HIS B 12 " pdb=" CD2 PHE D 176 " model vdw 1.161 3.740 nonbonded pdb=" CG HIS B 12 " pdb=" CD1 PHE D 176 " model vdw 1.165 3.560 nonbonded pdb=" CD2 HIS B 12 " pdb=" CA PHE D 176 " model vdw 1.174 3.690 ... (remaining 77280 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 55 through 313 or resid 336 through 565 or resid 588 throu \ gh 608)) } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.490 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5565 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 : 0.008 0.159 10386 Z= 0.359 Angle : 1.004 22.350 14046 Z= 0.568 Chirality : 0.053 0.230 1556 Planarity : 0.008 0.079 1769 Dihedral : 10.285 77.111 3863 Min Nonbonded Distance : 0.707 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.12 % Favored : 93.71 % Rotamer: Outliers : 0.70 % Allowed : 1.93 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.04 (0.19), residues: 1209 helix: -1.48 (0.14), residues: 817 sheet: 0.48 (1.77), residues: 14 loop : -3.08 (0.26), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP A 65 HIS 0.008 0.002 HIS B 12 PHE 0.040 0.003 PHE D 176 TYR 0.027 0.002 TYR B 382 ARG 0.007 0.001 ARG B 20 Details of bonding type rmsd hydrogen bonds : bond 0.15065 ( 596) hydrogen bonds : angle 6.13579 ( 1755) metal coordination : bond 0.13637 ( 6) metal coordination : angle 14.44752 ( 6) SS BOND : bond 0.00336 ( 1) SS BOND : angle 2.25148 ( 2) covalent geometry : bond 0.00657 (10378) covalent geometry : angle 0.95809 (14038) Misc. bond : bond 0.15934 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 300 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.6376 (m-70) cc_final: 0.6137 (m90) REVERT: A 199 ASN cc_start: 0.8173 (m-40) cc_final: 0.7769 (m-40) REVERT: A 200 TRP cc_start: 0.4857 (m100) cc_final: 0.4055 (m100) REVERT: A 255 SER cc_start: 0.7910 (m) cc_final: 0.7503 (t) REVERT: A 376 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7943 (tp30) REVERT: A 377 LEU cc_start: 0.7665 (tp) cc_final: 0.7381 (mt) REVERT: A 387 LEU cc_start: 0.7712 (mt) cc_final: 0.7222 (mp) REVERT: A 399 GLN cc_start: 0.8380 (tt0) cc_final: 0.8070 (tm-30) REVERT: A 436 LYS cc_start: 0.8667 (mttm) cc_final: 0.8323 (mmmt) REVERT: A 473 TYR cc_start: 0.6980 (t80) cc_final: 0.6458 (t80) REVERT: A 517 LEU cc_start: 0.7584 (tp) cc_final: 0.7064 (mt) REVERT: A 560 LYS cc_start: 0.7862 (mttt) cc_final: 0.7000 (ttpt) REVERT: B 38 GLN cc_start: 0.7797 (mt0) cc_final: 0.7546 (mt0) REVERT: B 43 MET cc_start: 0.7752 (mmm) cc_final: 0.7316 (tpt) REVERT: B 378 ASP cc_start: 0.5908 (m-30) cc_final: 0.5626 (m-30) REVERT: D 127 ASP cc_start: 0.6904 (p0) cc_final: 0.6004 (t0) REVERT: D 159 ARG cc_start: 0.4592 (mtt90) cc_final: 0.4038 (tpp-160) outliers start: 8 outliers final: 1 residues processed: 306 average time/residue: 0.2823 time to fit residues: 114.0333 Evaluate side-chains 159 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 142 GLN A 189 HIS A 394 ASN A 399 GLN A 461 GLN A 474 GLN A 543 ASN B 66 GLN B 67 ASN B 228 HIS B 303 GLN B 406 GLN B 445 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.187101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.166220 restraints weight = 16941.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.169174 restraints weight = 10285.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.171190 restraints weight = 7336.539| |-----------------------------------------------------------------------------| r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10386 Z= 0.143 Angle : 0.610 10.274 14046 Z= 0.322 Chirality : 0.039 0.203 1556 Planarity : 0.005 0.070 1769 Dihedral : 4.984 29.413 1341 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.36 % Allowed : 9.02 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % 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: -0.69 (0.23), residues: 1209 helix: 0.35 (0.17), residues: 845 sheet: 0.35 (1.77), residues: 14 loop : -2.40 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 412 HIS 0.023 0.001 HIS B 12 PHE 0.018 0.002 PHE A 117 TYR 0.020 0.001 TYR A 126 ARG 0.004 0.001 ARG D 121 Details of bonding type rmsd hydrogen bonds : bond 0.04775 ( 596) hydrogen bonds : angle 4.34378 ( 1755) metal coordination : bond 0.00518 ( 6) metal coordination : angle 6.02642 ( 6) SS BOND : bond 0.00270 ( 1) SS BOND : angle 1.39456 ( 2) covalent geometry : bond 0.00287 (10378) covalent geometry : angle 0.59720 (14038) Misc. bond : bond 0.00648 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 TYR cc_start: 0.6047 (m-80) cc_final: 0.5206 (m-80) REVERT: A 387 LEU cc_start: 0.7887 (mt) cc_final: 0.7649 (mp) REVERT: B 9 LYS cc_start: 0.7575 (mtmm) cc_final: 0.6899 (tttp) REVERT: B 308 LYS cc_start: 0.7828 (tttm) cc_final: 0.7621 (tttm) REVERT: B 426 ASP cc_start: 0.6718 (t0) cc_final: 0.6330 (t0) REVERT: B 444 ASN cc_start: 0.8209 (t0) cc_final: 0.7773 (m-40) REVERT: B 591 ARG cc_start: 0.6501 (ttm-80) cc_final: 0.6299 (ttp-170) REVERT: D 21 LYS cc_start: 0.8398 (mmmt) cc_final: 0.7870 (mmtm) REVERT: D 127 ASP cc_start: 0.5382 (p0) cc_final: 0.5036 (t0) REVERT: D 134 ILE cc_start: 0.6513 (mt) cc_final: 0.6262 (mt) outliers start: 27 outliers final: 13 residues processed: 209 average time/residue: 0.2381 time to fit residues: 68.7281 Evaluate side-chains 140 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain D residue 17 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 109 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 31 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 82 optimal weight: 0.0010 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 433 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.183941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.162836 restraints weight = 17145.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.165817 restraints weight = 10475.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.167833 restraints weight = 7497.000| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10386 Z= 0.118 Angle : 0.550 8.544 14046 Z= 0.286 Chirality : 0.038 0.163 1556 Planarity : 0.005 0.055 1769 Dihedral : 4.501 26.027 1340 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.01 % Allowed : 12.52 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % 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: 0.17 (0.24), residues: 1209 helix: 1.06 (0.18), residues: 847 sheet: 0.05 (1.71), residues: 14 loop : -2.28 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 412 HIS 0.017 0.001 HIS B 12 PHE 0.013 0.001 PHE A 127 TYR 0.025 0.001 TYR A 126 ARG 0.006 0.000 ARG D 121 Details of bonding type rmsd hydrogen bonds : bond 0.04249 ( 596) hydrogen bonds : angle 4.03868 ( 1755) metal coordination : bond 0.00350 ( 6) metal coordination : angle 4.54408 ( 6) SS BOND : bond 0.00218 ( 1) SS BOND : angle 0.54247 ( 2) covalent geometry : bond 0.00246 (10378) covalent geometry : angle 0.54215 (14038) Misc. bond : bond 0.00844 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TRP cc_start: 0.4617 (m100) cc_final: 0.4172 (m100) REVERT: A 204 MET cc_start: 0.5872 (mmt) cc_final: 0.5597 (tpp) REVERT: B 9 LYS cc_start: 0.7545 (mtmm) cc_final: 0.6806 (tttp) REVERT: B 266 ASN cc_start: 0.8632 (t0) cc_final: 0.8387 (t0) REVERT: B 307 ARG cc_start: 0.7558 (mmp80) cc_final: 0.7200 (mmp-170) REVERT: B 308 LYS cc_start: 0.7902 (tttm) cc_final: 0.7690 (tttm) REVERT: B 444 ASN cc_start: 0.8092 (t0) cc_final: 0.7768 (m110) REVERT: B 458 MET cc_start: 0.4963 (OUTLIER) cc_final: 0.4696 (ptp) REVERT: B 543 ASN cc_start: 0.7634 (m-40) cc_final: 0.7420 (m110) REVERT: D 77 MET cc_start: 0.7086 (ttp) cc_final: 0.6495 (ttm) REVERT: D 127 ASP cc_start: 0.5519 (p0) cc_final: 0.5012 (t0) REVERT: D 128 GLN cc_start: 0.7028 (tp-100) cc_final: 0.6712 (tp-100) outliers start: 23 outliers final: 15 residues processed: 179 average time/residue: 0.2393 time to fit residues: 59.3066 Evaluate side-chains 146 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain D residue 17 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 98 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 45 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 303 GLN B 543 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.171554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.152680 restraints weight = 17344.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.155040 restraints weight = 11416.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.156650 restraints weight = 8590.844| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10386 Z= 0.206 Angle : 0.705 7.845 14046 Z= 0.370 Chirality : 0.044 0.187 1556 Planarity : 0.005 0.051 1769 Dihedral : 4.952 25.273 1340 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.96 % Favored : 94.95 % Rotamer: Outliers : 3.50 % Allowed : 12.52 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % 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: 0.00 (0.24), residues: 1209 helix: 0.94 (0.18), residues: 847 sheet: -0.75 (1.62), residues: 14 loop : -2.33 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP A 412 HIS 0.017 0.002 HIS B 12 PHE 0.023 0.002 PHE B 590 TYR 0.026 0.002 TYR A 158 ARG 0.005 0.001 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.06345 ( 596) hydrogen bonds : angle 4.55234 ( 1755) metal coordination : bond 0.00818 ( 6) metal coordination : angle 3.54650 ( 6) SS BOND : bond 0.00339 ( 1) SS BOND : angle 0.64707 ( 2) covalent geometry : bond 0.00471 (10378) covalent geometry : angle 0.70152 (14038) Misc. bond : bond 0.00753 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.5946 (mmt) cc_final: 0.5627 (tpp) REVERT: A 377 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.7931 (mt) REVERT: B 9 LYS cc_start: 0.7632 (mtmm) cc_final: 0.6883 (tttp) REVERT: B 376 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6546 (mp0) REVERT: B 417 MET cc_start: 0.7606 (mmt) cc_final: 0.7162 (ttm) REVERT: B 444 ASN cc_start: 0.8106 (t0) cc_final: 0.7893 (m110) REVERT: D 128 GLN cc_start: 0.7422 (tp-100) cc_final: 0.6725 (tp-100) REVERT: D 132 TYR cc_start: 0.8358 (m-10) cc_final: 0.7930 (m-10) outliers start: 40 outliers final: 24 residues processed: 186 average time/residue: 0.2219 time to fit residues: 58.1973 Evaluate side-chains 150 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain D residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 68 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN B 205 GLN B 235 GLN B 445 ASN B 598 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.171861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.152781 restraints weight = 17359.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.155234 restraints weight = 11219.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.156958 restraints weight = 8344.566| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.6539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10386 Z= 0.177 Angle : 0.630 9.544 14046 Z= 0.330 Chirality : 0.042 0.174 1556 Planarity : 0.005 0.045 1769 Dihedral : 4.766 25.345 1340 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.20 % Allowed : 13.40 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % 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: 0.20 (0.24), residues: 1209 helix: 1.07 (0.18), residues: 851 sheet: -0.71 (1.54), residues: 14 loop : -2.24 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP A 412 HIS 0.015 0.001 HIS B 12 PHE 0.018 0.002 PHE A 476 TYR 0.017 0.002 TYR A 158 ARG 0.004 0.001 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.05302 ( 596) hydrogen bonds : angle 4.29668 ( 1755) metal coordination : bond 0.00713 ( 6) metal coordination : angle 3.24347 ( 6) SS BOND : bond 0.00113 ( 1) SS BOND : angle 0.55681 ( 2) covalent geometry : bond 0.00408 (10378) covalent geometry : angle 0.62706 (14038) Misc. bond : bond 0.00758 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 144 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7832 (t0) REVERT: B 9 LYS cc_start: 0.7577 (mtmm) cc_final: 0.6772 (tttp) REVERT: B 308 LYS cc_start: 0.8287 (tttm) cc_final: 0.8050 (tttm) REVERT: B 316 VAL cc_start: 0.7000 (OUTLIER) cc_final: 0.6596 (m) REVERT: B 417 MET cc_start: 0.7661 (mmt) cc_final: 0.7241 (ttm) REVERT: B 460 MET cc_start: 0.7695 (tpt) cc_final: 0.7469 (tpt) REVERT: B 489 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8709 (mt) REVERT: B 591 ARG cc_start: 0.6942 (ttm-80) cc_final: 0.6703 (ttp-170) REVERT: D 21 LYS cc_start: 0.8082 (mmtt) cc_final: 0.7625 (mmtm) REVERT: D 128 GLN cc_start: 0.7365 (tp-100) cc_final: 0.7018 (tp40) REVERT: D 132 TYR cc_start: 0.8432 (m-10) cc_final: 0.7995 (m-10) outliers start: 48 outliers final: 33 residues processed: 181 average time/residue: 0.2106 time to fit residues: 54.7640 Evaluate side-chains 169 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 88 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 0.0070 chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN B 104 ASN B 235 GLN B 303 GLN B 444 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.174091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.155228 restraints weight = 17346.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.157852 restraints weight = 10893.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.159623 restraints weight = 7955.993| |-----------------------------------------------------------------------------| r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.6733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10386 Z= 0.130 Angle : 0.588 8.718 14046 Z= 0.304 Chirality : 0.039 0.142 1556 Planarity : 0.004 0.043 1769 Dihedral : 4.506 23.899 1340 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.50 % Allowed : 15.32 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % 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: 0.66 (0.25), residues: 1209 helix: 1.40 (0.18), residues: 844 sheet: -0.54 (1.51), residues: 14 loop : -1.94 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP A 412 HIS 0.014 0.001 HIS B 12 PHE 0.014 0.001 PHE B 590 TYR 0.014 0.001 TYR B 382 ARG 0.007 0.000 ARG B 4 Details of bonding type rmsd hydrogen bonds : bond 0.04647 ( 596) hydrogen bonds : angle 4.06157 ( 1755) metal coordination : bond 0.00500 ( 6) metal coordination : angle 4.69438 ( 6) SS BOND : bond 0.00322 ( 1) SS BOND : angle 0.74662 ( 2) covalent geometry : bond 0.00282 (10378) covalent geometry : angle 0.57999 (14038) Misc. bond : bond 0.00691 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.6917 (m-10) cc_final: 0.6507 (m-10) REVERT: A 204 MET cc_start: 0.5867 (mmt) cc_final: 0.5513 (tpp) REVERT: A 374 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8254 (ttm110) REVERT: B 9 LYS cc_start: 0.7507 (mtmm) cc_final: 0.6629 (tttp) REVERT: B 100 MET cc_start: 0.4627 (ppp) cc_final: 0.4326 (ppp) REVERT: B 308 LYS cc_start: 0.8325 (tttm) cc_final: 0.8112 (tttm) REVERT: B 316 VAL cc_start: 0.7027 (OUTLIER) cc_final: 0.6631 (m) REVERT: B 417 MET cc_start: 0.7576 (mmt) cc_final: 0.7260 (ttm) REVERT: D 21 LYS cc_start: 0.8063 (mmtt) cc_final: 0.7673 (mmtm) REVERT: D 128 GLN cc_start: 0.7285 (tp-100) cc_final: 0.6799 (tp-100) REVERT: D 132 TYR cc_start: 0.8449 (m-10) cc_final: 0.8006 (m-10) outliers start: 40 outliers final: 30 residues processed: 188 average time/residue: 0.2410 time to fit residues: 64.9620 Evaluate side-chains 169 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 88 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 116 optimal weight: 7.9990 chunk 54 optimal weight: 0.3980 chunk 94 optimal weight: 0.0980 chunk 81 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 119 optimal weight: 0.0770 chunk 80 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 0.0570 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.180671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.162387 restraints weight = 17438.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.165114 restraints weight = 10820.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.166930 restraints weight = 7791.613| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.6882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10386 Z= 0.110 Angle : 0.560 10.606 14046 Z= 0.287 Chirality : 0.038 0.193 1556 Planarity : 0.004 0.040 1769 Dihedral : 4.192 24.859 1340 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.54 % Allowed : 16.90 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % 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 (0.25), residues: 1209 helix: 1.59 (0.18), residues: 854 sheet: -0.10 (1.45), residues: 14 loop : -1.64 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP A 412 HIS 0.015 0.001 HIS B 12 PHE 0.022 0.001 PHE A 476 TYR 0.013 0.001 TYR B 301 ARG 0.007 0.000 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 596) hydrogen bonds : angle 3.80378 ( 1755) metal coordination : bond 0.00321 ( 6) metal coordination : angle 3.84713 ( 6) SS BOND : bond 0.00300 ( 1) SS BOND : angle 0.26720 ( 2) covalent geometry : bond 0.00221 (10378) covalent geometry : angle 0.55403 (14038) Misc. bond : bond 0.00657 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.5795 (mmm) cc_final: 0.5590 (mmm) REVERT: A 204 MET cc_start: 0.5922 (mmt) cc_final: 0.5654 (tpp) REVERT: A 300 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.8121 (t0) REVERT: A 500 PHE cc_start: 0.4709 (m-80) cc_final: 0.4490 (m-80) REVERT: B 9 LYS cc_start: 0.7224 (mtmm) cc_final: 0.6467 (tttp) REVERT: D 21 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7713 (mmtm) REVERT: D 128 GLN cc_start: 0.7129 (tp-100) cc_final: 0.6774 (tp40) REVERT: D 132 TYR cc_start: 0.8479 (m-10) cc_final: 0.8130 (m-10) outliers start: 29 outliers final: 18 residues processed: 171 average time/residue: 0.2026 time to fit residues: 50.2049 Evaluate side-chains 154 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 88 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 109 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 36 optimal weight: 0.0060 chunk 31 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 13 optimal weight: 0.2980 chunk 80 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.179300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.161010 restraints weight = 17344.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.163641 restraints weight = 10956.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.165391 restraints weight = 7981.982| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.6984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10386 Z= 0.111 Angle : 0.567 11.238 14046 Z= 0.289 Chirality : 0.038 0.169 1556 Planarity : 0.004 0.041 1769 Dihedral : 4.090 23.334 1340 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.19 % Allowed : 18.04 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.25), residues: 1209 helix: 1.63 (0.18), residues: 858 sheet: 0.20 (1.41), residues: 14 loop : -1.62 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP A 412 HIS 0.014 0.001 HIS B 12 PHE 0.024 0.001 PHE A 476 TYR 0.013 0.001 TYR B 301 ARG 0.005 0.000 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 596) hydrogen bonds : angle 3.81139 ( 1755) metal coordination : bond 0.00363 ( 6) metal coordination : angle 3.91585 ( 6) SS BOND : bond 0.00375 ( 1) SS BOND : angle 0.29979 ( 2) covalent geometry : bond 0.00231 (10378) covalent geometry : angle 0.56091 (14038) Misc. bond : bond 0.00650 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.5814 (mmt) cc_final: 0.5605 (tpp) REVERT: A 377 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.7852 (mt) REVERT: B 9 LYS cc_start: 0.7274 (mtmm) cc_final: 0.6493 (tttp) REVERT: D 21 LYS cc_start: 0.8062 (mmtt) cc_final: 0.7566 (mmtm) REVERT: D 128 GLN cc_start: 0.7071 (tp-100) cc_final: 0.6760 (tp40) REVERT: D 132 TYR cc_start: 0.8600 (m-10) cc_final: 0.8196 (m-10) outliers start: 25 outliers final: 23 residues processed: 160 average time/residue: 0.2149 time to fit residues: 50.1341 Evaluate side-chains 153 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 88 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 26 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 118 optimal weight: 0.0010 chunk 98 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 overall best weight: 3.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.169494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.150295 restraints weight = 17547.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.152803 restraints weight = 11227.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.154483 restraints weight = 8311.047| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.7243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10386 Z= 0.219 Angle : 0.712 10.770 14046 Z= 0.370 Chirality : 0.044 0.196 1556 Planarity : 0.005 0.042 1769 Dihedral : 4.740 23.424 1340 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.63 % Allowed : 18.13 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % 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: 0.50 (0.24), residues: 1209 helix: 1.24 (0.18), residues: 849 sheet: -0.33 (1.37), residues: 14 loop : -1.93 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.003 TRP A 412 HIS 0.012 0.002 HIS B 12 PHE 0.022 0.002 PHE A 476 TYR 0.021 0.002 TYR B 382 ARG 0.003 0.001 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.05833 ( 596) hydrogen bonds : angle 4.36967 ( 1755) metal coordination : bond 0.00998 ( 6) metal coordination : angle 3.49943 ( 6) SS BOND : bond 0.00275 ( 1) SS BOND : angle 0.16802 ( 2) covalent geometry : bond 0.00510 (10378) covalent geometry : angle 0.70891 (14038) Misc. bond : bond 0.00628 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 539 LYS cc_start: 0.7566 (tptt) cc_final: 0.7118 (tptt) REVERT: B 9 LYS cc_start: 0.7558 (mtmm) cc_final: 0.6718 (tttp) REVERT: B 103 MET cc_start: 0.6188 (mpp) cc_final: 0.4893 (mtm) REVERT: B 376 GLU cc_start: 0.7274 (mm-30) cc_final: 0.7065 (mp0) REVERT: B 489 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8772 (mt) REVERT: D 21 LYS cc_start: 0.8082 (mmtt) cc_final: 0.7588 (mmtm) outliers start: 30 outliers final: 24 residues processed: 157 average time/residue: 0.2062 time to fit residues: 47.5222 Evaluate side-chains 151 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 99 CYS Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 88 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 75 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 83 optimal weight: 0.0040 chunk 33 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 107 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.177086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.158871 restraints weight = 17369.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.161417 restraints weight = 11025.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.163149 restraints weight = 8066.179| |-----------------------------------------------------------------------------| r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.7340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10386 Z= 0.118 Angle : 0.583 9.816 14046 Z= 0.302 Chirality : 0.039 0.224 1556 Planarity : 0.004 0.041 1769 Dihedral : 4.316 25.046 1340 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.01 % Allowed : 18.91 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % 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: 1.03 (0.25), residues: 1209 helix: 1.56 (0.18), residues: 852 sheet: 0.15 (1.33), residues: 14 loop : -1.54 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP A 412 HIS 0.013 0.001 HIS B 12 PHE 0.022 0.001 PHE A 476 TYR 0.020 0.001 TYR A 78 ARG 0.003 0.000 ARG A 397 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 596) hydrogen bonds : angle 3.96777 ( 1755) metal coordination : bond 0.00351 ( 6) metal coordination : angle 2.89058 ( 6) SS BOND : bond 0.00291 ( 1) SS BOND : angle 0.15304 ( 2) covalent geometry : bond 0.00251 (10378) covalent geometry : angle 0.57981 (14038) Misc. bond : bond 0.00613 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.7852 (mt) REVERT: B 103 MET cc_start: 0.6259 (mpp) cc_final: 0.5409 (mtm) REVERT: D 21 LYS cc_start: 0.8140 (mmtt) cc_final: 0.7632 (mmtm) outliers start: 23 outliers final: 20 residues processed: 155 average time/residue: 0.2081 time to fit residues: 47.5338 Evaluate side-chains 145 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 99 CYS Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 88 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 16 optimal weight: 0.0870 chunk 116 optimal weight: 0.3980 chunk 105 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 48 optimal weight: 0.0570 chunk 98 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 GLN ** 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 = 0.4326 r_free = 0.4326 target = 0.179587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.161408 restraints weight = 17402.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.164084 restraints weight = 10910.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.165889 restraints weight = 7903.108| |-----------------------------------------------------------------------------| r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.7437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10386 Z= 0.113 Angle : 0.579 8.371 14046 Z= 0.296 Chirality : 0.039 0.178 1556 Planarity : 0.004 0.040 1769 Dihedral : 4.145 25.201 1340 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.75 % Allowed : 19.44 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % 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: 1.22 (0.25), residues: 1209 helix: 1.69 (0.18), residues: 858 sheet: 0.72 (1.33), residues: 14 loop : -1.54 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP A 412 HIS 0.014 0.001 HIS B 12 PHE 0.022 0.001 PHE A 476 TYR 0.019 0.001 TYR A 105 ARG 0.003 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 596) hydrogen bonds : angle 3.80965 ( 1755) metal coordination : bond 0.00412 ( 6) metal coordination : angle 3.82364 ( 6) SS BOND : bond 0.00207 ( 1) SS BOND : angle 0.50065 ( 2) covalent geometry : bond 0.00240 (10378) covalent geometry : angle 0.57396 (14038) Misc. bond : bond 0.00602 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3229.47 seconds wall clock time: 56 minutes 50.04 seconds (3410.04 seconds total)