Starting phenix.real_space_refine on Mon Aug 5 17:30:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wh8_37533/08_2024/8wh8_37533.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wh8_37533/08_2024/8wh8_37533.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/8wh8_37533/08_2024/8wh8_37533.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wh8_37533/08_2024/8wh8_37533.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wh8_37533/08_2024/8wh8_37533.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wh8_37533/08_2024/8wh8_37533.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= 0.003 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 P 252 5.49 5 S 29 5.16 5 C 8263 2.51 5 N 2636 2.21 5 O 3124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 14304 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 766 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "B" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 617 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "C" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 662 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 3, 'TRANS': 84} Chain: "D" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 694 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "E" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 695 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "F" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 710 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "G" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 700 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "H" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 716 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "I" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2544 Classifications: {'DNA': 125} Link IDs: {'rna3p': 124} Chain: "J" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2581 Classifications: {'DNA': 125} Link IDs: {'rna3p': 124} Chain: "K" Number of atoms: 3592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3592 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 16, 'TRANS': 426} Chain breaks: 1 Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.06, per 1000 atoms: 0.56 Number of scatterers: 14304 At special positions: 0 Unit cell: (131.76, 138.24, 117.72, 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) S 29 16.00 P 252 15.00 O 3124 8.00 N 2636 7.00 C 8263 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 7.46 Conformation dependent library (CDL) restraints added in 1.7 seconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 10 sheets defined 63.6% alpha, 4.4% beta 99 base pairs and 194 stacking pairs defined. Time for finding SS restraints: 6.32 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.524A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN A 55 " --> pdb=" O ILE A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.911A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.804A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.918A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.566A pdb=" N GLY B 28 " --> pdb=" O ASN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.055A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 38 through 40 No H-bonds generated for 'chain 'C' and resid 38 through 40' Processing helix chain 'C' and resid 46 through 75 removed outlier: 4.081A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 removed outlier: 3.625A pdb=" N ILE C 84 " --> pdb=" O VAL C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 98 Processing helix chain 'D' and resid 62 through 74 Processing helix chain 'D' and resid 80 through 109 removed outlier: 3.522A pdb=" N MET D 84 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 127 removed outlier: 3.604A pdb=" N ILE D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 149 removed outlier: 3.822A pdb=" N SER D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 55 Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 87 through 114 removed outlier: 3.680A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.711A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 40 Processing helix chain 'F' and resid 50 through 75 removed outlier: 4.243A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL F 57 " --> pdb=" O GLU F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.961A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 38 Processing helix chain 'G' and resid 46 through 75 removed outlier: 4.423A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG G 72 " --> pdb=" O GLY G 68 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP G 73 " --> pdb=" O ASN G 69 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.511A pdb=" N ILE G 84 " --> pdb=" O VAL G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 98 Processing helix chain 'H' and resid 62 through 74 removed outlier: 3.702A pdb=" N LYS H 68 " --> pdb=" O ILE H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 109 removed outlier: 3.553A pdb=" N MET H 87 " --> pdb=" O ALA H 83 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER H 89 " --> pdb=" O GLY H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 126 Processing helix chain 'H' and resid 129 through 148 removed outlier: 3.926A pdb=" N LYS H 133 " --> pdb=" O GLY H 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 204 through 220 Processing helix chain 'K' and resid 234 through 244 Processing helix chain 'K' and resid 258 through 272 removed outlier: 3.919A pdb=" N LEU K 262 " --> pdb=" O PRO K 258 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 294 removed outlier: 3.957A pdb=" N GLU K 290 " --> pdb=" O ASN K 286 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG K 292 " --> pdb=" O ARG K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 310 through 317 Processing helix chain 'K' and resid 317 through 323 removed outlier: 4.068A pdb=" N ILE K 321 " --> pdb=" O ASP K 317 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG K 323 " --> pdb=" O LYS K 319 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 339 Processing helix chain 'K' and resid 343 through 352 removed outlier: 3.874A pdb=" N HIS K 351 " --> pdb=" O ARG K 347 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU K 352 " --> pdb=" O GLU K 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 369 through 380 Processing helix chain 'K' and resid 416 through 425 removed outlier: 3.651A pdb=" N ILE K 423 " --> pdb=" O LYS K 419 " (cutoff:3.500A) Processing helix chain 'K' and resid 453 through 465 Processing helix chain 'K' and resid 488 through 499 Processing helix chain 'K' and resid 500 through 508 Processing helix chain 'K' and resid 518 through 522 Processing helix chain 'K' and resid 523 through 536 Processing helix chain 'K' and resid 550 through 564 removed outlier: 3.564A pdb=" N LYS K 563 " --> pdb=" O TYR K 559 " (cutoff:3.500A) Processing helix chain 'K' and resid 575 through 587 Processing helix chain 'K' and resid 623 through 635 removed outlier: 4.161A pdb=" N ASP K 627 " --> pdb=" O ASN K 623 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS K 634 " --> pdb=" O ALA K 630 " (cutoff:3.500A) Processing helix chain 'K' and resid 653 through 676 removed outlier: 3.654A pdb=" N VAL K 672 " --> pdb=" O LEU K 668 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN K 675 " --> pdb=" O VAL K 671 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY K 676 " --> pdb=" O VAL K 672 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.148A pdb=" N ARG A 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.462A pdb=" N ARG B 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.400A pdb=" N ARG C 43 " --> pdb=" O ILE D 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'F' and resid 97 through 98 removed outlier: 3.696A pdb=" N TYR F 98 " --> pdb=" O THR G 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.507A pdb=" N ARG G 43 " --> pdb=" O ILE H 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'K' and resid 278 through 280 removed outlier: 6.609A pdb=" N ILE K 279 " --> pdb=" O ILE K 308 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU K 254 " --> pdb=" O VAL K 331 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 443 through 450 removed outlier: 3.586A pdb=" N MET K 448 " --> pdb=" O ARG K 647 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER K 649 " --> pdb=" O MET K 448 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N CYS K 615 " --> pdb=" O TYR K 646 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU K 648 " --> pdb=" O CYS K 615 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU K 617 " --> pdb=" O LEU K 648 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N THR K 650 " --> pdb=" O LEU K 617 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU K 544 " --> pdb=" O ILE K 616 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 567 through 570 removed outlier: 6.350A pdb=" N CYS K 568 " --> pdb=" O LEU K 597 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 500 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 256 hydrogen bonds 508 hydrogen bond angles 0 basepair planarities 99 basepair parallelities 194 stacking parallelities Total time for adding SS restraints: 6.27 Time building geometry restraints manager: 7.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1702 1.28 - 1.42: 4706 1.42 - 1.55: 7948 1.55 - 1.69: 671 1.69 - 1.82: 48 Bond restraints: 15075 Sorted by residual: bond pdb=" C SER K 653 " pdb=" O SER K 653 " ideal model delta sigma weight residual 1.235 1.316 -0.081 1.02e-02 9.61e+03 6.26e+01 bond pdb=" C ILE K 235 " pdb=" O ILE K 235 " ideal model delta sigma weight residual 1.236 1.142 0.094 1.19e-02 7.06e+03 6.23e+01 bond pdb=" C VAL H 136 " pdb=" O VAL H 136 " ideal model delta sigma weight residual 1.237 1.148 0.089 1.14e-02 7.69e+03 6.04e+01 bond pdb=" N ASN K 222 " pdb=" CA ASN K 222 " ideal model delta sigma weight residual 1.457 1.538 -0.081 1.29e-02 6.01e+03 3.92e+01 bond pdb=" C4 ADP K 801 " pdb=" C5 ADP K 801 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 ... (remaining 15070 not shown) Histogram of bond angle deviations from ideal: 97.59 - 104.93: 1120 104.93 - 112.27: 7841 112.27 - 119.61: 5609 119.61 - 126.95: 6210 126.95 - 134.29: 636 Bond angle restraints: 21416 Sorted by residual: angle pdb=" O3' DC I 107 " pdb=" C3' DC I 107 " pdb=" C2' DC I 107 " ideal model delta sigma weight residual 111.50 126.73 -15.23 1.50e+00 4.44e-01 1.03e+02 angle pdb=" O3' DT J 50 " pdb=" C3' DT J 50 " pdb=" C2' DT J 50 " ideal model delta sigma weight residual 111.50 125.51 -14.01 1.50e+00 4.44e-01 8.73e+01 angle pdb=" N ARG F 17 " pdb=" CA ARG F 17 " pdb=" C ARG F 17 " ideal model delta sigma weight residual 111.14 101.23 9.91 1.08e+00 8.57e-01 8.41e+01 angle pdb=" N LEU K 259 " pdb=" CA LEU K 259 " pdb=" C LEU K 259 " ideal model delta sigma weight residual 111.14 119.57 -8.43 1.08e+00 8.57e-01 6.09e+01 angle pdb=" N LYS H 104 " pdb=" CA LYS H 104 " pdb=" C LYS H 104 " ideal model delta sigma weight residual 111.28 103.01 8.27 1.09e+00 8.42e-01 5.75e+01 ... (remaining 21411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.66: 7149 33.66 - 67.32: 1220 67.32 - 100.97: 32 100.97 - 134.63: 4 134.63 - 168.29: 5 Dihedral angle restraints: 8410 sinusoidal: 5091 harmonic: 3319 Sorted by residual: dihedral pdb=" O2A ADP K 801 " pdb=" O3A ADP K 801 " pdb=" PA ADP K 801 " pdb=" PB ADP K 801 " ideal model delta sinusoidal sigma weight residual 300.00 164.37 135.63 1 2.00e+01 2.50e-03 4.12e+01 dihedral pdb=" C4' ADP K 801 " pdb=" C5' ADP K 801 " pdb=" O5' ADP K 801 " pdb=" PA ADP K 801 " ideal model delta sinusoidal sigma weight residual 180.00 92.83 87.17 1 2.00e+01 2.50e-03 2.28e+01 dihedral pdb=" CA VAL B 81 " pdb=" C VAL B 81 " pdb=" N THR B 82 " pdb=" CA THR B 82 " ideal model delta harmonic sigma weight residual -180.00 -157.38 -22.62 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 8407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 2317 0.148 - 0.295: 108 0.295 - 0.443: 1 0.443 - 0.590: 0 0.590 - 0.738: 2 Chirality restraints: 2428 Sorted by residual: chirality pdb=" C3' DT J 50 " pdb=" C4' DT J 50 " pdb=" O3' DT J 50 " pdb=" C2' DT J 50 " both_signs ideal model delta sigma weight residual False -2.66 -1.92 -0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" C3' DC I 107 " pdb=" C4' DC I 107 " pdb=" O3' DC I 107 " pdb=" C2' DC I 107 " both_signs ideal model delta sigma weight residual False -2.66 -1.96 -0.70 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" CA LEU K 372 " pdb=" N LEU K 372 " pdb=" C LEU K 372 " pdb=" CB LEU K 372 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 2425 not shown) Planarity restraints: 1833 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER H 148 " 0.024 2.00e-02 2.50e+03 4.73e-02 2.23e+01 pdb=" C SER H 148 " -0.082 2.00e-02 2.50e+03 pdb=" O SER H 148 " 0.030 2.00e-02 2.50e+03 pdb=" N SER H 149 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU K 376 " 0.021 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C LEU K 376 " -0.075 2.00e-02 2.50e+03 pdb=" O LEU K 376 " 0.028 2.00e-02 2.50e+03 pdb=" N ASN K 377 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN K 277 " -0.020 2.00e-02 2.50e+03 4.14e-02 1.71e+01 pdb=" C ASN K 277 " 0.072 2.00e-02 2.50e+03 pdb=" O ASN K 277 " -0.026 2.00e-02 2.50e+03 pdb=" N ALA K 278 " -0.025 2.00e-02 2.50e+03 ... (remaining 1830 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3714 2.82 - 3.34: 13538 3.34 - 3.86: 25280 3.86 - 4.38: 30863 4.38 - 4.90: 43590 Nonbonded interactions: 116985 Sorted by model distance: nonbonded pdb=" CG2 VAL K 516 " pdb=" CG1 ILE K 519 " model vdw 2.300 3.860 nonbonded pdb=" CD1 ILE B 50 " pdb=" CG2 ILE E 119 " model vdw 2.307 3.880 nonbonded pdb=" O SER K 547 " pdb=" OG1 THR K 600 " model vdw 2.311 3.040 nonbonded pdb=" OD1 ASN K 368 " pdb=" N SER K 370 " model vdw 2.319 3.120 nonbonded pdb=" O ASN K 466 " pdb=" OG1 THR K 467 " model vdw 2.325 3.040 ... (remaining 116980 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' and resid 50 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 25 through 100) selection = (chain 'F' and resid 25 through 100) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 21 through 108) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 61 through 149) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 47.520 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 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 : 0.013 0.109 15075 Z= 0.784 Angle : 1.397 15.230 21416 Z= 0.972 Chirality : 0.071 0.738 2428 Planarity : 0.008 0.047 1833 Dihedral : 25.117 168.290 6268 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.89 % Allowed : 7.44 % Favored : 91.67 % Rotamer: Outliers : 0.72 % Allowed : 6.86 % Favored : 92.43 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.21), residues: 1129 helix: -1.60 (0.17), residues: 677 sheet: -2.93 (0.58), residues: 62 loop : -3.03 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP K 217 HIS 0.016 0.002 HIS H 74 PHE 0.028 0.003 PHE D 67 TYR 0.040 0.003 TYR K 329 ARG 0.006 0.001 ARG K 430 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 326 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.6445 (m110) cc_final: 0.5761 (m-40) REVERT: C 65 GLU cc_start: 0.7509 (tp30) cc_final: 0.7297 (tp30) REVERT: C 75 LYS cc_start: 0.8499 (mttp) cc_final: 0.8234 (tmtt) REVERT: E 54 TYR cc_start: 0.8331 (m-80) cc_final: 0.7823 (m-80) REVERT: E 123 ASP cc_start: 0.8983 (m-30) cc_final: 0.8733 (m-30) REVERT: F 52 GLU cc_start: 0.7781 (tp30) cc_final: 0.7317 (tp30) REVERT: G 36 LYS cc_start: 0.9028 (ttmt) cc_final: 0.8702 (mtpt) REVERT: H 113 THR cc_start: 0.9186 (m) cc_final: 0.8891 (p) REVERT: H 141 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8211 (mtmt) REVERT: K 269 ILE cc_start: 0.8514 (tt) cc_final: 0.8306 (mt) REVERT: K 296 MET cc_start: 0.8179 (mtp) cc_final: 0.7514 (mmp) REVERT: K 432 MET cc_start: 0.6988 (mmm) cc_final: 0.6731 (tpt) REVERT: K 446 ILE cc_start: 0.7555 (mt) cc_final: 0.7058 (tp) REVERT: K 452 MET cc_start: 0.7877 (ttp) cc_final: 0.7651 (ttt) REVERT: K 626 MET cc_start: 0.8521 (mmt) cc_final: 0.8311 (mmm) REVERT: K 667 LYS cc_start: 0.6950 (mtpt) cc_final: 0.6737 (mptt) REVERT: K 669 GLU cc_start: 0.8623 (tp30) cc_final: 0.8340 (tp30) outliers start: 7 outliers final: 1 residues processed: 328 average time/residue: 0.3732 time to fit residues: 162.1243 Evaluate side-chains 169 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 211 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 0.0000 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 40 optimal weight: 20.0000 chunk 63 optimal weight: 0.6980 chunk 78 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN D 134 HIS K 206 GLN K 286 ASN K 366 GLN ** K 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 462 HIS ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15075 Z= 0.224 Angle : 0.663 10.272 21416 Z= 0.379 Chirality : 0.039 0.155 2428 Planarity : 0.005 0.038 1833 Dihedral : 29.035 173.998 3977 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.34 % Favored : 95.48 % Rotamer: Outliers : 2.46 % Allowed : 14.12 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.25), residues: 1129 helix: 1.17 (0.20), residues: 688 sheet: -2.70 (0.60), residues: 61 loop : -2.14 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 265 HIS 0.008 0.001 HIS F 75 PHE 0.021 0.002 PHE H 67 TYR 0.012 0.001 TYR G 51 ARG 0.004 0.001 ARG K 636 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 196 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 65 GLU cc_start: 0.7807 (tp30) cc_final: 0.7396 (tp30) REVERT: C 75 LYS cc_start: 0.8762 (mttp) cc_final: 0.8287 (tmtt) REVERT: C 85 GLN cc_start: 0.8829 (tp40) cc_final: 0.8625 (tp40) REVERT: C 91 ASP cc_start: 0.7434 (t0) cc_final: 0.7190 (t0) REVERT: D 67 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.8322 (m-80) REVERT: D 118 GLU cc_start: 0.8342 (mp0) cc_final: 0.8096 (mp0) REVERT: E 54 TYR cc_start: 0.8202 (m-80) cc_final: 0.7990 (m-80) REVERT: G 36 LYS cc_start: 0.9157 (ttmt) cc_final: 0.8754 (ttmm) REVERT: H 84 MET cc_start: 0.8299 (mtm) cc_final: 0.8069 (mtm) REVERT: K 296 MET cc_start: 0.8200 (mtp) cc_final: 0.7515 (mmp) REVERT: K 516 VAL cc_start: 0.8151 (t) cc_final: 0.7931 (t) REVERT: K 570 ILE cc_start: 0.9090 (pt) cc_final: 0.8594 (mp) REVERT: K 608 ASN cc_start: 0.7765 (t0) cc_final: 0.7121 (p0) REVERT: K 626 MET cc_start: 0.8675 (mmt) cc_final: 0.8447 (mmt) outliers start: 24 outliers final: 12 residues processed: 211 average time/residue: 0.2694 time to fit residues: 81.5604 Evaluate side-chains 166 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 153 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 483 LYS Chi-restraints excluded: chain K residue 487 ASN Chi-restraints excluded: chain K residue 615 CYS Chi-restraints excluded: chain K residue 631 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 108 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 97 optimal weight: 0.0770 overall best weight: 1.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 120 GLN E 85 GLN G 85 GLN ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 522 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15075 Z= 0.258 Angle : 0.637 13.334 21416 Z= 0.359 Chirality : 0.038 0.291 2428 Planarity : 0.004 0.037 1833 Dihedral : 28.808 179.091 3973 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.96 % Favored : 94.86 % Rotamer: Outliers : 3.48 % Allowed : 15.56 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1129 helix: 1.86 (0.20), residues: 694 sheet: -2.31 (0.65), residues: 60 loop : -2.03 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 217 HIS 0.009 0.001 HIS F 75 PHE 0.017 0.002 PHE H 67 TYR 0.010 0.001 TYR D 65 ARG 0.004 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 171 time to evaluate : 1.265 Fit side-chains revert: symmetry clash REVERT: C 42 GLU cc_start: 0.7587 (mp0) cc_final: 0.7270 (mp0) REVERT: C 75 LYS cc_start: 0.8698 (mttp) cc_final: 0.8336 (tmtt) REVERT: C 78 ARG cc_start: 0.6802 (ttm-80) cc_final: 0.6344 (mtt-85) REVERT: C 85 GLN cc_start: 0.8806 (tp40) cc_final: 0.8603 (tp40) REVERT: C 91 ASP cc_start: 0.7584 (t0) cc_final: 0.7332 (t0) REVERT: D 67 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8414 (m-80) REVERT: E 54 TYR cc_start: 0.8265 (m-80) cc_final: 0.7888 (m-80) REVERT: G 57 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8323 (tm-30) REVERT: G 74 ASN cc_start: 0.8872 (m-40) cc_final: 0.7820 (t0) REVERT: H 86 ILE cc_start: 0.9522 (mm) cc_final: 0.9228 (mt) REVERT: K 212 TRP cc_start: 0.7920 (t-100) cc_final: 0.7522 (t-100) REVERT: K 294 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6037 (pptt) REVERT: K 296 MET cc_start: 0.8276 (mtp) cc_final: 0.7530 (mmp) REVERT: K 448 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8132 (ptp) REVERT: K 486 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8597 (mm) REVERT: K 608 ASN cc_start: 0.7937 (t0) cc_final: 0.7200 (p0) REVERT: K 626 MET cc_start: 0.8602 (mmt) cc_final: 0.8362 (mmm) outliers start: 34 outliers final: 20 residues processed: 194 average time/residue: 0.2778 time to fit residues: 76.5938 Evaluate side-chains 171 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 147 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain K residue 260 SER Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 294 LYS Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 448 MET Chi-restraints excluded: chain K residue 483 LYS Chi-restraints excluded: chain K residue 486 LEU Chi-restraints excluded: chain K residue 529 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 63 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 chunk 115 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 625 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15075 Z= 0.192 Angle : 0.583 8.194 21416 Z= 0.333 Chirality : 0.036 0.154 2428 Planarity : 0.004 0.035 1833 Dihedral : 28.527 173.992 3973 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.81 % Favored : 96.10 % Rotamer: Outliers : 3.48 % Allowed : 16.27 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.26), residues: 1129 helix: 2.18 (0.20), residues: 700 sheet: -2.18 (0.60), residues: 60 loop : -1.93 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 265 HIS 0.007 0.001 HIS F 75 PHE 0.013 0.001 PHE H 67 TYR 0.010 0.001 TYR G 51 ARG 0.004 0.000 ARG K 288 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 169 time to evaluate : 1.199 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7865 (mt-10) REVERT: C 42 GLU cc_start: 0.7593 (mp0) cc_final: 0.7321 (mp0) REVERT: C 65 GLU cc_start: 0.8433 (tp30) cc_final: 0.7733 (tp30) REVERT: C 75 LYS cc_start: 0.8701 (mttp) cc_final: 0.8301 (tptp) REVERT: C 78 ARG cc_start: 0.6819 (ttm-80) cc_final: 0.6352 (mtt-85) REVERT: C 85 GLN cc_start: 0.8805 (tp40) cc_final: 0.8583 (tp40) REVERT: C 91 ASP cc_start: 0.7653 (t0) cc_final: 0.7380 (t0) REVERT: D 67 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8369 (m-80) REVERT: D 118 GLU cc_start: 0.8565 (mp0) cc_final: 0.8160 (mp0) REVERT: E 54 TYR cc_start: 0.8167 (m-80) cc_final: 0.7613 (m-80) REVERT: E 56 LYS cc_start: 0.6862 (pttt) cc_final: 0.5847 (tppt) REVERT: G 57 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8336 (tm-30) REVERT: G 74 ASN cc_start: 0.8812 (m-40) cc_final: 0.7862 (t0) REVERT: G 90 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8353 (m-40) REVERT: H 86 ILE cc_start: 0.9384 (mm) cc_final: 0.9147 (mt) REVERT: K 212 TRP cc_start: 0.7760 (t-100) cc_final: 0.7525 (t-100) REVERT: K 296 MET cc_start: 0.8274 (mtp) cc_final: 0.7539 (mmp) REVERT: K 608 ASN cc_start: 0.8043 (t0) cc_final: 0.7342 (p0) REVERT: K 622 TRP cc_start: 0.8599 (OUTLIER) cc_final: 0.8368 (m-10) REVERT: K 626 MET cc_start: 0.8652 (mmt) cc_final: 0.8058 (mmm) outliers start: 34 outliers final: 23 residues processed: 190 average time/residue: 0.2622 time to fit residues: 72.8878 Evaluate side-chains 177 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 65 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 260 SER Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 483 LYS Chi-restraints excluded: chain K residue 487 ASN Chi-restraints excluded: chain K residue 615 CYS Chi-restraints excluded: chain K residue 622 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 32 optimal weight: 0.0870 chunk 43 optimal weight: 0.7980 overall best weight: 2.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS K 287 GLN ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 15075 Z= 0.332 Angle : 0.659 7.231 21416 Z= 0.371 Chirality : 0.040 0.283 2428 Planarity : 0.004 0.036 1833 Dihedral : 28.726 169.320 3973 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.14 % Favored : 94.77 % Rotamer: Outliers : 3.79 % Allowed : 17.09 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.25), residues: 1129 helix: 1.90 (0.20), residues: 700 sheet: -2.18 (0.59), residues: 64 loop : -2.07 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 265 HIS 0.006 0.001 HIS F 75 PHE 0.012 0.002 PHE E 67 TYR 0.013 0.001 TYR B 72 ARG 0.007 0.001 ARG K 288 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 156 time to evaluate : 1.509 Fit side-chains revert: symmetry clash REVERT: C 65 GLU cc_start: 0.8370 (tp30) cc_final: 0.7656 (tp30) REVERT: C 75 LYS cc_start: 0.8701 (mttp) cc_final: 0.8400 (tptp) REVERT: C 78 ARG cc_start: 0.6946 (ttm-80) cc_final: 0.6534 (mtt-85) REVERT: D 67 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8493 (m-80) REVERT: E 54 TYR cc_start: 0.8323 (m-80) cc_final: 0.7794 (m-80) REVERT: G 57 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8480 (tm-30) REVERT: G 90 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8395 (m-40) REVERT: H 86 ILE cc_start: 0.9584 (mm) cc_final: 0.9326 (mt) REVERT: K 212 TRP cc_start: 0.7760 (t-100) cc_final: 0.7541 (t-100) REVERT: K 296 MET cc_start: 0.8191 (mtp) cc_final: 0.7562 (mmp) REVERT: K 608 ASN cc_start: 0.8230 (t0) cc_final: 0.7519 (p0) REVERT: K 622 TRP cc_start: 0.8571 (OUTLIER) cc_final: 0.8266 (m-10) outliers start: 37 outliers final: 29 residues processed: 183 average time/residue: 0.2642 time to fit residues: 71.3291 Evaluate side-chains 175 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 143 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 65 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 260 SER Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 483 LYS Chi-restraints excluded: chain K residue 487 ASN Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 622 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 60 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 134 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 287 GLN ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15075 Z= 0.207 Angle : 0.582 6.842 21416 Z= 0.331 Chirality : 0.036 0.218 2428 Planarity : 0.004 0.033 1833 Dihedral : 28.443 170.147 3973 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.99 % Favored : 95.93 % Rotamer: Outliers : 3.68 % Allowed : 17.91 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.26), residues: 1129 helix: 2.22 (0.20), residues: 699 sheet: -1.76 (0.58), residues: 68 loop : -1.89 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 622 HIS 0.006 0.001 HIS F 75 PHE 0.019 0.001 PHE K 240 TYR 0.010 0.001 TYR G 51 ARG 0.003 0.000 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 150 time to evaluate : 1.278 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.7849 (mtm) cc_final: 0.7602 (mtt) REVERT: C 65 GLU cc_start: 0.8387 (tp30) cc_final: 0.7718 (tp30) REVERT: C 75 LYS cc_start: 0.8631 (mttp) cc_final: 0.8363 (tptp) REVERT: C 78 ARG cc_start: 0.6957 (ttm-80) cc_final: 0.6456 (mtt-85) REVERT: D 67 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.8419 (m-80) REVERT: D 118 GLU cc_start: 0.8704 (mp0) cc_final: 0.8233 (mp0) REVERT: E 54 TYR cc_start: 0.8282 (m-80) cc_final: 0.7687 (m-80) REVERT: G 57 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8389 (tm-30) REVERT: G 73 ASP cc_start: 0.8630 (m-30) cc_final: 0.7831 (t0) REVERT: G 74 ASN cc_start: 0.8865 (m-40) cc_final: 0.7838 (t0) REVERT: G 90 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8410 (m-40) REVERT: H 86 ILE cc_start: 0.9487 (mm) cc_final: 0.9244 (mt) REVERT: K 212 TRP cc_start: 0.7844 (t-100) cc_final: 0.7571 (t-100) REVERT: K 296 MET cc_start: 0.8142 (mtp) cc_final: 0.7647 (mmp) REVERT: K 608 ASN cc_start: 0.8266 (t0) cc_final: 0.7603 (p0) outliers start: 36 outliers final: 22 residues processed: 177 average time/residue: 0.2747 time to fit residues: 70.9636 Evaluate side-chains 171 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 147 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 260 SER Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 478 ARG Chi-restraints excluded: chain K residue 483 LYS Chi-restraints excluded: chain K residue 487 ASN Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 615 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 94 optimal weight: 0.0040 chunk 109 optimal weight: 0.3980 chunk 72 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15075 Z= 0.182 Angle : 0.567 7.425 21416 Z= 0.321 Chirality : 0.035 0.208 2428 Planarity : 0.003 0.034 1833 Dihedral : 28.354 168.780 3973 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.61 % Favored : 95.31 % Rotamer: Outliers : 2.46 % Allowed : 18.83 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.26), residues: 1129 helix: 2.42 (0.20), residues: 699 sheet: -1.57 (0.59), residues: 65 loop : -1.76 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 217 HIS 0.006 0.001 HIS F 75 PHE 0.019 0.001 PHE K 240 TYR 0.009 0.001 TYR G 51 ARG 0.002 0.000 ARG K 347 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 162 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: C 65 GLU cc_start: 0.8366 (tp30) cc_final: 0.7647 (tp30) REVERT: C 75 LYS cc_start: 0.8570 (mttp) cc_final: 0.8355 (tptp) REVERT: C 78 ARG cc_start: 0.6919 (ttm-80) cc_final: 0.6417 (mtt-85) REVERT: D 67 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8407 (m-80) REVERT: D 118 GLU cc_start: 0.8593 (mp0) cc_final: 0.8199 (mp0) REVERT: G 57 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8338 (tm-30) REVERT: G 73 ASP cc_start: 0.8516 (m-30) cc_final: 0.7772 (t0) REVERT: G 74 ASN cc_start: 0.8766 (m-40) cc_final: 0.7811 (t0) REVERT: G 78 ARG cc_start: 0.8429 (mtm110) cc_final: 0.8145 (mtp-110) REVERT: G 90 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8443 (m-40) REVERT: H 86 ILE cc_start: 0.9425 (mm) cc_final: 0.9174 (mt) REVERT: K 212 TRP cc_start: 0.7822 (t-100) cc_final: 0.7534 (t-100) REVERT: K 296 MET cc_start: 0.8117 (mtp) cc_final: 0.7629 (mmp) REVERT: K 350 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.6757 (ttpt) REVERT: K 354 MET cc_start: 0.7546 (mtm) cc_final: 0.6958 (mtm) REVERT: K 608 ASN cc_start: 0.8208 (t0) cc_final: 0.7602 (p0) outliers start: 24 outliers final: 12 residues processed: 178 average time/residue: 0.2176 time to fit residues: 55.3978 Evaluate side-chains 163 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 85 GLN Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 350 LYS Chi-restraints excluded: chain K residue 570 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 101 optimal weight: 0.0770 chunk 117 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS E 55 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.6064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15075 Z= 0.168 Angle : 0.567 9.721 21416 Z= 0.318 Chirality : 0.035 0.169 2428 Planarity : 0.003 0.039 1833 Dihedral : 28.275 167.372 3973 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.16 % Favored : 95.75 % Rotamer: Outliers : 2.05 % Allowed : 19.04 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.26), residues: 1129 helix: 2.51 (0.20), residues: 705 sheet: -1.32 (0.62), residues: 68 loop : -1.67 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 217 HIS 0.005 0.001 HIS F 75 PHE 0.024 0.001 PHE K 240 TYR 0.009 0.001 TYR G 51 ARG 0.002 0.000 ARG K 347 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 159 time to evaluate : 1.309 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7909 (mt-10) REVERT: C 65 GLU cc_start: 0.8382 (tp30) cc_final: 0.7672 (tp30) REVERT: C 78 ARG cc_start: 0.6936 (ttm-80) cc_final: 0.6425 (mtt-85) REVERT: D 67 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8400 (m-80) REVERT: D 118 GLU cc_start: 0.8552 (mp0) cc_final: 0.8198 (mp0) REVERT: G 57 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8342 (tm-30) REVERT: G 73 ASP cc_start: 0.8455 (m-30) cc_final: 0.7791 (t0) REVERT: G 74 ASN cc_start: 0.8693 (m-40) cc_final: 0.7884 (t0) REVERT: G 78 ARG cc_start: 0.8345 (mtm110) cc_final: 0.8037 (mtp-110) REVERT: G 85 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8376 (tp-100) REVERT: G 90 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8376 (m-40) REVERT: H 86 ILE cc_start: 0.9407 (mm) cc_final: 0.9162 (mt) REVERT: K 212 TRP cc_start: 0.7785 (t-100) cc_final: 0.7495 (t-100) REVERT: K 296 MET cc_start: 0.7790 (mtp) cc_final: 0.7550 (mmp) REVERT: K 608 ASN cc_start: 0.8284 (t0) cc_final: 0.7737 (p0) outliers start: 20 outliers final: 14 residues processed: 172 average time/residue: 0.2850 time to fit residues: 70.0256 Evaluate side-chains 167 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 150 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 85 GLN Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 478 ARG Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 615 CYS Chi-restraints excluded: chain K residue 622 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 94 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS F 75 HIS H 88 ASN ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.6113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 15075 Z= 0.347 Angle : 0.662 9.443 21416 Z= 0.368 Chirality : 0.039 0.212 2428 Planarity : 0.004 0.041 1833 Dihedral : 28.543 163.230 3973 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.69 % Favored : 95.22 % Rotamer: Outliers : 2.46 % Allowed : 19.34 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.25), residues: 1129 helix: 2.07 (0.20), residues: 703 sheet: -1.31 (0.63), residues: 57 loop : -1.86 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 265 HIS 0.003 0.001 HIS D 74 PHE 0.030 0.002 PHE K 240 TYR 0.011 0.002 TYR D 65 ARG 0.004 0.001 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 155 time to evaluate : 1.360 Fit side-chains revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8820 (m-30) cc_final: 0.8591 (m-30) REVERT: C 65 GLU cc_start: 0.8429 (tp30) cc_final: 0.7688 (tp30) REVERT: C 78 ARG cc_start: 0.6824 (ttm-80) cc_final: 0.6419 (mtt-85) REVERT: D 67 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.8488 (m-80) REVERT: D 118 GLU cc_start: 0.8716 (mp0) cc_final: 0.8242 (mp0) REVERT: G 57 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8476 (tm-30) REVERT: G 78 ARG cc_start: 0.8396 (mtm110) cc_final: 0.8115 (mtp-110) REVERT: G 90 ASN cc_start: 0.8741 (OUTLIER) cc_final: 0.8396 (m-40) REVERT: H 86 ILE cc_start: 0.9591 (mm) cc_final: 0.9325 (mt) REVERT: K 212 TRP cc_start: 0.7820 (t-100) cc_final: 0.7545 (t-100) REVERT: K 296 MET cc_start: 0.7927 (mtp) cc_final: 0.7515 (mmp) REVERT: K 354 MET cc_start: 0.7351 (mtm) cc_final: 0.6862 (mtm) REVERT: K 608 ASN cc_start: 0.8284 (t0) cc_final: 0.7832 (p0) outliers start: 24 outliers final: 20 residues processed: 175 average time/residue: 0.2817 time to fit residues: 70.8326 Evaluate side-chains 167 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 85 GLN Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain K residue 260 SER Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 478 ARG Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 615 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.6266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15075 Z= 0.232 Angle : 0.613 10.035 21416 Z= 0.342 Chirality : 0.036 0.180 2428 Planarity : 0.004 0.038 1833 Dihedral : 28.385 164.344 3973 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Rotamer: Outliers : 2.35 % Allowed : 19.65 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.26), residues: 1129 helix: 2.30 (0.20), residues: 702 sheet: -1.11 (0.66), residues: 56 loop : -1.83 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 265 HIS 0.009 0.001 HIS K 295 PHE 0.030 0.001 PHE K 240 TYR 0.010 0.001 TYR G 51 ARG 0.002 0.000 ARG D 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: C 65 GLU cc_start: 0.8472 (tp30) cc_final: 0.7817 (tp30) REVERT: C 78 ARG cc_start: 0.6873 (ttm-80) cc_final: 0.6311 (mtt-85) REVERT: C 91 ASP cc_start: 0.8103 (t0) cc_final: 0.7620 (t0) REVERT: D 67 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8437 (m-80) REVERT: D 118 GLU cc_start: 0.8719 (mp0) cc_final: 0.8266 (mp0) REVERT: G 57 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8393 (tm-30) REVERT: G 73 ASP cc_start: 0.8597 (m-30) cc_final: 0.7834 (t0) REVERT: G 74 ASN cc_start: 0.8932 (m-40) cc_final: 0.7901 (t0) REVERT: G 78 ARG cc_start: 0.8313 (mtm110) cc_final: 0.8022 (mtp-110) REVERT: G 85 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8038 (tp-100) REVERT: G 90 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8415 (m-40) REVERT: H 86 ILE cc_start: 0.9530 (mm) cc_final: 0.9286 (mt) REVERT: K 212 TRP cc_start: 0.7770 (t-100) cc_final: 0.7508 (t-100) REVERT: K 296 MET cc_start: 0.7918 (mtp) cc_final: 0.7596 (mmp) REVERT: K 354 MET cc_start: 0.7458 (mtm) cc_final: 0.6982 (mtm) REVERT: K 608 ASN cc_start: 0.8315 (t0) cc_final: 0.7863 (p0) outliers start: 23 outliers final: 17 residues processed: 167 average time/residue: 0.2722 time to fit residues: 65.9177 Evaluate side-chains 166 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 85 GLN Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 478 ARG Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 615 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 106 optimal weight: 0.0170 chunk 44 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 93 optimal weight: 0.0670 chunk 6 optimal weight: 0.8980 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS ** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.108955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.075157 restraints weight = 39650.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.075384 restraints weight = 21815.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.076066 restraints weight = 15726.350| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.6528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15075 Z= 0.168 Angle : 0.580 9.707 21416 Z= 0.324 Chirality : 0.035 0.177 2428 Planarity : 0.004 0.042 1833 Dihedral : 28.207 163.586 3973 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Rotamer: Outliers : 1.43 % Allowed : 20.27 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.26), residues: 1129 helix: 2.53 (0.20), residues: 705 sheet: -1.28 (0.60), residues: 66 loop : -1.60 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 265 HIS 0.008 0.001 HIS K 295 PHE 0.033 0.001 PHE K 240 TYR 0.016 0.001 TYR K 253 ARG 0.002 0.000 ARG E 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2504.23 seconds wall clock time: 47 minutes 10.98 seconds (2830.98 seconds total)