Starting phenix.real_space_refine on Sun Jul 21 09:53:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wh8_37533/07_2024/8wh8_37533.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wh8_37533/07_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_37533/07_2024/8wh8_37533.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wh8_37533/07_2024/8wh8_37533.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wh8_37533/07_2024/8wh8_37533.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wh8_37533/07_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-5388/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: 8.52, per 1000 atoms: 0.60 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: 7.07 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: 5.79 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: 6.00 Time building geometry restraints manager: 7.61 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 2.440 nonbonded pdb=" OD1 ASN K 368 " pdb=" N SER K 370 " model vdw 2.319 2.520 nonbonded pdb=" O ASN K 466 " pdb=" OG1 THR K 467 " model vdw 2.325 2.440 ... (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 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 46.100 Find NCS groups from input model: 0.310 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: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.660 ------------------------------------------------------------------------------- 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 : 1.239 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: 0.3802 time to fit residues: 165.6542 Evaluate side-chains 169 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 1.303 ------------------------------------------------------------------------------- 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: 5.9990 chunk 101 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 105 optimal weight: 8.9990 chunk 40 optimal weight: 20.0000 chunk 63 optimal weight: 0.6980 chunk 78 optimal weight: 9.9990 chunk 121 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3283 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= 0.213 Angle : 0.650 7.898 21416 Z= 0.373 Chirality : 0.038 0.179 2428 Planarity : 0.005 0.038 1833 Dihedral : 29.018 173.381 3977 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.61 % Favored : 95.22 % Rotamer: Outliers : 2.35 % Allowed : 14.53 % Favored : 83.11 % 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: -0.32 (0.25), residues: 1129 helix: 1.07 (0.20), residues: 688 sheet: -2.78 (0.59), residues: 64 loop : -2.18 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 217 HIS 0.008 0.001 HIS F 75 PHE 0.021 0.001 PHE H 67 TYR 0.011 0.001 TYR G 51 ARG 0.005 0.001 ARG K 431 *********************** 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 223 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 200 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 65 GLU cc_start: 0.7735 (tp30) cc_final: 0.7255 (tp30) REVERT: C 75 LYS cc_start: 0.8699 (mttp) cc_final: 0.8258 (tmtt) REVERT: C 91 ASP cc_start: 0.7449 (t0) cc_final: 0.7245 (t0) REVERT: D 67 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.8307 (m-80) REVERT: G 36 LYS cc_start: 0.9147 (ttmt) cc_final: 0.8829 (ttmm) REVERT: H 84 MET cc_start: 0.8202 (mtm) cc_final: 0.7949 (mtm) REVERT: K 296 MET cc_start: 0.8194 (mtp) cc_final: 0.7498 (mmp) REVERT: K 486 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8408 (mm) REVERT: K 516 VAL cc_start: 0.8059 (t) cc_final: 0.7822 (t) REVERT: K 570 ILE cc_start: 0.9087 (pt) cc_final: 0.8588 (mp) REVERT: K 608 ASN cc_start: 0.7681 (t0) cc_final: 0.7140 (p0) outliers start: 23 outliers final: 12 residues processed: 215 average time/residue: 0.2754 time to fit residues: 85.3410 Evaluate side-chains 163 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 149 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 VAL 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 100 ASP 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 486 LEU 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: 0.9990 chunk 101 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 131 optimal weight: 8.9990 chunk 108 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 G 85 GLN K 367 ASN ** 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: 0.8235 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 15075 Z= 0.361 Angle : 0.691 13.107 21416 Z= 0.388 Chirality : 0.041 0.185 2428 Planarity : 0.005 0.037 1833 Dihedral : 28.995 178.826 3973 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.67 % Favored : 94.24 % Rotamer: Outliers : 4.40 % Allowed : 15.05 % Favored : 80.55 % 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: 0.33 (0.26), residues: 1129 helix: 1.65 (0.20), residues: 694 sheet: -2.49 (0.57), residues: 74 loop : -2.10 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP K 217 HIS 0.009 0.001 HIS F 75 PHE 0.019 0.002 PHE H 67 TYR 0.012 0.002 TYR B 72 ARG 0.008 0.001 ARG K 531 *********************** 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 209 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 166 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8252 (tt0) cc_final: 0.8022 (tt0) REVERT: C 65 GLU cc_start: 0.8351 (tp30) cc_final: 0.7693 (tp30) REVERT: C 75 LYS cc_start: 0.8699 (mttp) cc_final: 0.8355 (tmtt) REVERT: D 67 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8520 (m-80) REVERT: G 57 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8381 (tm-30) REVERT: K 212 TRP cc_start: 0.7959 (t-100) cc_final: 0.7579 (t-100) REVERT: K 296 MET cc_start: 0.8261 (mtp) cc_final: 0.7531 (mmp) REVERT: K 516 VAL cc_start: 0.8249 (t) cc_final: 0.8037 (t) REVERT: K 608 ASN cc_start: 0.7800 (t0) cc_final: 0.7324 (p0) outliers start: 43 outliers final: 26 residues processed: 193 average time/residue: 0.2909 time to fit residues: 80.1336 Evaluate side-chains 175 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 147 THR 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 G residue 80 VAL Chi-restraints excluded: chain G residue 85 GLN Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 260 SER Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 446 ILE Chi-restraints excluded: chain K residue 483 LYS Chi-restraints excluded: chain K residue 486 LEU Chi-restraints excluded: chain K residue 529 LEU Chi-restraints excluded: chain K residue 571 ASP Chi-restraints excluded: chain K residue 615 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 115 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN E 55 GLN ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 625 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4892 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= 0.195 Angle : 0.584 8.761 21416 Z= 0.335 Chirality : 0.036 0.148 2428 Planarity : 0.004 0.037 1833 Dihedral : 28.650 175.293 3973 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.25 % Favored : 95.66 % Rotamer: Outliers : 3.38 % Allowed : 16.58 % Favored : 80.04 % 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: 1.03 (0.26), residues: 1129 helix: 2.20 (0.20), residues: 693 sheet: -2.08 (0.59), residues: 72 loop : -1.83 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 265 HIS 0.006 0.001 HIS F 75 PHE 0.013 0.001 PHE E 78 TYR 0.010 0.001 TYR G 51 ARG 0.007 0.000 ARG E 134 *********************** 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 197 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 164 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.7707 (mtm) cc_final: 0.7454 (mtt) REVERT: C 65 GLU cc_start: 0.8400 (tp30) cc_final: 0.7665 (tp30) REVERT: C 75 LYS cc_start: 0.8744 (mttp) cc_final: 0.8400 (tmtt) REVERT: D 67 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8412 (m-80) REVERT: G 57 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8377 (tm-30) REVERT: G 74 ASN cc_start: 0.8813 (m-40) cc_final: 0.7823 (t0) REVERT: G 78 ARG cc_start: 0.8599 (mtm110) cc_final: 0.8085 (ptp-170) REVERT: G 85 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8162 (tp-100) REVERT: H 86 ILE cc_start: 0.9435 (mm) cc_final: 0.9192 (mt) REVERT: K 212 TRP cc_start: 0.7782 (t-100) cc_final: 0.7570 (t-100) REVERT: K 296 MET cc_start: 0.8187 (mtp) cc_final: 0.7563 (mmp) REVERT: K 608 ASN cc_start: 0.7919 (t0) cc_final: 0.7372 (p0) REVERT: K 622 TRP cc_start: 0.8594 (OUTLIER) cc_final: 0.8056 (m-10) outliers start: 33 outliers final: 21 residues processed: 184 average time/residue: 0.2938 time to fit residues: 76.6421 Evaluate side-chains 173 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 149 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 112 ILE 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 65 GLU 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 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 343 CYS Chi-restraints excluded: chain K residue 446 ILE Chi-restraints excluded: chain K residue 483 LYS Chi-restraints excluded: chain K residue 486 LEU 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: 0.5980 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 32 optimal weight: 0.0070 chunk 43 optimal weight: 1.9990 overall best weight: 1.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15075 Z= 0.204 Angle : 0.575 8.300 21416 Z= 0.330 Chirality : 0.036 0.146 2428 Planarity : 0.004 0.038 1833 Dihedral : 28.531 171.324 3973 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.96 % Favored : 94.95 % Rotamer: Outliers : 2.87 % Allowed : 17.60 % Favored : 79.53 % 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: 1.15 (0.26), residues: 1129 helix: 2.30 (0.20), residues: 699 sheet: -1.97 (0.59), residues: 72 loop : -1.89 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 622 HIS 0.006 0.001 HIS F 75 PHE 0.010 0.001 PHE H 67 TYR 0.009 0.001 TYR G 51 ARG 0.013 0.000 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 179 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 151 time to evaluate : 1.375 Fit side-chains revert: symmetry clash REVERT: C 65 GLU cc_start: 0.8443 (tp30) cc_final: 0.7768 (tp30) REVERT: C 75 LYS cc_start: 0.8755 (mttp) cc_final: 0.8377 (tptp) REVERT: C 91 ASP cc_start: 0.8008 (t0) cc_final: 0.7254 (t0) REVERT: D 67 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8428 (m-80) REVERT: G 57 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8384 (tm-30) REVERT: G 74 ASN cc_start: 0.8810 (m-40) cc_final: 0.7852 (t0) REVERT: G 78 ARG cc_start: 0.8643 (mtm110) cc_final: 0.8142 (ptp-170) REVERT: H 86 ILE cc_start: 0.9457 (mm) cc_final: 0.9206 (mt) REVERT: K 212 TRP cc_start: 0.7771 (t-100) cc_final: 0.7547 (t-100) REVERT: K 296 MET cc_start: 0.8191 (mtp) cc_final: 0.7581 (mmp) REVERT: K 608 ASN cc_start: 0.7959 (t0) cc_final: 0.7415 (p0) outliers start: 28 outliers final: 19 residues processed: 171 average time/residue: 0.2641 time to fit residues: 65.3834 Evaluate side-chains 161 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 80 THR Chi-restraints excluded: chain E residue 112 ILE 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 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 343 CYS Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 446 ILE Chi-restraints excluded: chain K residue 483 LYS Chi-restraints excluded: chain K residue 615 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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: 0.8198 moved from start: 0.5480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15075 Z= 0.215 Angle : 0.582 7.702 21416 Z= 0.330 Chirality : 0.036 0.278 2428 Planarity : 0.004 0.036 1833 Dihedral : 28.467 169.108 3973 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.14 % Favored : 94.77 % Rotamer: Outliers : 3.28 % Allowed : 18.32 % 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: 1.23 (0.26), residues: 1129 helix: 2.36 (0.20), residues: 696 sheet: -1.74 (0.61), residues: 72 loop : -1.86 (0.30), residues: 361 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 0.009 0.001 PHE H 67 TYR 0.009 0.001 TYR K 325 ARG 0.004 0.000 ARG K 431 *********************** 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 178 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 146 time to evaluate : 2.114 Fit side-chains revert: symmetry clash REVERT: C 65 GLU cc_start: 0.8537 (tp30) cc_final: 0.7797 (tp30) REVERT: C 75 LYS cc_start: 0.8647 (mttp) cc_final: 0.8396 (tptp) REVERT: D 67 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8430 (m-80) REVERT: G 57 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8402 (tm-30) REVERT: G 74 ASN cc_start: 0.8842 (m-40) cc_final: 0.7866 (t0) REVERT: G 78 ARG cc_start: 0.8632 (mtm110) cc_final: 0.8076 (ptp-170) REVERT: H 86 ILE cc_start: 0.9514 (mm) cc_final: 0.9253 (mt) REVERT: K 212 TRP cc_start: 0.7702 (t-100) cc_final: 0.7461 (t-100) REVERT: K 296 MET cc_start: 0.8167 (mtp) cc_final: 0.7523 (mmp) REVERT: K 486 LEU cc_start: 0.8411 (mm) cc_final: 0.8154 (mm) REVERT: K 608 ASN cc_start: 0.8043 (t0) cc_final: 0.7541 (p0) outliers start: 32 outliers final: 22 residues processed: 170 average time/residue: 0.2749 time to fit residues: 68.7993 Evaluate side-chains 165 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 142 time to evaluate : 1.300 ------------------------------------------------------------------------------- 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 112 ILE 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 65 GLU Chi-restraints excluded: chain G residue 80 VAL 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 343 CYS Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 446 ILE Chi-restraints excluded: chain K residue 483 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 59 optimal weight: 0.0670 chunk 79 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN D 134 HIS ** 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: 0.8227 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15075 Z= 0.243 Angle : 0.605 12.178 21416 Z= 0.339 Chirality : 0.037 0.229 2428 Planarity : 0.004 0.042 1833 Dihedral : 28.493 167.596 3973 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.14 % Favored : 94.77 % Rotamer: Outliers : 3.07 % Allowed : 19.55 % Favored : 77.38 % 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: 1.23 (0.26), residues: 1129 helix: 2.31 (0.20), residues: 697 sheet: -0.99 (0.64), residues: 55 loop : -1.90 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 265 HIS 0.006 0.001 HIS F 75 PHE 0.020 0.001 PHE K 240 TYR 0.009 0.001 TYR K 325 ARG 0.002 0.000 ARG G 30 *********************** 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 178 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 148 time to evaluate : 1.212 Fit side-chains revert: symmetry clash REVERT: C 65 GLU cc_start: 0.8588 (tp30) cc_final: 0.7909 (tp30) REVERT: C 75 LYS cc_start: 0.8607 (mttp) cc_final: 0.8366 (tptp) REVERT: D 67 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.8374 (m-80) REVERT: G 57 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8422 (tm-30) REVERT: G 74 ASN cc_start: 0.8879 (m-40) cc_final: 0.7893 (t0) REVERT: G 78 ARG cc_start: 0.8554 (mtm110) cc_final: 0.7998 (ptp-170) REVERT: H 84 MET cc_start: 0.8702 (ttm) cc_final: 0.8262 (tpp) REVERT: H 86 ILE cc_start: 0.9539 (mm) cc_final: 0.9276 (mt) REVERT: K 212 TRP cc_start: 0.7756 (t-100) cc_final: 0.7494 (t-100) REVERT: K 296 MET cc_start: 0.8128 (mtp) cc_final: 0.7676 (mmp) REVERT: K 315 MET cc_start: 0.8369 (mmm) cc_final: 0.8169 (mmm) REVERT: K 354 MET cc_start: 0.7441 (mtm) cc_final: 0.6820 (mtm) REVERT: K 483 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7578 (pttm) REVERT: K 486 LEU cc_start: 0.8282 (mm) cc_final: 0.7769 (mm) REVERT: K 608 ASN cc_start: 0.8117 (t0) cc_final: 0.7656 (p0) outliers start: 30 outliers final: 21 residues processed: 172 average time/residue: 0.2925 time to fit residues: 72.7102 Evaluate side-chains 164 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 GLN 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 80 THR 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 36 LYS Chi-restraints excluded: chain G residue 80 VAL 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 343 CYS Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 446 ILE Chi-restraints excluded: chain K residue 483 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 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: 0.8980 chunk 101 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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** ** K 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.5982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15075 Z= 0.289 Angle : 0.622 8.097 21416 Z= 0.350 Chirality : 0.038 0.245 2428 Planarity : 0.004 0.042 1833 Dihedral : 28.539 165.603 3973 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.14 % Favored : 94.77 % Rotamer: Outliers : 2.87 % Allowed : 19.96 % Favored : 77.18 % 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: 1.10 (0.26), residues: 1129 helix: 2.24 (0.20), residues: 690 sheet: -1.16 (0.61), residues: 65 loop : -1.94 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 265 HIS 0.006 0.001 HIS F 75 PHE 0.026 0.001 PHE K 240 TYR 0.011 0.001 TYR K 325 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 174 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 1.317 Fit side-chains revert: symmetry clash REVERT: C 65 GLU cc_start: 0.8621 (tp30) cc_final: 0.7932 (tp30) REVERT: C 75 LYS cc_start: 0.8602 (mttp) cc_final: 0.8397 (tptp) REVERT: D 67 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8464 (m-80) REVERT: G 57 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8404 (tm-30) REVERT: G 78 ARG cc_start: 0.8567 (mtm110) cc_final: 0.8027 (ptp-170) REVERT: H 84 MET cc_start: 0.8773 (ttm) cc_final: 0.8439 (tpp) REVERT: H 86 ILE cc_start: 0.9576 (mm) cc_final: 0.9309 (mt) REVERT: K 212 TRP cc_start: 0.7705 (t-100) cc_final: 0.7457 (t-100) REVERT: K 296 MET cc_start: 0.8109 (mtp) cc_final: 0.7650 (mmp) REVERT: K 320 ARG cc_start: 0.6421 (tpt170) cc_final: 0.6164 (tpt170) REVERT: K 483 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7713 (pttm) REVERT: K 486 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8168 (mm) REVERT: K 516 VAL cc_start: 0.8070 (t) cc_final: 0.7858 (t) REVERT: K 608 ASN cc_start: 0.8228 (t0) cc_final: 0.7788 (p0) outliers start: 28 outliers final: 20 residues processed: 167 average time/residue: 0.2741 time to fit residues: 66.1766 Evaluate side-chains 160 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 137 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 81 ASP 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 36 LYS Chi-restraints excluded: chain G residue 80 VAL 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 343 CYS Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 446 ILE Chi-restraints excluded: chain K residue 483 LYS Chi-restraints excluded: chain K residue 486 LEU Chi-restraints excluded: chain K residue 529 LEU 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: 0.2980 chunk 123 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 108 optimal weight: 0.1980 chunk 113 optimal weight: 0.0000 chunk 119 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 18 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 644 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.6212 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= 0.169 Angle : 0.570 7.770 21416 Z= 0.321 Chirality : 0.035 0.189 2428 Planarity : 0.003 0.041 1833 Dihedral : 28.335 165.681 3973 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.99 % Favored : 95.93 % Rotamer: Outliers : 2.05 % Allowed : 20.37 % Favored : 77.58 % 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: 1.47 (0.26), residues: 1129 helix: 2.49 (0.20), residues: 702 sheet: -0.97 (0.62), residues: 65 loop : -1.86 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 622 HIS 0.006 0.001 HIS F 75 PHE 0.028 0.001 PHE K 240 TYR 0.021 0.001 TYR K 618 ARG 0.003 0.000 ARG K 431 *********************** 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 173 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 153 time to evaluate : 1.286 Fit side-chains revert: symmetry clash REVERT: C 65 GLU cc_start: 0.8547 (tp30) cc_final: 0.7907 (tp30) REVERT: D 67 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.8364 (m-80) REVERT: E 56 LYS cc_start: 0.7133 (pttt) cc_final: 0.6136 (tppt) REVERT: E 73 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6992 (mt-10) REVERT: G 57 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8375 (tm-30) REVERT: G 73 ASP cc_start: 0.8447 (m-30) cc_final: 0.7712 (t0) REVERT: G 74 ASN cc_start: 0.8797 (m-40) cc_final: 0.7829 (t0) REVERT: G 78 ARG cc_start: 0.8492 (mtm110) cc_final: 0.7827 (ptp-110) REVERT: H 84 MET cc_start: 0.8532 (ttm) cc_final: 0.8146 (tpp) REVERT: H 86 ILE cc_start: 0.9435 (mm) cc_final: 0.9194 (mt) REVERT: K 212 TRP cc_start: 0.7761 (t-100) cc_final: 0.7482 (t-100) REVERT: K 354 MET cc_start: 0.7337 (mtm) cc_final: 0.6871 (mtm) REVERT: K 432 MET cc_start: 0.6371 (tpt) cc_final: 0.6162 (tpt) REVERT: K 486 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8026 (mm) REVERT: K 608 ASN cc_start: 0.8159 (t0) cc_final: 0.7808 (p0) outliers start: 20 outliers final: 12 residues processed: 168 average time/residue: 0.2585 time to fit residues: 62.6758 Evaluate side-chains 158 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 144 time to evaluate : 1.334 ------------------------------------------------------------------------------- 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 F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain K residue 260 SER Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 343 CYS Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 446 ILE Chi-restraints excluded: chain K residue 486 LEU 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: 0.6980 chunk 88 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** H 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.6347 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= 0.189 Angle : 0.584 12.809 21416 Z= 0.325 Chirality : 0.035 0.185 2428 Planarity : 0.004 0.043 1833 Dihedral : 28.338 162.784 3973 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.69 % Favored : 95.22 % Rotamer: Outliers : 1.74 % Allowed : 20.37 % Favored : 77.89 % 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: 1.52 (0.26), residues: 1129 helix: 2.50 (0.20), residues: 704 sheet: -0.80 (0.67), residues: 56 loop : -1.81 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 265 HIS 0.009 0.001 HIS K 295 PHE 0.034 0.001 PHE K 240 TYR 0.010 0.001 TYR G 51 ARG 0.003 0.000 ARG K 347 ********************** 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 160 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 1.303 Fit side-chains revert: symmetry clash REVERT: C 65 GLU cc_start: 0.8546 (tp30) cc_final: 0.7967 (tp30) REVERT: D 67 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8458 (m-80) REVERT: E 56 LYS cc_start: 0.7048 (pttt) cc_final: 0.6139 (tppt) REVERT: G 57 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8406 (tm-30) REVERT: G 73 ASP cc_start: 0.8541 (m-30) cc_final: 0.7852 (t0) REVERT: G 74 ASN cc_start: 0.8793 (m-40) cc_final: 0.7889 (t0) REVERT: G 78 ARG cc_start: 0.8443 (mtm110) cc_final: 0.8121 (mtp-110) REVERT: H 84 MET cc_start: 0.8556 (ttm) cc_final: 0.8164 (tpp) REVERT: H 86 ILE cc_start: 0.9460 (mm) cc_final: 0.9195 (mt) REVERT: K 212 TRP cc_start: 0.7740 (t-100) cc_final: 0.7461 (t-100) REVERT: K 296 MET cc_start: 0.6956 (mmm) cc_final: 0.6749 (mmp) REVERT: K 354 MET cc_start: 0.7317 (mtm) cc_final: 0.6881 (mtm) REVERT: K 432 MET cc_start: 0.6471 (tpt) cc_final: 0.6233 (tpt) REVERT: K 486 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8263 (mm) REVERT: K 608 ASN cc_start: 0.8189 (t0) cc_final: 0.7825 (p0) outliers start: 17 outliers final: 13 residues processed: 155 average time/residue: 0.2740 time to fit residues: 61.3354 Evaluate side-chains 156 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 141 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 K residue 260 SER Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 343 CYS Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 446 ILE Chi-restraints excluded: chain K residue 486 LEU 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: 0.0570 chunk 98 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.0000 chunk 106 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 overall best weight: 0.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.108388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.075095 restraints weight = 39512.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.075152 restraints weight = 22405.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.075408 restraints weight = 17824.836| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.6462 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= 0.170 Angle : 0.568 12.313 21416 Z= 0.318 Chirality : 0.035 0.171 2428 Planarity : 0.003 0.042 1833 Dihedral : 28.245 161.292 3973 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.39 % Rotamer: Outliers : 1.54 % Allowed : 20.57 % Favored : 77.89 % 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: 1.63 (0.26), residues: 1129 helix: 2.57 (0.20), residues: 704 sheet: -0.69 (0.67), residues: 56 loop : -1.74 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 265 HIS 0.006 0.001 HIS K 295 PHE 0.033 0.001 PHE K 240 TYR 0.011 0.001 TYR G 51 ARG 0.002 0.000 ARG K 347 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2542.99 seconds wall clock time: 48 minutes 6.41 seconds (2886.41 seconds total)