Starting phenix.real_space_refine on Wed Sep 25 11:01:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f07_4163/09_2024/6f07_4163.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f07_4163/09_2024/6f07_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f07_4163/09_2024/6f07_4163.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f07_4163/09_2024/6f07_4163.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f07_4163/09_2024/6f07_4163.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f07_4163/09_2024/6f07_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-5461/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: 5.94, per 1000 atoms: 0.59 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=0, symmetry=0 Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.1 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: 1.06 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: 2.57 Time building geometry restraints manager: 2.79 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: 0.56 - 1.43: 8 1.43 - 2.30: 28 2.30 - 3.16: 8494 3.16 - 4.03: 24622 4.03 - 4.90: 44139 Warning: very small nonbonded interaction distances. Nonbonded interactions: 77291 Sorted by model distance: nonbonded pdb=" NE2 HIS B 12 " pdb=" N PHE D 176 " model vdw 0.559 3.200 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 ... (remaining 77286 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: 0.850 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.490 Find NCS groups from input model: 0.330 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.990 ------------------------------------------------------------------------------- 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 : 0.007 0.068 10378 Z= 0.422 Angle : 0.958 13.656 14038 Z= 0.565 Chirality : 0.053 0.230 1556 Planarity : 0.008 0.079 1769 Dihedral : 10.285 77.111 3863 Min Nonbonded Distance : 0.559 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 *********************** 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 fitting. rotamer outliers: 8 poor density : 300 time to evaluate : 1.030 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: 0.2714 time to fit residues: 109.1277 Evaluate side-chains 159 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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: 10.0000 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 12 HIS B 66 GLN B 67 ASN B 303 GLN B 406 GLN B 445 ASN B 543 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5640 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10378 Z= 0.175 Angle : 0.595 9.225 14038 Z= 0.318 Chirality : 0.039 0.201 1556 Planarity : 0.005 0.069 1769 Dihedral : 5.035 29.722 1341 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.45 % Allowed : 9.11 % Favored : 88.44 % 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: 844 sheet: 0.34 (1.77), residues: 14 loop : -2.43 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 412 HIS 0.017 0.001 HIS B 12 PHE 0.019 0.001 PHE A 117 TYR 0.019 0.001 TYR A 126 ARG 0.005 0.000 ARG D 121 *********************** 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 223 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 195 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 PHE cc_start: 0.6791 (t80) cc_final: 0.6175 (t80) REVERT: A 199 ASN cc_start: 0.7883 (m-40) cc_final: 0.7518 (m-40) REVERT: A 255 SER cc_start: 0.7796 (m) cc_final: 0.7373 (t) REVERT: A 376 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7665 (tp30) REVERT: A 387 LEU cc_start: 0.7590 (mt) cc_final: 0.7240 (mp) REVERT: A 399 GLN cc_start: 0.8363 (tt0) cc_final: 0.8006 (pp30) REVERT: A 473 TYR cc_start: 0.6844 (t80) cc_final: 0.6138 (t80) REVERT: A 517 LEU cc_start: 0.7706 (tp) cc_final: 0.7311 (mt) REVERT: B 9 LYS cc_start: 0.6583 (mtmm) cc_final: 0.5613 (tttp) REVERT: B 11 LYS cc_start: 0.5761 (pttt) cc_final: 0.4682 (mttp) REVERT: B 43 MET cc_start: 0.7625 (mmm) cc_final: 0.7018 (tpt) REVERT: B 102 TRP cc_start: 0.4547 (m100) cc_final: 0.3657 (t-100) REVERT: B 376 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7029 (mm-30) REVERT: B 426 ASP cc_start: 0.7881 (t0) cc_final: 0.6958 (t0) REVERT: B 440 SER cc_start: 0.8034 (t) cc_final: 0.7624 (p) REVERT: B 444 ASN cc_start: 0.7319 (t0) cc_final: 0.6713 (m-40) REVERT: B 543 ASN cc_start: 0.7233 (OUTLIER) cc_final: 0.6715 (m-40) REVERT: B 591 ARG cc_start: 0.6483 (ttm-80) cc_final: 0.5745 (ttp-170) REVERT: D 21 LYS cc_start: 0.8313 (mmmt) cc_final: 0.7805 (mmtm) REVERT: D 24 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6239 (mm-30) REVERT: D 77 MET cc_start: 0.7472 (ttp) cc_final: 0.7195 (ttp) REVERT: D 127 ASP cc_start: 0.7328 (p0) cc_final: 0.6353 (t0) REVERT: D 159 ARG cc_start: 0.4390 (mtt90) cc_final: 0.3930 (tpp-160) outliers start: 28 outliers final: 13 residues processed: 212 average time/residue: 0.2328 time to fit residues: 68.1382 Evaluate side-chains 145 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 B residue 543 ASN 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 61 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 37 optimal weight: 0.0370 chunk 89 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 228 HIS B 433 HIS B 598 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5703 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10378 Z= 0.168 Angle : 0.556 8.797 14038 Z= 0.292 Chirality : 0.038 0.154 1556 Planarity : 0.005 0.056 1769 Dihedral : 4.485 26.022 1340 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.36 % Allowed : 11.65 % Favored : 85.99 % 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: 0.18 (0.24), residues: 1209 helix: 1.05 (0.18), residues: 846 sheet: 0.41 (1.74), residues: 14 loop : -2.25 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 412 HIS 0.003 0.001 HIS D 96 PHE 0.012 0.001 PHE B 415 TYR 0.026 0.002 TYR A 126 ARG 0.005 0.000 ARG B 146 *********************** 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 195 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 168 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 TYR cc_start: 0.5586 (m-80) cc_final: 0.5126 (m-80) REVERT: A 200 TRP cc_start: 0.4620 (m100) cc_final: 0.4061 (m100) REVERT: A 204 MET cc_start: 0.3652 (mmt) cc_final: 0.3442 (tpp) REVERT: A 255 SER cc_start: 0.7834 (m) cc_final: 0.7552 (p) REVERT: A 387 LEU cc_start: 0.7794 (mt) cc_final: 0.7479 (mp) REVERT: A 399 GLN cc_start: 0.8451 (tt0) cc_final: 0.8024 (pp30) REVERT: A 473 TYR cc_start: 0.6914 (t80) cc_final: 0.6504 (t80) REVERT: B 9 LYS cc_start: 0.6368 (mtmm) cc_final: 0.5336 (tttp) REVERT: B 11 LYS cc_start: 0.6689 (pttt) cc_final: 0.5544 (mttp) REVERT: B 43 MET cc_start: 0.7537 (mmm) cc_final: 0.6951 (tpt) REVERT: B 102 TRP cc_start: 0.4398 (m100) cc_final: 0.4037 (m100) REVERT: B 307 ARG cc_start: 0.7023 (mmp80) cc_final: 0.6819 (mmp80) REVERT: B 376 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7198 (mm-30) REVERT: B 426 ASP cc_start: 0.8217 (t0) cc_final: 0.7814 (t0) REVERT: B 440 SER cc_start: 0.8198 (t) cc_final: 0.7790 (p) REVERT: B 444 ASN cc_start: 0.7345 (t0) cc_final: 0.6728 (m110) REVERT: B 488 ASP cc_start: 0.7403 (m-30) cc_final: 0.7176 (m-30) REVERT: D 24 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6619 (mm-30) REVERT: D 159 ARG cc_start: 0.4474 (mtt90) cc_final: 0.4072 (tpp-160) outliers start: 27 outliers final: 16 residues processed: 189 average time/residue: 0.2369 time to fit residues: 62.7591 Evaluate side-chains 154 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 138 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL 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 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 442 ILE 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 83 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 74 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 128 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5809 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10378 Z= 0.238 Angle : 0.609 8.142 14038 Z= 0.323 Chirality : 0.041 0.141 1556 Planarity : 0.005 0.048 1769 Dihedral : 4.595 24.047 1340 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.06 % Allowed : 12.08 % Favored : 84.85 % 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: 0.30 (0.24), residues: 1209 helix: 1.17 (0.18), residues: 845 sheet: -0.28 (1.69), residues: 14 loop : -2.25 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP A 412 HIS 0.005 0.001 HIS D 96 PHE 0.023 0.002 PHE A 476 TYR 0.020 0.002 TYR A 158 ARG 0.006 0.001 ARG B 34 *********************** 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 194 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 159 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ASN cc_start: 0.6303 (t0) cc_final: 0.6009 (t0) REVERT: A 173 TYR cc_start: 0.5826 (m-80) cc_final: 0.5320 (m-10) REVERT: A 200 TRP cc_start: 0.4527 (m100) cc_final: 0.4140 (m100) REVERT: A 204 MET cc_start: 0.3579 (mmt) cc_final: 0.3350 (tpp) REVERT: A 377 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7065 (mt) REVERT: A 387 LEU cc_start: 0.7877 (mt) cc_final: 0.7589 (mp) REVERT: A 399 GLN cc_start: 0.8556 (tt0) cc_final: 0.8058 (pp30) REVERT: A 473 TYR cc_start: 0.6786 (t80) cc_final: 0.6468 (t80) REVERT: B 9 LYS cc_start: 0.5982 (mtmm) cc_final: 0.4991 (tttp) REVERT: B 11 LYS cc_start: 0.6112 (pttt) cc_final: 0.4714 (mttp) REVERT: B 43 MET cc_start: 0.7575 (mmm) cc_final: 0.7044 (tpt) REVERT: B 82 GLN cc_start: 0.7172 (mm-40) cc_final: 0.6635 (pm20) REVERT: B 184 SER cc_start: 0.6857 (t) cc_final: 0.6423 (p) REVERT: B 226 MET cc_start: 0.7030 (ttm) cc_final: 0.6770 (ttt) REVERT: B 376 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7090 (mp0) REVERT: B 417 MET cc_start: 0.5640 (mmt) cc_final: 0.5017 (ttm) REVERT: B 426 ASP cc_start: 0.7978 (t0) cc_final: 0.7315 (t0) REVERT: B 440 SER cc_start: 0.8171 (t) cc_final: 0.7763 (p) REVERT: B 444 ASN cc_start: 0.7434 (t0) cc_final: 0.6840 (m110) REVERT: B 488 ASP cc_start: 0.7599 (m-30) cc_final: 0.7343 (m-30) REVERT: D 21 LYS cc_start: 0.8136 (mmtt) cc_final: 0.7683 (mmtm) REVERT: D 24 GLU cc_start: 0.7675 (mt-10) cc_final: 0.6606 (mm-30) REVERT: D 30 LYS cc_start: 0.7944 (tptp) cc_final: 0.7710 (ttmt) REVERT: D 31 ASN cc_start: 0.6834 (OUTLIER) cc_final: 0.6545 (p0) REVERT: D 132 TYR cc_start: 0.7614 (m-10) cc_final: 0.7310 (m-10) REVERT: D 143 ILE cc_start: 0.5187 (mm) cc_final: 0.4558 (mm) REVERT: D 146 LEU cc_start: 0.7943 (tp) cc_final: 0.7688 (pp) REVERT: D 159 ARG cc_start: 0.4951 (mtt90) cc_final: 0.4382 (tpp-160) outliers start: 35 outliers final: 21 residues processed: 184 average time/residue: 0.2246 time to fit residues: 57.6998 Evaluate side-chains 153 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 223 CYS 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 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 231 ILE 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 470 ILE Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 31 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 GLN B 598 GLN D 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5753 moved from start: 0.5913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10378 Z= 0.148 Angle : 0.537 9.409 14038 Z= 0.280 Chirality : 0.038 0.248 1556 Planarity : 0.004 0.044 1769 Dihedral : 4.270 24.216 1340 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.36 % Allowed : 14.36 % Favored : 83.27 % 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: 0.81 (0.25), residues: 1209 helix: 1.52 (0.18), residues: 847 sheet: -0.05 (1.69), residues: 14 loop : -1.95 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 412 HIS 0.004 0.001 HIS A 456 PHE 0.010 0.001 PHE B 590 TYR 0.014 0.001 TYR B 301 ARG 0.004 0.000 ARG A 375 *********************** 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 188 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 161 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TRP cc_start: 0.4492 (m100) cc_final: 0.4116 (m100) REVERT: A 387 LEU cc_start: 0.7842 (mt) cc_final: 0.7578 (mp) REVERT: A 399 GLN cc_start: 0.8566 (tt0) cc_final: 0.8060 (pp30) REVERT: A 460 MET cc_start: 0.4300 (tpp) cc_final: 0.4042 (tpp) REVERT: A 473 TYR cc_start: 0.6932 (t80) cc_final: 0.6554 (t80) REVERT: B 9 LYS cc_start: 0.5858 (mtmm) cc_final: 0.4914 (tttp) REVERT: B 11 LYS cc_start: 0.6617 (pttt) cc_final: 0.5316 (mttp) REVERT: B 82 GLN cc_start: 0.7335 (mm-40) cc_final: 0.6795 (pm20) REVERT: B 120 GLU cc_start: 0.9027 (tp30) cc_final: 0.8415 (tt0) REVERT: B 184 SER cc_start: 0.7029 (t) cc_final: 0.6689 (p) REVERT: B 316 VAL cc_start: 0.6302 (OUTLIER) cc_final: 0.5927 (m) REVERT: B 376 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7077 (mp0) REVERT: B 417 MET cc_start: 0.5535 (mmt) cc_final: 0.5061 (ttt) REVERT: B 426 ASP cc_start: 0.8059 (t0) cc_final: 0.7653 (t0) REVERT: B 440 SER cc_start: 0.8186 (t) cc_final: 0.7898 (p) REVERT: B 444 ASN cc_start: 0.7440 (t0) cc_final: 0.6996 (m110) REVERT: B 488 ASP cc_start: 0.7520 (m-30) cc_final: 0.7240 (m-30) REVERT: B 591 ARG cc_start: 0.6984 (ttm-80) cc_final: 0.6669 (ttp-170) REVERT: D 21 LYS cc_start: 0.8023 (mmtt) cc_final: 0.7521 (mmtm) REVERT: D 24 GLU cc_start: 0.7431 (mt-10) cc_final: 0.6350 (mm-30) REVERT: D 132 TYR cc_start: 0.7500 (m-10) cc_final: 0.7256 (m-10) REVERT: D 159 ARG cc_start: 0.4771 (mtt90) cc_final: 0.4299 (tpp-160) outliers start: 27 outliers final: 20 residues processed: 179 average time/residue: 0.2148 time to fit residues: 54.6350 Evaluate side-chains 160 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 139 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 223 CYS 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 456 HIS 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 113 optimal weight: 0.0980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5788 moved from start: 0.6248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10378 Z= 0.180 Angle : 0.550 8.574 14038 Z= 0.290 Chirality : 0.039 0.239 1556 Planarity : 0.004 0.044 1769 Dihedral : 4.282 22.532 1340 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.24 % Allowed : 13.84 % Favored : 82.92 % 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: 0.85 (0.25), residues: 1209 helix: 1.56 (0.18), residues: 848 sheet: -0.50 (1.62), residues: 14 loop : -1.97 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP A 412 HIS 0.006 0.001 HIS B 152 PHE 0.019 0.001 PHE A 476 TYR 0.015 0.001 TYR A 158 ARG 0.005 0.000 ARG A 375 *********************** 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 191 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 154 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TRP cc_start: 0.6641 (m100) cc_final: 0.6357 (m100) REVERT: A 200 TRP cc_start: 0.4430 (m100) cc_final: 0.4145 (m100) REVERT: A 387 LEU cc_start: 0.7858 (mt) cc_final: 0.7601 (mp) REVERT: A 399 GLN cc_start: 0.8597 (tt0) cc_final: 0.8100 (pp30) REVERT: B 9 LYS cc_start: 0.5824 (mtmm) cc_final: 0.4894 (tttp) REVERT: B 11 LYS cc_start: 0.6761 (pttt) cc_final: 0.6402 (pttm) REVERT: B 82 GLN cc_start: 0.7408 (mm-40) cc_final: 0.6890 (pm20) REVERT: B 120 GLU cc_start: 0.9035 (tp30) cc_final: 0.8417 (tt0) REVERT: B 184 SER cc_start: 0.7017 (t) cc_final: 0.6709 (p) REVERT: B 316 VAL cc_start: 0.6406 (OUTLIER) cc_final: 0.5979 (m) REVERT: B 376 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7026 (mp0) REVERT: B 417 MET cc_start: 0.5639 (mmt) cc_final: 0.4982 (ttm) REVERT: B 421 TYR cc_start: 0.6990 (m-80) cc_final: 0.6639 (m-10) REVERT: B 426 ASP cc_start: 0.8103 (t0) cc_final: 0.7832 (m-30) REVERT: B 440 SER cc_start: 0.8155 (t) cc_final: 0.7839 (p) REVERT: B 444 ASN cc_start: 0.7728 (t0) cc_final: 0.7099 (m110) REVERT: B 446 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6968 (m-10) REVERT: B 488 ASP cc_start: 0.7574 (m-30) cc_final: 0.7345 (m-30) REVERT: B 591 ARG cc_start: 0.7016 (ttm-80) cc_final: 0.6541 (ttp-170) REVERT: D 21 LYS cc_start: 0.8042 (mmtt) cc_final: 0.7559 (mmtm) REVERT: D 24 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6609 (tp30) REVERT: D 128 GLN cc_start: 0.5877 (tp40) cc_final: 0.4883 (tp-100) REVERT: D 132 TYR cc_start: 0.7613 (m-10) cc_final: 0.7287 (m-10) REVERT: D 146 LEU cc_start: 0.7959 (tp) cc_final: 0.7611 (pp) REVERT: D 159 ARG cc_start: 0.5052 (mtt90) cc_final: 0.4330 (tpp-160) outliers start: 37 outliers final: 27 residues processed: 180 average time/residue: 0.2088 time to fit residues: 54.2476 Evaluate side-chains 169 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 140 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 378 ASP 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 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 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 316 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 446 PHE Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 459 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5757 moved from start: 0.6464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10378 Z= 0.147 Angle : 0.514 7.638 14038 Z= 0.271 Chirality : 0.038 0.235 1556 Planarity : 0.004 0.040 1769 Dihedral : 4.096 24.600 1340 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.80 % Allowed : 14.89 % Favored : 82.31 % 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: 1.09 (0.25), residues: 1209 helix: 1.72 (0.18), residues: 847 sheet: 0.01 (1.68), residues: 14 loop : -1.82 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP A 412 HIS 0.003 0.001 HIS A 456 PHE 0.019 0.001 PHE A 476 TYR 0.018 0.001 TYR D 32 ARG 0.006 0.000 ARG A 375 *********************** 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 186 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 154 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TRP cc_start: 0.6652 (m100) cc_final: 0.6415 (m100) REVERT: A 200 TRP cc_start: 0.4433 (m100) cc_final: 0.4211 (m100) REVERT: A 226 MET cc_start: 0.6275 (mmt) cc_final: 0.6026 (mmt) REVERT: A 387 LEU cc_start: 0.7795 (mt) cc_final: 0.7546 (mp) REVERT: A 399 GLN cc_start: 0.8624 (tt0) cc_final: 0.8147 (pp30) REVERT: A 556 PHE cc_start: 0.6900 (OUTLIER) cc_final: 0.6687 (t80) REVERT: B 11 LYS cc_start: 0.7087 (pttt) cc_final: 0.6346 (ptpt) REVERT: B 82 GLN cc_start: 0.7357 (mm-40) cc_final: 0.6825 (pm20) REVERT: B 120 GLU cc_start: 0.8979 (tp30) cc_final: 0.8447 (tt0) REVERT: B 184 SER cc_start: 0.6888 (t) cc_final: 0.6592 (p) REVERT: B 316 VAL cc_start: 0.6277 (m) cc_final: 0.5867 (m) REVERT: B 376 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7170 (mp0) REVERT: B 417 MET cc_start: 0.5539 (mmt) cc_final: 0.4979 (ttm) REVERT: B 426 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7749 (m-30) REVERT: B 440 SER cc_start: 0.8172 (t) cc_final: 0.7877 (p) REVERT: B 444 ASN cc_start: 0.7779 (t0) cc_final: 0.7186 (m110) REVERT: B 446 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.6987 (m-10) REVERT: B 488 ASP cc_start: 0.7588 (m-30) cc_final: 0.7337 (m-30) REVERT: D 24 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6639 (tp30) REVERT: D 77 MET cc_start: 0.7313 (mmm) cc_final: 0.6854 (tpt) REVERT: D 128 GLN cc_start: 0.5932 (tp40) cc_final: 0.4845 (tp-100) REVERT: D 132 TYR cc_start: 0.7600 (m-10) cc_final: 0.7297 (m-10) REVERT: D 159 ARG cc_start: 0.5101 (mtt90) cc_final: 0.4411 (tpp-160) outliers start: 32 outliers final: 20 residues processed: 176 average time/residue: 0.2151 time to fit residues: 53.8374 Evaluate side-chains 166 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 143 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 176 VAL 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 456 HIS Chi-restraints excluded: chain A residue 531 ASP 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 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 426 ASP Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 446 PHE Chi-restraints excluded: chain B residue 459 VAL 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 136 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.0970 chunk 70 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5752 moved from start: 0.6639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10378 Z= 0.148 Angle : 0.532 8.938 14038 Z= 0.276 Chirality : 0.038 0.237 1556 Planarity : 0.004 0.041 1769 Dihedral : 4.039 23.297 1340 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.63 % Allowed : 15.32 % Favored : 82.05 % 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: 1.18 (0.25), residues: 1209 helix: 1.76 (0.18), residues: 848 sheet: 0.06 (1.64), residues: 14 loop : -1.70 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP A 412 HIS 0.005 0.001 HIS A 456 PHE 0.020 0.001 PHE A 476 TYR 0.014 0.001 TYR B 301 ARG 0.004 0.000 ARG A 375 *********************** 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 174 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 144 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TRP cc_start: 0.4494 (m100) cc_final: 0.4271 (m100) REVERT: A 387 LEU cc_start: 0.7758 (mt) cc_final: 0.7505 (mp) REVERT: A 399 GLN cc_start: 0.8632 (tt0) cc_final: 0.8162 (pp30) REVERT: B 11 LYS cc_start: 0.7030 (pttt) cc_final: 0.6373 (ptpt) REVERT: B 82 GLN cc_start: 0.7392 (mm-40) cc_final: 0.6863 (pm20) REVERT: B 120 GLU cc_start: 0.8963 (tp30) cc_final: 0.8431 (tt0) REVERT: B 184 SER cc_start: 0.6878 (t) cc_final: 0.6583 (p) REVERT: B 316 VAL cc_start: 0.6055 (m) cc_final: 0.5657 (m) REVERT: B 376 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7158 (mp0) REVERT: B 417 MET cc_start: 0.5518 (mmt) cc_final: 0.5073 (ttt) REVERT: B 426 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7657 (m-30) REVERT: B 440 SER cc_start: 0.8147 (t) cc_final: 0.7839 (p) REVERT: B 444 ASN cc_start: 0.7914 (t0) cc_final: 0.7330 (m-40) REVERT: B 446 PHE cc_start: 0.7362 (OUTLIER) cc_final: 0.7098 (m-10) REVERT: D 21 LYS cc_start: 0.8427 (tppt) cc_final: 0.7998 (tttt) REVERT: D 24 GLU cc_start: 0.7323 (mt-10) cc_final: 0.6469 (tp30) REVERT: D 128 GLN cc_start: 0.5814 (tp40) cc_final: 0.4886 (tp-100) REVERT: D 132 TYR cc_start: 0.7613 (m-10) cc_final: 0.7290 (m-10) REVERT: D 146 LEU cc_start: 0.7907 (tp) cc_final: 0.7550 (pp) REVERT: D 159 ARG cc_start: 0.5127 (mtt90) cc_final: 0.4343 (tpp-160) outliers start: 30 outliers final: 26 residues processed: 166 average time/residue: 0.2141 time to fit residues: 50.8412 Evaluate side-chains 165 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 223 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 550 LEU 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 275 LEU 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 426 ASP Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 446 PHE Chi-restraints excluded: chain B residue 459 VAL 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 136 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN B 235 GLN B 598 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5861 moved from start: 0.6970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10378 Z= 0.313 Angle : 0.680 11.747 14038 Z= 0.356 Chirality : 0.044 0.234 1556 Planarity : 0.005 0.045 1769 Dihedral : 4.681 23.890 1340 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.98 % Allowed : 15.76 % Favored : 81.26 % 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: 0.62 (0.24), residues: 1209 helix: 1.35 (0.18), residues: 845 sheet: -0.29 (1.54), residues: 14 loop : -1.93 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.003 TRP A 412 HIS 0.006 0.001 HIS D 96 PHE 0.023 0.002 PHE B 590 TYR 0.019 0.002 TYR A 158 ARG 0.005 0.001 ARG B 26 *********************** 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 175 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 141 time to evaluate : 1.156 Fit side-chains revert: symmetry clash REVERT: A 200 TRP cc_start: 0.4612 (m100) cc_final: 0.4378 (m100) REVERT: A 387 LEU cc_start: 0.7781 (mt) cc_final: 0.7518 (mp) REVERT: A 399 GLN cc_start: 0.8609 (tt0) cc_final: 0.8169 (pp30) REVERT: A 527 LEU cc_start: 0.5919 (tp) cc_final: 0.5592 (tt) REVERT: A 539 LYS cc_start: 0.5871 (tptt) cc_final: 0.5654 (tptt) REVERT: B 4 ARG cc_start: 0.7144 (mmp-170) cc_final: 0.6713 (mmp-170) REVERT: B 11 LYS cc_start: 0.6993 (pttt) cc_final: 0.6236 (ptpp) REVERT: B 19 ARG cc_start: 0.5756 (ttm-80) cc_final: 0.5245 (ptp-170) REVERT: B 43 MET cc_start: 0.6574 (mmt) cc_final: 0.6340 (mmt) REVERT: B 82 GLN cc_start: 0.7430 (mm110) cc_final: 0.6973 (pm20) REVERT: B 120 GLU cc_start: 0.8905 (tp30) cc_final: 0.8402 (tt0) REVERT: B 376 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7019 (mp0) REVERT: B 417 MET cc_start: 0.5663 (mmt) cc_final: 0.5025 (ttm) REVERT: B 426 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7516 (t70) REVERT: B 440 SER cc_start: 0.8136 (t) cc_final: 0.7825 (p) REVERT: B 444 ASN cc_start: 0.7608 (t0) cc_final: 0.7131 (m110) REVERT: B 446 PHE cc_start: 0.7402 (OUTLIER) cc_final: 0.7168 (m-10) REVERT: D 24 GLU cc_start: 0.7597 (mt-10) cc_final: 0.6856 (tp30) REVERT: D 157 MET cc_start: 0.6989 (mmm) cc_final: 0.6660 (mmm) REVERT: D 159 ARG cc_start: 0.5127 (mtt90) cc_final: 0.4253 (tpp-160) outliers start: 34 outliers final: 25 residues processed: 169 average time/residue: 0.2151 time to fit residues: 52.0521 Evaluate side-chains 153 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER 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 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 456 HIS 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 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 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 424 THR Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 446 PHE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 532 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 111 optimal weight: 0.0030 chunk 96 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 103 optimal weight: 0.0980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN B 142 GLN B 235 GLN B 406 GLN D 128 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5767 moved from start: 0.7095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10378 Z= 0.153 Angle : 0.579 11.167 14038 Z= 0.300 Chirality : 0.039 0.244 1556 Planarity : 0.004 0.041 1769 Dihedral : 4.263 24.994 1340 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.58 % Allowed : 18.04 % Favored : 80.39 % 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: 1.06 (0.25), residues: 1209 helix: 1.65 (0.18), residues: 847 sheet: 0.01 (1.53), residues: 14 loop : -1.71 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 412 HIS 0.005 0.001 HIS A 456 PHE 0.024 0.001 PHE A 398 TYR 0.014 0.001 TYR B 301 ARG 0.004 0.000 ARG A 375 ********************** 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 163 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 145 time to evaluate : 1.190 Fit side-chains revert: symmetry clash REVERT: A 200 TRP cc_start: 0.4562 (m100) cc_final: 0.4273 (m100) REVERT: A 377 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7223 (mt) REVERT: A 387 LEU cc_start: 0.7846 (mt) cc_final: 0.7635 (mp) REVERT: A 399 GLN cc_start: 0.8672 (tt0) cc_final: 0.8250 (pp30) REVERT: B 11 LYS cc_start: 0.7652 (pttt) cc_final: 0.7118 (ptpt) REVERT: B 19 ARG cc_start: 0.5639 (ttm-80) cc_final: 0.5251 (ptp-170) REVERT: B 43 MET cc_start: 0.6405 (mmt) cc_final: 0.6167 (mmt) REVERT: B 82 GLN cc_start: 0.7373 (mm110) cc_final: 0.6902 (pm20) REVERT: B 120 GLU cc_start: 0.8861 (tp30) cc_final: 0.8336 (tt0) REVERT: B 376 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7145 (mp0) REVERT: B 417 MET cc_start: 0.5514 (mmt) cc_final: 0.5094 (ttt) REVERT: B 440 SER cc_start: 0.8165 (t) cc_final: 0.7873 (p) REVERT: B 444 ASN cc_start: 0.7865 (t0) cc_final: 0.7258 (m110) REVERT: B 446 PHE cc_start: 0.7412 (OUTLIER) cc_final: 0.7177 (m-10) REVERT: D 21 LYS cc_start: 0.8390 (tppt) cc_final: 0.7932 (tttt) REVERT: D 24 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6608 (mm-30) REVERT: D 86 VAL cc_start: 0.8596 (p) cc_final: 0.8207 (m) REVERT: D 132 TYR cc_start: 0.8025 (m-10) cc_final: 0.7726 (m-10) REVERT: D 157 MET cc_start: 0.6916 (mmm) cc_final: 0.6571 (mmm) REVERT: D 159 ARG cc_start: 0.5062 (mtt90) cc_final: 0.4409 (tpp-160) outliers start: 18 outliers final: 15 residues processed: 159 average time/residue: 0.2102 time to fit residues: 47.8641 Evaluate side-chains 154 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 SER 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 456 HIS Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 550 LEU 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 446 PHE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain D residue 35 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.171004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.152317 restraints weight = 17245.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.154767 restraints weight = 11144.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.156404 restraints weight = 8274.305| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.7214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10378 Z= 0.251 Angle : 0.634 9.573 14038 Z= 0.330 Chirality : 0.042 0.244 1556 Planarity : 0.004 0.043 1769 Dihedral : 4.487 24.440 1340 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.54 % Allowed : 17.60 % Favored : 79.86 % 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: 0.83 (0.24), residues: 1209 helix: 1.50 (0.18), residues: 848 sheet: -0.15 (1.54), residues: 14 loop : -1.84 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP A 412 HIS 0.004 0.001 HIS D 96 PHE 0.018 0.002 PHE B 590 TYR 0.016 0.002 TYR A 158 ARG 0.004 0.001 ARG B 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2022.02 seconds wall clock time: 36 minutes 55.58 seconds (2215.58 seconds total)