Starting phenix.real_space_refine on Thu Mar 14 23:52:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f07_4163/03_2024/6f07_4163.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f07_4163/03_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_4163/03_2024/6f07_4163.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f07_4163/03_2024/6f07_4163.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f07_4163/03_2024/6f07_4163.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f07_4163/03_2024/6f07_4163.pdb" } 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 Residue "B ARG 26": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.60, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.98 Conformation dependent library (CDL) restraints added in 1.8 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: 1.07 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: 2.87 Time building geometry restraints manager: 4.31 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: 99.06 - 106.06: 189 106.06 - 113.06: 5555 113.06 - 120.06: 3978 120.06 - 127.06: 4211 127.06 - 134.06: 105 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 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: 0.560 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: 3.600 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.710 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.480 ------------------------------------------------------------------------------- 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 : 1.247 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: 0.2728 time to fit residues: 109.4905 Evaluate side-chains 159 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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: 0.9980 chunk 92 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 399 GLN B 406 GLN B 445 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5637 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10378 Z= 0.172 Angle : 0.581 8.844 14038 Z= 0.310 Chirality : 0.038 0.192 1556 Planarity : 0.005 0.070 1769 Dihedral : 4.981 30.090 1341 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.45 % Allowed : 9.54 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.60 (0.23), residues: 1209 helix: 0.48 (0.17), residues: 835 sheet: 0.35 (1.74), residues: 14 loop : -2.49 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 412 HIS 0.022 0.001 HIS B 12 PHE 0.018 0.002 PHE A 117 TYR 0.020 0.001 TYR A 126 ARG 0.004 0.000 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 222 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 194 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 PHE cc_start: 0.6808 (t80) cc_final: 0.6231 (t80) REVERT: A 199 ASN cc_start: 0.7720 (m-40) cc_final: 0.7291 (m-40) REVERT: A 255 SER cc_start: 0.7763 (m) cc_final: 0.7303 (p) REVERT: A 376 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7662 (tp30) REVERT: A 387 LEU cc_start: 0.7593 (mt) cc_final: 0.7255 (mp) REVERT: A 399 GLN cc_start: 0.8367 (tt0) cc_final: 0.8015 (pp30) REVERT: A 473 TYR cc_start: 0.6722 (t80) cc_final: 0.6123 (t80) REVERT: A 517 LEU cc_start: 0.7703 (tp) cc_final: 0.7215 (mt) REVERT: A 560 LYS cc_start: 0.7597 (mttt) cc_final: 0.6920 (ttpt) REVERT: B 9 LYS cc_start: 0.6466 (mtmm) cc_final: 0.5573 (tttp) REVERT: B 11 LYS cc_start: 0.6110 (pttt) cc_final: 0.5089 (mttp) REVERT: B 43 MET cc_start: 0.7631 (mmm) cc_final: 0.7095 (tpt) REVERT: B 102 TRP cc_start: 0.4503 (m100) cc_final: 0.3616 (t-100) REVERT: B 204 MET cc_start: 0.5030 (mtp) cc_final: 0.4802 (mtp) REVERT: B 226 MET cc_start: 0.6263 (mtm) cc_final: 0.6044 (mtt) REVERT: B 376 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7004 (mm-30) REVERT: B 426 ASP cc_start: 0.7881 (t0) cc_final: 0.6936 (t0) REVERT: B 440 SER cc_start: 0.8039 (t) cc_final: 0.7635 (p) REVERT: B 444 ASN cc_start: 0.7323 (t0) cc_final: 0.6715 (m-40) REVERT: B 591 ARG cc_start: 0.6496 (ttm-80) cc_final: 0.5880 (ttp-170) REVERT: D 21 LYS cc_start: 0.8331 (mmmt) cc_final: 0.7851 (mmtm) REVERT: D 24 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6290 (mm-30) REVERT: D 77 MET cc_start: 0.7388 (ttp) cc_final: 0.7138 (ttp) REVERT: D 159 ARG cc_start: 0.4362 (mtt90) cc_final: 0.3935 (tpp-160) outliers start: 28 outliers final: 14 residues processed: 210 average time/residue: 0.2341 time to fit residues: 67.6174 Evaluate side-chains 150 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 136 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 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 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 61 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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** B 104 ASN B 228 HIS B 303 GLN B 433 HIS B 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5742 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10378 Z= 0.192 Angle : 0.569 8.753 14038 Z= 0.301 Chirality : 0.039 0.151 1556 Planarity : 0.005 0.059 1769 Dihedral : 4.595 27.979 1340 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.71 % Allowed : 11.30 % 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: 0.11 (0.24), residues: 1209 helix: 1.02 (0.18), residues: 855 sheet: 0.13 (1.69), residues: 14 loop : -2.40 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 412 HIS 0.003 0.001 HIS D 96 PHE 0.014 0.002 PHE B 415 TYR 0.019 0.002 TYR A 126 ARG 0.004 0.001 ARG D 121 *********************** 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 198 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 167 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASN cc_start: 0.7663 (m-40) cc_final: 0.7411 (m-40) REVERT: A 204 MET cc_start: 0.3549 (mmt) cc_final: 0.3339 (tpp) REVERT: A 255 SER cc_start: 0.7925 (m) cc_final: 0.7590 (p) REVERT: A 376 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7503 (tp30) REVERT: A 377 LEU cc_start: 0.7670 (tp) cc_final: 0.7053 (mt) REVERT: A 387 LEU cc_start: 0.7809 (mt) cc_final: 0.7505 (mp) REVERT: A 399 GLN cc_start: 0.8502 (tt0) cc_final: 0.8058 (pp30) REVERT: A 595 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7740 (tp30) REVERT: B 9 LYS cc_start: 0.5944 (mtmm) cc_final: 0.5013 (tttp) REVERT: B 11 LYS cc_start: 0.6321 (pttt) cc_final: 0.5040 (mttp) REVERT: B 43 MET cc_start: 0.7689 (mmm) cc_final: 0.7135 (tpt) REVERT: B 102 TRP cc_start: 0.4513 (m100) cc_final: 0.4051 (m100) REVERT: B 158 TYR cc_start: 0.6772 (OUTLIER) cc_final: 0.6010 (m-10) REVERT: B 184 SER cc_start: 0.6980 (t) cc_final: 0.6520 (p) REVERT: B 316 VAL cc_start: 0.6231 (OUTLIER) cc_final: 0.5794 (m) REVERT: B 376 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7087 (mm-30) REVERT: B 417 MET cc_start: 0.5733 (mmt) cc_final: 0.4979 (ttm) REVERT: B 440 SER cc_start: 0.8189 (t) cc_final: 0.7860 (p) REVERT: B 444 ASN cc_start: 0.7385 (t0) cc_final: 0.6831 (m110) REVERT: B 458 MET cc_start: 0.3983 (OUTLIER) cc_final: 0.3690 (ptp) REVERT: B 543 ASN cc_start: 0.7059 (OUTLIER) cc_final: 0.6666 (m-40) REVERT: D 24 GLU cc_start: 0.7474 (mt-10) cc_final: 0.6754 (mm-30) REVERT: D 127 ASP cc_start: 0.6770 (p0) cc_final: 0.5270 (t0) REVERT: D 128 GLN cc_start: 0.5879 (tp-100) cc_final: 0.5600 (tp-100) REVERT: D 130 MET cc_start: 0.6196 (tpp) cc_final: 0.5901 (tpp) REVERT: D 159 ARG cc_start: 0.4559 (mtt90) cc_final: 0.3945 (tpp-160) outliers start: 31 outliers final: 16 residues processed: 191 average time/residue: 0.2142 time to fit residues: 56.1031 Evaluate side-chains 152 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 302 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 B residue 158 TYR 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 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 543 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.2980 chunk 57 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN D 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5774 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10378 Z= 0.196 Angle : 0.561 7.367 14038 Z= 0.296 Chirality : 0.039 0.124 1556 Planarity : 0.004 0.046 1769 Dihedral : 4.412 25.022 1340 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.89 % Allowed : 12.96 % Favored : 84.15 % 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: 0.48 (0.25), residues: 1209 helix: 1.28 (0.18), residues: 853 sheet: -0.11 (1.64), residues: 14 loop : -2.18 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 412 HIS 0.004 0.001 HIS B 189 PHE 0.020 0.002 PHE A 476 TYR 0.022 0.002 TYR A 158 ARG 0.004 0.000 ARG B 146 *********************** 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 190 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 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 200 TRP cc_start: 0.4607 (m100) cc_final: 0.4055 (m100) REVERT: A 204 MET cc_start: 0.3632 (mmt) cc_final: 0.3405 (tpp) REVERT: A 376 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7496 (tp30) REVERT: A 387 LEU cc_start: 0.7861 (mt) cc_final: 0.7578 (mp) REVERT: A 399 GLN cc_start: 0.8524 (tt0) cc_final: 0.8045 (pp30) REVERT: A 595 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7765 (tp30) REVERT: B 7 GLN cc_start: 0.6782 (mm110) cc_final: 0.6566 (mm110) REVERT: B 11 LYS cc_start: 0.5210 (pttt) cc_final: 0.3962 (mttp) REVERT: B 43 MET cc_start: 0.7575 (mmm) cc_final: 0.6907 (tpt) REVERT: B 102 TRP cc_start: 0.4027 (m100) cc_final: 0.3766 (m100) REVERT: B 120 GLU cc_start: 0.9022 (tp30) cc_final: 0.8430 (tt0) REVERT: B 184 SER cc_start: 0.6619 (t) cc_final: 0.6249 (p) REVERT: B 316 VAL cc_start: 0.6246 (OUTLIER) cc_final: 0.5810 (m) REVERT: B 376 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7118 (mp0) REVERT: B 417 MET cc_start: 0.5637 (mmt) cc_final: 0.5024 (ttt) REVERT: B 440 SER cc_start: 0.8236 (t) cc_final: 0.7847 (p) REVERT: B 444 ASN cc_start: 0.7439 (t0) cc_final: 0.6895 (m110) REVERT: B 458 MET cc_start: 0.4112 (OUTLIER) cc_final: 0.3883 (ptp) REVERT: B 591 ARG cc_start: 0.7029 (ttm-80) cc_final: 0.6701 (ttp-170) REVERT: D 21 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7686 (mmtm) REVERT: D 24 GLU cc_start: 0.7662 (mt-10) cc_final: 0.6715 (mm-30) REVERT: D 31 ASN cc_start: 0.7077 (OUTLIER) cc_final: 0.6812 (p0) REVERT: D 77 MET cc_start: 0.7043 (ttt) cc_final: 0.6748 (ttt) REVERT: D 128 GLN cc_start: 0.5917 (tp-100) cc_final: 0.5045 (tp-100) REVERT: D 132 TYR cc_start: 0.7611 (m-10) cc_final: 0.7145 (m-10) REVERT: D 159 ARG cc_start: 0.4938 (mtt90) cc_final: 0.4305 (tpp-160) outliers start: 33 outliers final: 21 residues processed: 182 average time/residue: 0.2072 time to fit residues: 53.3389 Evaluate side-chains 161 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 137 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 356 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 531 ASP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 30 CYS 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 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 532 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: 0.9990 chunk 1 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 81 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5761 moved from start: 0.5933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10378 Z= 0.161 Angle : 0.531 8.581 14038 Z= 0.277 Chirality : 0.038 0.231 1556 Planarity : 0.004 0.045 1769 Dihedral : 4.220 24.786 1340 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.89 % Allowed : 14.36 % Favored : 82.75 % 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: 852 sheet: -0.04 (1.57), residues: 14 loop : -2.02 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP A 412 HIS 0.003 0.001 HIS D 96 PHE 0.019 0.001 PHE A 476 TYR 0.018 0.001 TYR A 509 ARG 0.005 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 192 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 159 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TRP cc_start: 0.6544 (m100) cc_final: 0.6210 (m100) REVERT: A 200 TRP cc_start: 0.4631 (m100) cc_final: 0.4206 (m100) REVERT: A 387 LEU cc_start: 0.7874 (mt) cc_final: 0.7611 (mp) REVERT: A 399 GLN cc_start: 0.8599 (tt0) cc_final: 0.8086 (pp30) REVERT: A 595 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7762 (tp30) REVERT: B 11 LYS cc_start: 0.6040 (pttt) cc_final: 0.4817 (mttp) REVERT: B 43 MET cc_start: 0.7531 (mmm) cc_final: 0.6903 (tpt) REVERT: B 120 GLU cc_start: 0.9009 (tp30) cc_final: 0.8413 (tt0) REVERT: B 184 SER cc_start: 0.6534 (t) cc_final: 0.6222 (p) REVERT: B 316 VAL cc_start: 0.6110 (OUTLIER) cc_final: 0.5789 (m) REVERT: B 376 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7044 (mp0) REVERT: B 417 MET cc_start: 0.5508 (mmt) cc_final: 0.5113 (ttt) REVERT: B 426 ASP cc_start: 0.8110 (t0) cc_final: 0.7056 (t0) REVERT: B 440 SER cc_start: 0.8183 (t) cc_final: 0.7883 (p) REVERT: B 444 ASN cc_start: 0.7442 (t0) cc_final: 0.6972 (m110) REVERT: B 458 MET cc_start: 0.4126 (OUTLIER) cc_final: 0.3861 (ptp) REVERT: D 21 LYS cc_start: 0.8059 (mmtt) cc_final: 0.7558 (mmtm) REVERT: D 24 GLU cc_start: 0.7533 (mt-10) cc_final: 0.6468 (mm-30) REVERT: D 31 ASN cc_start: 0.7090 (OUTLIER) cc_final: 0.6804 (p0) REVERT: D 77 MET cc_start: 0.7199 (ttt) cc_final: 0.6776 (ttt) REVERT: D 128 GLN cc_start: 0.5880 (tp-100) cc_final: 0.5320 (tp40) REVERT: D 132 TYR cc_start: 0.7732 (m-10) cc_final: 0.7275 (m-10) REVERT: D 159 ARG cc_start: 0.5027 (mtt90) cc_final: 0.4332 (tpp-160) outliers start: 33 outliers final: 23 residues processed: 182 average time/residue: 0.2165 time to fit residues: 55.9349 Evaluate side-chains 166 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 153 SER 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 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 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 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 459 VAL Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 35 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 118 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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** B 66 GLN B 205 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN B 445 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5759 moved from start: 0.6230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10378 Z= 0.155 Angle : 0.514 7.023 14038 Z= 0.270 Chirality : 0.038 0.248 1556 Planarity : 0.004 0.043 1769 Dihedral : 4.136 25.851 1340 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.98 % Allowed : 14.71 % 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: 1.02 (0.25), residues: 1209 helix: 1.67 (0.18), residues: 854 sheet: 0.21 (1.60), residues: 14 loop : -1.95 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP A 412 HIS 0.002 0.000 HIS D 96 PHE 0.024 0.001 PHE A 476 TYR 0.019 0.001 TYR A 509 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 185 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 151 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TRP cc_start: 0.4501 (m100) cc_final: 0.4210 (m100) REVERT: A 387 LEU cc_start: 0.7787 (mt) cc_final: 0.7535 (mp) REVERT: A 460 MET cc_start: 0.3903 (OUTLIER) cc_final: 0.3588 (ttm) REVERT: A 474 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7873 (pt0) REVERT: A 500 PHE cc_start: 0.5453 (m-80) cc_final: 0.5173 (m-80) REVERT: A 595 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7757 (tp30) REVERT: B 43 MET cc_start: 0.7502 (mmm) cc_final: 0.6881 (tpt) REVERT: B 120 GLU cc_start: 0.9037 (tp30) cc_final: 0.8476 (tt0) REVERT: B 266 ASN cc_start: 0.6778 (t0) cc_final: 0.6454 (t0) REVERT: B 376 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7174 (mp0) REVERT: B 417 MET cc_start: 0.5520 (mmt) cc_final: 0.4923 (ttm) REVERT: B 426 ASP cc_start: 0.8074 (t70) cc_final: 0.7605 (t70) REVERT: B 440 SER cc_start: 0.8164 (t) cc_final: 0.7869 (p) REVERT: B 444 ASN cc_start: 0.7849 (t0) cc_final: 0.7225 (m110) REVERT: B 446 PHE cc_start: 0.7240 (OUTLIER) cc_final: 0.7024 (m-10) REVERT: B 591 ARG cc_start: 0.7043 (ttm-80) cc_final: 0.6685 (ttp-170) REVERT: D 21 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7507 (mmtm) REVERT: D 24 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6404 (mm-30) REVERT: D 31 ASN cc_start: 0.7099 (OUTLIER) cc_final: 0.6761 (p0) REVERT: D 77 MET cc_start: 0.7220 (ttt) cc_final: 0.6789 (ttt) REVERT: D 128 GLN cc_start: 0.5845 (tp-100) cc_final: 0.5131 (tp40) REVERT: D 132 TYR cc_start: 0.7736 (m-10) cc_final: 0.7250 (m-10) REVERT: D 159 ARG cc_start: 0.5010 (mtt90) cc_final: 0.4332 (tpp-160) outliers start: 34 outliers final: 27 residues processed: 174 average time/residue: 0.2026 time to fit residues: 50.8611 Evaluate side-chains 171 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 140 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE 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 424 THR Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 474 GLN 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 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 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 470 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 35 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5757 moved from start: 0.6471 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= 0.152 Angle : 0.509 8.664 14038 Z= 0.268 Chirality : 0.038 0.248 1556 Planarity : 0.004 0.042 1769 Dihedral : 4.038 26.168 1340 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.33 % Allowed : 14.71 % Favored : 81.96 % 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: 1.12 (0.25), residues: 1209 helix: 1.74 (0.18), residues: 854 sheet: 0.51 (1.59), residues: 14 loop : -1.90 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP A 412 HIS 0.003 0.001 HIS D 96 PHE 0.022 0.001 PHE A 476 TYR 0.019 0.001 TYR A 509 ARG 0.004 0.000 ARG A 83 *********************** 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 185 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 147 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TRP cc_start: 0.4471 (m100) cc_final: 0.4212 (m100) REVERT: A 387 LEU cc_start: 0.7740 (mt) cc_final: 0.7491 (mp) REVERT: A 460 MET cc_start: 0.3899 (OUTLIER) cc_final: 0.3547 (ttm) REVERT: A 500 PHE cc_start: 0.5721 (m-80) cc_final: 0.5216 (m-80) REVERT: A 595 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7781 (tp30) REVERT: B 7 GLN cc_start: 0.6825 (mm110) cc_final: 0.6424 (mm110) REVERT: B 11 LYS cc_start: 0.6247 (pttt) cc_final: 0.5294 (ptpt) REVERT: B 27 MET cc_start: 0.7135 (mmp) cc_final: 0.6610 (mmm) REVERT: B 43 MET cc_start: 0.7479 (mmm) cc_final: 0.6861 (tpt) REVERT: B 120 GLU cc_start: 0.9028 (tp30) cc_final: 0.8470 (tt0) REVERT: B 266 ASN cc_start: 0.6782 (t0) cc_final: 0.6455 (t0) REVERT: B 376 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7184 (mp0) REVERT: B 417 MET cc_start: 0.5527 (mmt) cc_final: 0.5077 (ttm) REVERT: B 440 SER cc_start: 0.8152 (t) cc_final: 0.7836 (p) REVERT: B 444 ASN cc_start: 0.7851 (t0) cc_final: 0.7224 (m-40) REVERT: B 446 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.7081 (m-10) REVERT: B 458 MET cc_start: 0.4000 (OUTLIER) cc_final: 0.3744 (ptp) REVERT: B 591 ARG cc_start: 0.7030 (ttm-80) cc_final: 0.6698 (ttp-170) REVERT: D 21 LYS cc_start: 0.7989 (mmtt) cc_final: 0.7471 (mmtm) REVERT: D 24 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6556 (tp30) REVERT: D 31 ASN cc_start: 0.7135 (OUTLIER) cc_final: 0.6831 (p0) REVERT: D 77 MET cc_start: 0.7300 (ttt) cc_final: 0.6849 (ttt) REVERT: D 128 GLN cc_start: 0.5879 (tp-100) cc_final: 0.5529 (tp40) REVERT: D 159 ARG cc_start: 0.4985 (mtt90) cc_final: 0.4305 (tpp-160) outliers start: 38 outliers final: 30 residues processed: 175 average time/residue: 0.2072 time to fit residues: 52.5196 Evaluate side-chains 175 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 141 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 255 SER 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 460 MET 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 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 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 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 470 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 35 ASP 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: 4.9990 chunk 70 optimal weight: 10.0000 chunk 35 optimal weight: 0.2980 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5813 moved from start: 0.6748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10378 Z= 0.207 Angle : 0.580 11.607 14038 Z= 0.303 Chirality : 0.040 0.239 1556 Planarity : 0.004 0.045 1769 Dihedral : 4.285 26.464 1340 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.33 % Allowed : 15.85 % Favored : 80.82 % 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: 0.92 (0.25), residues: 1209 helix: 1.59 (0.18), residues: 854 sheet: 0.25 (1.51), residues: 14 loop : -1.97 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.002 TRP A 412 HIS 0.004 0.001 HIS D 96 PHE 0.019 0.002 PHE A 476 TYR 0.020 0.002 TYR A 509 ARG 0.003 0.000 ARG B 146 *********************** 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 184 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 146 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TRP cc_start: 0.4516 (m100) cc_final: 0.4273 (m100) REVERT: A 387 LEU cc_start: 0.7759 (mt) cc_final: 0.7550 (mt) REVERT: A 436 LYS cc_start: 0.8396 (mmmt) cc_final: 0.7981 (mttm) REVERT: A 460 MET cc_start: 0.3758 (OUTLIER) cc_final: 0.3147 (ttp) REVERT: A 500 PHE cc_start: 0.5780 (m-80) cc_final: 0.5284 (m-80) REVERT: A 539 LYS cc_start: 0.5758 (tptt) cc_final: 0.5553 (tptt) REVERT: A 595 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7801 (tp30) REVERT: B 11 LYS cc_start: 0.6850 (pttt) cc_final: 0.5922 (ptpt) REVERT: B 43 MET cc_start: 0.7489 (mmm) cc_final: 0.6911 (tpt) REVERT: B 120 GLU cc_start: 0.8945 (tp30) cc_final: 0.8488 (tt0) REVERT: B 184 SER cc_start: 0.6638 (t) cc_final: 0.6344 (p) REVERT: B 376 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7150 (mp0) REVERT: B 417 MET cc_start: 0.5615 (mmt) cc_final: 0.5118 (ttm) REVERT: B 440 SER cc_start: 0.8096 (t) cc_final: 0.7769 (p) REVERT: B 444 ASN cc_start: 0.7754 (t0) cc_final: 0.7264 (m110) REVERT: B 446 PHE cc_start: 0.7409 (OUTLIER) cc_final: 0.7206 (m-10) REVERT: B 458 MET cc_start: 0.4082 (OUTLIER) cc_final: 0.3865 (ptp) REVERT: B 591 ARG cc_start: 0.7019 (ttm-80) cc_final: 0.6624 (ttp-170) REVERT: D 21 LYS cc_start: 0.7936 (mmtt) cc_final: 0.7442 (mmtm) REVERT: D 24 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6587 (tp30) REVERT: D 31 ASN cc_start: 0.7069 (OUTLIER) cc_final: 0.6842 (p0) REVERT: D 77 MET cc_start: 0.7373 (ttt) cc_final: 0.6917 (ttt) REVERT: D 159 ARG cc_start: 0.5195 (mtt90) cc_final: 0.4454 (tpp-160) outliers start: 38 outliers final: 33 residues processed: 174 average time/residue: 0.2092 time to fit residues: 51.7559 Evaluate side-chains 172 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 135 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE 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 255 SER 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 460 MET 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 84 ASP 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 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 22 ILE Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 35 ASP 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: 0.1980 chunk 102 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 86 optimal weight: 0.0870 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 115 optimal weight: 0.1980 overall best weight: 0.8960 ------------------------------------------------------------------------------- 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** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5769 moved from start: 0.6878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10378 Z= 0.153 Angle : 0.533 10.343 14038 Z= 0.277 Chirality : 0.038 0.256 1556 Planarity : 0.004 0.042 1769 Dihedral : 4.104 27.254 1340 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.89 % Allowed : 16.64 % Favored : 80.47 % 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: 1.71 (0.18), residues: 854 sheet: 0.60 (1.49), residues: 14 loop : -1.85 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 412 HIS 0.003 0.001 HIS D 96 PHE 0.026 0.001 PHE A 476 TYR 0.014 0.001 TYR A 158 ARG 0.003 0.000 ARG B 146 *********************** 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 179 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 146 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TRP cc_start: 0.4489 (m100) cc_final: 0.4250 (m100) REVERT: A 377 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7072 (mt) REVERT: A 387 LEU cc_start: 0.7792 (mt) cc_final: 0.7588 (mt) REVERT: A 436 LYS cc_start: 0.8412 (mmmt) cc_final: 0.8013 (mttp) REVERT: A 460 MET cc_start: 0.3831 (OUTLIER) cc_final: 0.3490 (ttm) REVERT: A 500 PHE cc_start: 0.5739 (m-80) cc_final: 0.5255 (m-80) REVERT: A 595 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7790 (tp30) REVERT: B 11 LYS cc_start: 0.6896 (pttt) cc_final: 0.5970 (ptpt) REVERT: B 43 MET cc_start: 0.7431 (mmm) cc_final: 0.6812 (tpt) REVERT: B 120 GLU cc_start: 0.8944 (tp30) cc_final: 0.8428 (tt0) REVERT: B 266 ASN cc_start: 0.6745 (t0) cc_final: 0.6430 (t0) REVERT: B 376 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7048 (mp0) REVERT: B 417 MET cc_start: 0.5490 (mmt) cc_final: 0.5048 (ttm) REVERT: B 440 SER cc_start: 0.8129 (t) cc_final: 0.7811 (p) REVERT: B 444 ASN cc_start: 0.7746 (t0) cc_final: 0.7245 (m-40) REVERT: B 458 MET cc_start: 0.3961 (OUTLIER) cc_final: 0.3693 (ptp) REVERT: D 21 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7596 (mmtm) REVERT: D 24 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6575 (tp30) REVERT: D 31 ASN cc_start: 0.7128 (OUTLIER) cc_final: 0.6831 (p0) REVERT: D 77 MET cc_start: 0.7389 (ttt) cc_final: 0.6882 (ttt) REVERT: D 146 LEU cc_start: 0.7859 (tp) cc_final: 0.7488 (pp) REVERT: D 159 ARG cc_start: 0.4946 (mtt90) cc_final: 0.4226 (tpp-160) outliers start: 33 outliers final: 26 residues processed: 170 average time/residue: 0.2091 time to fit residues: 50.8984 Evaluate side-chains 174 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 144 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 255 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 460 MET Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 532 SER 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 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 458 MET Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 80 optimal weight: 0.6980 chunk 121 optimal weight: 10.0000 chunk 111 optimal weight: 0.0980 chunk 96 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5744 moved from start: 0.6992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10378 Z= 0.141 Angle : 0.533 11.139 14038 Z= 0.274 Chirality : 0.038 0.275 1556 Planarity : 0.004 0.041 1769 Dihedral : 3.992 27.182 1340 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.71 % Allowed : 16.73 % 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: 1.20 (0.25), residues: 1209 helix: 1.76 (0.18), residues: 854 sheet: 0.92 (1.50), residues: 14 loop : -1.77 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 412 HIS 0.003 0.000 HIS D 96 PHE 0.025 0.001 PHE A 476 TYR 0.029 0.001 TYR A 143 ARG 0.004 0.000 ARG A 83 ********************** 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 189 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 158 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TRP cc_start: 0.4435 (m100) cc_final: 0.4195 (m100) REVERT: A 377 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7101 (mt) REVERT: A 436 LYS cc_start: 0.8407 (mmmt) cc_final: 0.7936 (mtmm) REVERT: A 460 MET cc_start: 0.3780 (OUTLIER) cc_final: 0.3457 (ttm) REVERT: A 500 PHE cc_start: 0.5791 (m-80) cc_final: 0.5221 (m-80) REVERT: A 591 ARG cc_start: 0.6740 (mpt180) cc_final: 0.6513 (mpp-170) REVERT: A 595 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7779 (tp30) REVERT: B 43 MET cc_start: 0.7400 (mmm) cc_final: 0.6795 (tpt) REVERT: B 120 GLU cc_start: 0.8932 (tp30) cc_final: 0.8430 (tt0) REVERT: B 177 GLU cc_start: 0.6738 (pp20) cc_final: 0.5797 (tp30) REVERT: B 266 ASN cc_start: 0.6655 (t0) cc_final: 0.6366 (t0) REVERT: B 376 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7161 (mp0) REVERT: B 417 MET cc_start: 0.5426 (mmt) cc_final: 0.4996 (ttm) REVERT: B 440 SER cc_start: 0.8182 (t) cc_final: 0.7875 (p) REVERT: B 444 ASN cc_start: 0.7784 (t0) cc_final: 0.7178 (m-40) REVERT: B 458 MET cc_start: 0.3924 (OUTLIER) cc_final: 0.3655 (ptp) REVERT: D 21 LYS cc_start: 0.8005 (mmtt) cc_final: 0.7496 (mmtm) REVERT: D 24 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6563 (tp30) REVERT: D 31 ASN cc_start: 0.7169 (OUTLIER) cc_final: 0.6817 (p0) REVERT: D 33 LEU cc_start: 0.8493 (tp) cc_final: 0.7867 (tp) REVERT: D 77 MET cc_start: 0.7341 (ttt) cc_final: 0.6913 (ttt) REVERT: D 159 ARG cc_start: 0.4893 (mtt90) cc_final: 0.4264 (tpp-160) outliers start: 31 outliers final: 24 residues processed: 180 average time/residue: 0.2067 time to fit residues: 53.0053 Evaluate side-chains 169 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 141 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 460 MET 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 84 ASP 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 426 ASP Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain D residue 31 ASN 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: 0.9990 chunk 89 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 0.0670 chunk 5 optimal weight: 6.9990 overall best weight: 1.5724 ------------------------------------------------------------------------------- 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** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 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 = 0.4278 r_free = 0.4278 target = 0.174244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.155312 restraints weight = 17040.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.157913 restraints weight = 10661.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.159710 restraints weight = 7751.481| |-----------------------------------------------------------------------------| r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.7117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10378 Z= 0.196 Angle : 0.589 10.248 14038 Z= 0.302 Chirality : 0.040 0.259 1556 Planarity : 0.004 0.042 1769 Dihedral : 4.169 27.072 1340 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.63 % Allowed : 18.48 % Favored : 78.90 % 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: 1.65 (0.18), residues: 855 sheet: 0.55 (1.44), residues: 14 loop : -1.85 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 412 HIS 0.004 0.001 HIS D 96 PHE 0.023 0.002 PHE A 476 TYR 0.022 0.002 TYR A 143 ARG 0.003 0.000 ARG A 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2014.76 seconds wall clock time: 37 minutes 7.07 seconds (2227.07 seconds total)