Starting phenix.real_space_refine on Fri Sep 27 20:31:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1t_34431/09_2024/8h1t_34431.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1t_34431/09_2024/8h1t_34431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1t_34431/09_2024/8h1t_34431.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1t_34431/09_2024/8h1t_34431.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1t_34431/09_2024/8h1t_34431.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1t_34431/09_2024/8h1t_34431.cif" } resolution = 3.0 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= -0.013 sd= 1.080 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 334 5.49 5 S 28 5.16 5 C 9881 2.51 5 N 3214 2.21 5 O 3908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17365 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 858 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "D" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 737 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 838 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 737 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3398 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Chain: "J" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3449 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Chain: "K" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 520 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "L" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2433 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 15, 'TRANS': 285} Chain breaks: 2 Chain: "M" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "N" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 903 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Time building chain proxies: 10.66, per 1000 atoms: 0.61 Number of scatterers: 17365 At special positions: 0 Unit cell: (121, 118, 159, 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 28 16.00 P 334 15.00 O 3908 8.00 N 3214 7.00 C 9881 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.65 Conformation dependent library (CDL) restraints added in 1.5 seconds 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2468 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 14 sheets defined 61.6% alpha, 5.7% beta 166 base pairs and 273 stacking pairs defined. Time for finding SS restraints: 8.29 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.982A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 48 through 76 removed outlier: 4.078A pdb=" N GLU B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.538A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 38 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.471A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 58 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.925A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.516A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.651A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.512A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.347A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.526A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.559A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.658A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 49 removed outlier: 4.154A pdb=" N LEU K 42 " --> pdb=" O PRO K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 69 Processing helix chain 'K' and resid 75 through 85 Processing helix chain 'L' and resid 11 through 23 Processing helix chain 'L' and resid 54 through 60 Processing helix chain 'L' and resid 74 through 80 Processing helix chain 'L' and resid 90 through 102 Processing helix chain 'L' and resid 109 through 120 Processing helix chain 'L' and resid 123 through 133 Processing helix chain 'L' and resid 134 through 144 removed outlier: 3.616A pdb=" N HIS L 144 " --> pdb=" O ALA L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 152 Processing helix chain 'L' and resid 202 through 218 Processing helix chain 'L' and resid 236 through 243 removed outlier: 3.990A pdb=" N LYS L 240 " --> pdb=" O ASP L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 648 through 668 removed outlier: 3.545A pdb=" N THR L 668 " --> pdb=" O ASP L 664 " (cutoff:3.500A) Processing helix chain 'L' and resid 671 through 686 Processing helix chain 'L' and resid 687 through 695 removed outlier: 3.625A pdb=" N LEU L 691 " --> pdb=" O MET L 687 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU L 693 " --> pdb=" O ALA L 689 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 removed outlier: 3.548A pdb=" N VAL M 26 " --> pdb=" O THR M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'M' and resid 55 through 59 Processing helix chain 'N' and resid 263 through 268 Processing helix chain 'N' and resid 269 through 275 Processing helix chain 'N' and resid 277 through 286 removed outlier: 3.732A pdb=" N PHE N 286 " --> pdb=" O GLN N 282 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 327 Processing helix chain 'N' and resid 330 through 352 removed outlier: 4.396A pdb=" N ARG N 336 " --> pdb=" O GLU N 332 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU N 344 " --> pdb=" O GLU N 340 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS N 345 " --> pdb=" O MET N 341 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS N 346 " --> pdb=" O GLU N 342 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL N 347 " --> pdb=" O LYS N 343 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN N 349 " --> pdb=" O LYS N 345 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N TRP N 350 " --> pdb=" O LYS N 346 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS N 351 " --> pdb=" O VAL N 347 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.038A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.450A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.464A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.577A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.026A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.223A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 56 through 57 Processing sheet with id=AB2, first strand: chain 'L' and resid 8 through 9 removed outlier: 3.770A pdb=" N LEU L 8 " --> pdb=" O GLY M 75 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 28 through 30 removed outlier: 4.375A pdb=" N ALA L 167 " --> pdb=" O TRP L 52 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE L 191 " --> pdb=" O GLU L 182 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 12 through 15 Processing sheet with id=AB5, first strand: chain 'N' and resid 293 through 295 598 hydrogen bonds defined for protein. 1749 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 429 hydrogen bonds 858 hydrogen bond angles 0 basepair planarities 166 basepair parallelities 273 stacking parallelities Total time for adding SS restraints: 7.72 Time building geometry restraints manager: 5.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3600 1.33 - 1.45: 5397 1.45 - 1.57: 8649 1.57 - 1.69: 666 1.69 - 1.81: 48 Bond restraints: 18360 Sorted by residual: bond pdb=" N ARG M 74 " pdb=" CA ARG M 74 " ideal model delta sigma weight residual 1.452 1.490 -0.037 1.25e-02 6.40e+03 9.00e+00 bond pdb=" N GLY M 75 " pdb=" CA GLY M 75 " ideal model delta sigma weight residual 1.447 1.475 -0.028 1.03e-02 9.43e+03 7.23e+00 bond pdb=" N GLU L 7 " pdb=" CA GLU L 7 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.55e+00 bond pdb=" N LYS A 122 " pdb=" CA LYS A 122 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.77e+00 bond pdb=" N LEU M 73 " pdb=" CA LEU M 73 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.50e-02 4.44e+03 5.18e+00 ... (remaining 18355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 26027 2.32 - 4.63: 173 4.63 - 6.95: 8 6.95 - 9.26: 0 9.26 - 11.58: 1 Bond angle restraints: 26209 Sorted by residual: angle pdb=" C GLY M 75 " pdb=" N GLY M 76 " pdb=" CA GLY M 76 " ideal model delta sigma weight residual 121.70 133.28 -11.58 1.80e+00 3.09e-01 4.14e+01 angle pdb=" O GLY M 75 " pdb=" C GLY M 75 " pdb=" N GLY M 76 " ideal model delta sigma weight residual 123.92 127.46 -3.54 9.60e-01 1.09e+00 1.36e+01 angle pdb=" N PHE L 660 " pdb=" CA PHE L 660 " pdb=" C PHE L 660 " ideal model delta sigma weight residual 111.36 107.39 3.97 1.09e+00 8.42e-01 1.33e+01 angle pdb=" C1' DG J 159 " pdb=" N9 DG J 159 " pdb=" C4 DG J 159 " ideal model delta sigma weight residual 127.00 122.04 4.96 1.50e+00 4.44e-01 1.10e+01 angle pdb=" CA ARG M 74 " pdb=" C ARG M 74 " pdb=" O ARG M 74 " ideal model delta sigma weight residual 121.82 118.26 3.56 1.21e+00 6.83e-01 8.68e+00 ... (remaining 26204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.39: 8216 27.39 - 54.78: 1664 54.78 - 82.17: 308 82.17 - 109.56: 4 109.56 - 136.96: 2 Dihedral angle restraints: 10194 sinusoidal: 6377 harmonic: 3817 Sorted by residual: dihedral pdb=" C4' DC J 119 " pdb=" C3' DC J 119 " pdb=" O3' DC J 119 " pdb=" P DT J 120 " ideal model delta sinusoidal sigma weight residual 220.00 83.04 136.96 1 3.50e+01 8.16e-04 1.36e+01 dihedral pdb=" C4' DG J 27 " pdb=" C3' DG J 27 " pdb=" O3' DG J 27 " pdb=" P DT J 28 " ideal model delta sinusoidal sigma weight residual 220.00 87.80 132.20 1 3.50e+01 8.16e-04 1.31e+01 dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 163.41 16.59 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 10191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2194 0.034 - 0.068: 558 0.068 - 0.103: 144 0.103 - 0.137: 54 0.137 - 0.171: 10 Chirality restraints: 2960 Sorted by residual: chirality pdb=" C3' DG J 159 " pdb=" C4' DG J 159 " pdb=" O3' DG J 159 " pdb=" C2' DG J 159 " both_signs ideal model delta sigma weight residual False -2.66 -2.83 0.17 2.00e-01 2.50e+01 7.32e-01 chirality pdb=" C3' DC J 7 " pdb=" C4' DC J 7 " pdb=" O3' DC J 7 " pdb=" C2' DC J 7 " both_signs ideal model delta sigma weight residual False -2.66 -2.50 -0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" C3' DG J 10 " pdb=" C4' DG J 10 " pdb=" O3' DG J 10 " pdb=" C2' DG J 10 " both_signs ideal model delta sigma weight residual False -2.66 -2.82 0.16 2.00e-01 2.50e+01 6.28e-01 ... (remaining 2957 not shown) Planarity restraints: 2176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS L 659 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.79e+00 pdb=" C LYS L 659 " -0.034 2.00e-02 2.50e+03 pdb=" O LYS L 659 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE L 660 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL L 234 " -0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO L 235 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO L 235 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 235 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 165 " 0.013 2.00e-02 2.50e+03 9.02e-03 1.83e+00 pdb=" N1 DC I 165 " -0.020 2.00e-02 2.50e+03 pdb=" C2 DC I 165 " 0.011 2.00e-02 2.50e+03 pdb=" O2 DC I 165 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DC I 165 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DC I 165 " 0.002 2.00e-02 2.50e+03 pdb=" N4 DC I 165 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DC I 165 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DC I 165 " -0.001 2.00e-02 2.50e+03 ... (remaining 2173 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 1 2.05 - 2.76: 2413 2.76 - 3.47: 24272 3.47 - 4.19: 47582 4.19 - 4.90: 72594 Nonbonded interactions: 146862 Sorted by model distance: nonbonded pdb=" NZ LYS C 119 " pdb=" C GLY M 76 " model vdw 1.336 3.350 nonbonded pdb=" CD1 LEU M 73 " pdb=" O ARG M 74 " model vdw 2.164 3.460 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.247 3.040 nonbonded pdb=" NZ LYS C 119 " pdb=" O GLY M 76 " model vdw 2.259 3.120 nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.278 3.040 ... (remaining 146857 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 22 through 101) } ncs_group { reference = (chain 'C' and resid 11 through 118) selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.96 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 15.330 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: 0.000 Extract box with map and model: 2.710 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 44.850 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 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:14.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 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 : 0.003 0.037 18360 Z= 0.149 Angle : 0.532 11.575 26209 Z= 0.325 Chirality : 0.037 0.171 2960 Planarity : 0.003 0.041 2176 Dihedral : 24.612 136.956 7726 Min Nonbonded Distance : 1.336 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % 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: 2.26 (0.24), residues: 1295 helix: 2.55 (0.19), residues: 759 sheet: -0.00 (0.61), residues: 70 loop : -0.02 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 320 HIS 0.003 0.000 HIS L 169 PHE 0.005 0.001 PHE C 25 TYR 0.006 0.001 TYR C 50 ARG 0.002 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7555 (pm20) cc_final: 0.7220 (pm20) REVERT: B 84 MET cc_start: 0.8037 (tpt) cc_final: 0.7802 (tpt) REVERT: C 23 LEU cc_start: 0.8181 (tp) cc_final: 0.7872 (mt) REVERT: C 24 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8353 (mm-40) REVERT: C 90 ASP cc_start: 0.8592 (t0) cc_final: 0.8152 (t70) REVERT: C 92 GLU cc_start: 0.7722 (pm20) cc_final: 0.7348 (pm20) REVERT: D 34 LYS cc_start: 0.8060 (mppt) cc_final: 0.7780 (mppt) REVERT: D 115 THR cc_start: 0.8675 (m) cc_final: 0.8463 (m) REVERT: D 120 LYS cc_start: 0.8026 (tttp) cc_final: 0.7718 (tttp) REVERT: E 64 LYS cc_start: 0.8403 (mtmt) cc_final: 0.8193 (mtmm) REVERT: F 77 LYS cc_start: 0.8364 (mmtm) cc_final: 0.8049 (mmmm) REVERT: F 84 MET cc_start: 0.8561 (tpt) cc_final: 0.8285 (mmm) REVERT: G 73 ASN cc_start: 0.8682 (t0) cc_final: 0.8264 (t0) REVERT: H 34 LYS cc_start: 0.7711 (tptm) cc_final: 0.7331 (mmtm) REVERT: H 47 GLN cc_start: 0.8660 (tt0) cc_final: 0.8339 (tt0) REVERT: K 74 LYS cc_start: 0.8516 (mmtp) cc_final: 0.8185 (tppt) REVERT: L 204 ASP cc_start: 0.8030 (t0) cc_final: 0.7760 (t0) REVERT: L 654 VAL cc_start: 0.9040 (p) cc_final: 0.8660 (m) REVERT: L 655 GLU cc_start: 0.8653 (pt0) cc_final: 0.8428 (tp30) REVERT: L 658 LYS cc_start: 0.9193 (mttt) cc_final: 0.8980 (tppt) REVERT: L 695 ASN cc_start: 0.8667 (m-40) cc_final: 0.8461 (m110) REVERT: M 38 PRO cc_start: 0.8112 (Cg_exo) cc_final: 0.7826 (Cg_endo) REVERT: N 286 PHE cc_start: 0.7411 (m-80) cc_final: 0.6780 (m-80) REVERT: N 305 SER cc_start: 0.8360 (m) cc_final: 0.8046 (t) REVERT: N 333 MET cc_start: 0.8773 (ttt) cc_final: 0.8364 (tmt) REVERT: N 334 GLN cc_start: 0.8836 (tp40) cc_final: 0.8562 (tp40) REVERT: N 337 ILE cc_start: 0.8294 (mt) cc_final: 0.6833 (mt) outliers start: 0 outliers final: 1 residues processed: 351 average time/residue: 1.4465 time to fit residues: 557.6932 Evaluate side-chains 230 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 229 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 27 GLN B 93 GLN C 38 ASN D 47 GLN E 39 HIS E 93 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 84 HIS L 193 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18360 Z= 0.216 Angle : 0.589 14.725 26209 Z= 0.332 Chirality : 0.035 0.187 2960 Planarity : 0.004 0.051 2176 Dihedral : 29.024 136.197 5084 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.03 % Allowed : 15.49 % Favored : 81.48 % 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: 2.17 (0.24), residues: 1295 helix: 2.44 (0.19), residues: 785 sheet: -0.21 (0.61), residues: 71 loop : -0.09 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 196 HIS 0.006 0.001 HIS D 109 PHE 0.026 0.002 PHE L 118 TYR 0.013 0.001 TYR E 54 ARG 0.009 0.001 ARG M 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 242 time to evaluate : 1.446 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8732 (mm) cc_final: 0.8474 (mt) REVERT: B 35 ARG cc_start: 0.8453 (mtp85) cc_final: 0.7939 (mtt90) REVERT: B 74 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7349 (tm-30) REVERT: C 90 ASP cc_start: 0.8459 (t0) cc_final: 0.7412 (t70) REVERT: D 34 LYS cc_start: 0.8092 (mppt) cc_final: 0.7822 (mppt) REVERT: D 57 LYS cc_start: 0.8272 (tppp) cc_final: 0.7829 (tptt) REVERT: E 59 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.6860 (pm20) REVERT: F 77 LYS cc_start: 0.8671 (mmtm) cc_final: 0.8224 (mmmm) REVERT: F 88 TYR cc_start: 0.8730 (m-10) cc_final: 0.8260 (m-80) REVERT: G 73 ASN cc_start: 0.8657 (t0) cc_final: 0.8209 (t0) REVERT: G 95 LYS cc_start: 0.8622 (tppt) cc_final: 0.8408 (tptt) REVERT: H 34 LYS cc_start: 0.7713 (tptm) cc_final: 0.7209 (mmtm) REVERT: H 47 GLN cc_start: 0.8617 (tt0) cc_final: 0.8294 (tt0) REVERT: H 83 TYR cc_start: 0.8186 (m-10) cc_final: 0.7800 (m-10) REVERT: L 51 LYS cc_start: 0.8571 (tttt) cc_final: 0.8236 (tptm) REVERT: L 204 ASP cc_start: 0.8429 (t0) cc_final: 0.8073 (t0) REVERT: L 654 VAL cc_start: 0.9080 (p) cc_final: 0.8797 (m) REVERT: L 655 GLU cc_start: 0.8689 (pt0) cc_final: 0.8482 (tp30) REVERT: L 659 LYS cc_start: 0.9044 (pttt) cc_final: 0.8754 (tmmt) REVERT: L 685 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7118 (tm-30) REVERT: L 695 ASN cc_start: 0.8737 (m-40) cc_final: 0.8479 (m110) REVERT: L 710 HIS cc_start: 0.7166 (OUTLIER) cc_final: 0.6797 (m-70) REVERT: N 286 PHE cc_start: 0.7402 (m-80) cc_final: 0.6977 (m-80) REVERT: N 305 SER cc_start: 0.8464 (m) cc_final: 0.8131 (t) REVERT: N 322 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8421 (mm-30) REVERT: N 333 MET cc_start: 0.8639 (ttt) cc_final: 0.8383 (tmm) REVERT: N 334 GLN cc_start: 0.8784 (tp40) cc_final: 0.8433 (tp40) REVERT: N 337 ILE cc_start: 0.8231 (mt) cc_final: 0.7201 (mt) outliers start: 34 outliers final: 17 residues processed: 260 average time/residue: 1.2711 time to fit residues: 367.9280 Evaluate side-chains 233 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 212 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain K residue 63 LYS Chi-restraints excluded: chain L residue 129 TYR Chi-restraints excluded: chain L residue 172 SER Chi-restraints excluded: chain L residue 202 TRP Chi-restraints excluded: chain L residue 685 GLU Chi-restraints excluded: chain L residue 710 HIS Chi-restraints excluded: chain M residue 4 PHE Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 308 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 120 optimal weight: 0.0670 chunk 98 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 27 GLN E 113 HIS E 125 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 84 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18360 Z= 0.236 Angle : 0.595 23.294 26209 Z= 0.331 Chirality : 0.036 0.144 2960 Planarity : 0.004 0.032 2176 Dihedral : 29.169 135.884 5082 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.19 % Allowed : 16.83 % Favored : 78.98 % 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: 1.95 (0.23), residues: 1295 helix: 2.23 (0.19), residues: 795 sheet: -0.24 (0.61), residues: 71 loop : -0.20 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 196 HIS 0.004 0.001 HIS F 75 PHE 0.027 0.002 PHE L 122 TYR 0.019 0.002 TYR F 88 ARG 0.005 0.001 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 226 time to evaluate : 1.552 Fit side-chains revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8622 (mtp85) cc_final: 0.8415 (mtp85) REVERT: B 74 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7674 (tm-30) REVERT: B 79 LYS cc_start: 0.8252 (mttt) cc_final: 0.7937 (mttt) REVERT: B 84 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8087 (tpp) REVERT: C 90 ASP cc_start: 0.8332 (t0) cc_final: 0.7824 (t70) REVERT: D 57 LYS cc_start: 0.8352 (tppp) cc_final: 0.7961 (tptp) REVERT: D 68 ASP cc_start: 0.9024 (t70) cc_final: 0.8823 (t0) REVERT: E 59 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.6925 (pm20) REVERT: F 35 ARG cc_start: 0.8622 (ttm-80) cc_final: 0.8128 (mtp85) REVERT: F 77 LYS cc_start: 0.8668 (mmtm) cc_final: 0.8349 (mmmm) REVERT: F 80 THR cc_start: 0.8999 (OUTLIER) cc_final: 0.8713 (p) REVERT: G 73 ASN cc_start: 0.8677 (t0) cc_final: 0.8224 (t0) REVERT: G 92 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7819 (mt-10) REVERT: H 34 LYS cc_start: 0.7613 (tptm) cc_final: 0.7216 (mmtm) REVERT: H 47 GLN cc_start: 0.8632 (tt0) cc_final: 0.8286 (tt0) REVERT: H 86 ARG cc_start: 0.7558 (mmt90) cc_final: 0.7082 (mmt90) REVERT: L 90 SER cc_start: 0.6851 (m) cc_final: 0.6353 (p) REVERT: L 204 ASP cc_start: 0.8512 (t0) cc_final: 0.8153 (t0) REVERT: L 659 LYS cc_start: 0.9046 (pttt) cc_final: 0.8704 (ttpp) REVERT: L 665 GLN cc_start: 0.9286 (tp-100) cc_final: 0.8959 (tp-100) REVERT: L 693 GLU cc_start: 0.8193 (pp20) cc_final: 0.7983 (pp20) REVERT: L 694 GLN cc_start: 0.8558 (mt0) cc_final: 0.8060 (mt0) REVERT: L 695 ASN cc_start: 0.8722 (m-40) cc_final: 0.8399 (m110) REVERT: L 710 HIS cc_start: 0.7308 (OUTLIER) cc_final: 0.6987 (m-70) REVERT: N 305 SER cc_start: 0.8589 (m) cc_final: 0.8240 (t) REVERT: N 322 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8528 (mm-30) REVERT: N 337 ILE cc_start: 0.8294 (mt) cc_final: 0.7226 (mt) outliers start: 47 outliers final: 20 residues processed: 248 average time/residue: 1.2387 time to fit residues: 343.2826 Evaluate side-chains 225 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 200 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain K residue 63 LYS Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 129 TYR Chi-restraints excluded: chain L residue 202 TRP Chi-restraints excluded: chain L residue 679 ILE Chi-restraints excluded: chain L residue 710 HIS Chi-restraints excluded: chain M residue 4 PHE Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 324 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 2.9990 chunk 108 optimal weight: 0.0010 chunk 75 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN C 24 GLN C 89 ASN C 94 ASN D 47 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 84 HIS ** N 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18360 Z= 0.203 Angle : 0.592 27.812 26209 Z= 0.322 Chirality : 0.035 0.153 2960 Planarity : 0.004 0.034 2176 Dihedral : 29.174 135.657 5082 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.92 % Allowed : 18.52 % Favored : 77.56 % 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: 1.99 (0.23), residues: 1295 helix: 2.25 (0.19), residues: 794 sheet: -0.21 (0.62), residues: 71 loop : -0.15 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 202 HIS 0.004 0.001 HIS F 75 PHE 0.029 0.002 PHE L 122 TYR 0.010 0.001 TYR H 83 ARG 0.007 0.000 ARG M 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 223 time to evaluate : 1.621 Fit side-chains REVERT: A 79 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.6946 (tttt) REVERT: B 74 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7887 (tm-30) REVERT: B 79 LYS cc_start: 0.8186 (mttt) cc_final: 0.7904 (mttt) REVERT: B 84 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8120 (tpp) REVERT: C 41 GLU cc_start: 0.8199 (tt0) cc_final: 0.7903 (tt0) REVERT: C 90 ASP cc_start: 0.8285 (t0) cc_final: 0.7603 (t70) REVERT: C 92 GLU cc_start: 0.7813 (pm20) cc_final: 0.7579 (pm20) REVERT: D 57 LYS cc_start: 0.8384 (tppp) cc_final: 0.7940 (tptp) REVERT: D 84 ASN cc_start: 0.8806 (m110) cc_final: 0.8562 (m-40) REVERT: E 42 ARG cc_start: 0.7898 (mtm-85) cc_final: 0.7159 (mtt180) REVERT: E 59 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.6922 (pm20) REVERT: E 60 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7562 (mt) REVERT: E 73 GLU cc_start: 0.7767 (tt0) cc_final: 0.7271 (tt0) REVERT: E 125 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8350 (mp10) REVERT: F 77 LYS cc_start: 0.8636 (mmtm) cc_final: 0.8356 (mmmm) REVERT: G 92 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7854 (mt-10) REVERT: H 34 LYS cc_start: 0.7509 (tptm) cc_final: 0.7133 (mmtm) REVERT: H 47 GLN cc_start: 0.8682 (tt0) cc_final: 0.8340 (tt0) REVERT: H 86 ARG cc_start: 0.7615 (mmt90) cc_final: 0.7376 (mmt90) REVERT: L 90 SER cc_start: 0.6928 (m) cc_final: 0.6387 (p) REVERT: L 204 ASP cc_start: 0.8510 (t0) cc_final: 0.8141 (t0) REVERT: L 659 LYS cc_start: 0.9076 (pttt) cc_final: 0.8637 (mmtm) REVERT: L 665 GLN cc_start: 0.9254 (tp-100) cc_final: 0.8969 (tp40) REVERT: L 685 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: L 694 GLN cc_start: 0.8519 (mt0) cc_final: 0.8250 (mt0) REVERT: L 695 ASN cc_start: 0.8623 (m-40) cc_final: 0.8318 (m110) REVERT: L 710 HIS cc_start: 0.7378 (OUTLIER) cc_final: 0.7017 (m-70) REVERT: N 305 SER cc_start: 0.8627 (m) cc_final: 0.8268 (t) REVERT: N 322 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8520 (mm-30) outliers start: 44 outliers final: 27 residues processed: 246 average time/residue: 1.1894 time to fit residues: 327.4692 Evaluate side-chains 237 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 202 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 63 LYS Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 129 TYR Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 202 TRP Chi-restraints excluded: chain L residue 685 GLU Chi-restraints excluded: chain L residue 710 HIS Chi-restraints excluded: chain M residue 4 PHE Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 324 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN C 94 ASN D 109 HIS ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN L 78 ASN N 282 GLN ** N 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18360 Z= 0.245 Angle : 0.594 19.340 26209 Z= 0.331 Chirality : 0.035 0.170 2960 Planarity : 0.004 0.046 2176 Dihedral : 29.246 135.080 5082 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.92 % Allowed : 19.86 % Favored : 76.22 % 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: 1.87 (0.23), residues: 1295 helix: 2.15 (0.18), residues: 793 sheet: -0.17 (0.65), residues: 69 loop : -0.19 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 202 HIS 0.004 0.001 HIS F 75 PHE 0.019 0.002 PHE L 118 TYR 0.013 0.002 TYR H 83 ARG 0.009 0.001 ARG M 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 217 time to evaluate : 1.502 Fit side-chains REVERT: A 79 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.6935 (tttt) REVERT: B 79 LYS cc_start: 0.8243 (mttt) cc_final: 0.7950 (mttt) REVERT: B 84 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8180 (tpp) REVERT: C 41 GLU cc_start: 0.8144 (tt0) cc_final: 0.7853 (tt0) REVERT: C 90 ASP cc_start: 0.8363 (t0) cc_final: 0.7553 (t70) REVERT: C 92 GLU cc_start: 0.7870 (pm20) cc_final: 0.7587 (pm20) REVERT: D 57 LYS cc_start: 0.8374 (tppp) cc_final: 0.7889 (tptp) REVERT: D 84 ASN cc_start: 0.8841 (m110) cc_final: 0.8593 (m-40) REVERT: E 42 ARG cc_start: 0.7917 (mtm-85) cc_final: 0.7160 (mtt180) REVERT: E 59 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.6960 (pm20) REVERT: E 73 GLU cc_start: 0.7868 (tt0) cc_final: 0.7372 (tt0) REVERT: F 35 ARG cc_start: 0.8613 (ttm-80) cc_final: 0.8229 (mtp85) REVERT: F 77 LYS cc_start: 0.8615 (mmtm) cc_final: 0.8315 (mmmm) REVERT: G 92 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7824 (mt-10) REVERT: H 34 LYS cc_start: 0.7532 (tptm) cc_final: 0.7105 (mmtm) REVERT: H 47 GLN cc_start: 0.8594 (tt0) cc_final: 0.8291 (tt0) REVERT: L 204 ASP cc_start: 0.8626 (t0) cc_final: 0.8257 (t70) REVERT: L 652 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7249 (pt0) REVERT: L 659 LYS cc_start: 0.9027 (pttt) cc_final: 0.8589 (mmtm) REVERT: L 665 GLN cc_start: 0.9276 (tp-100) cc_final: 0.9042 (tp40) REVERT: L 685 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7815 (tm-30) REVERT: L 694 GLN cc_start: 0.8555 (mt0) cc_final: 0.8266 (mt0) REVERT: N 305 SER cc_start: 0.8755 (m) cc_final: 0.8431 (p) REVERT: N 322 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8550 (mm-30) outliers start: 44 outliers final: 21 residues processed: 240 average time/residue: 1.2377 time to fit residues: 331.4604 Evaluate side-chains 237 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 211 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 63 LYS Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 129 TYR Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 202 TRP Chi-restraints excluded: chain L residue 652 GLU Chi-restraints excluded: chain L residue 685 GLU Chi-restraints excluded: chain L residue 698 VAL Chi-restraints excluded: chain M residue 4 PHE Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 41 GLN Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 324 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 90 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 153 optimal weight: 0.0770 chunk 127 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 93 GLN D 63 ASN E 39 HIS E 125 GLN ** N 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18360 Z= 0.193 Angle : 0.586 17.072 26209 Z= 0.325 Chirality : 0.035 0.155 2960 Planarity : 0.004 0.038 2176 Dihedral : 29.225 135.458 5082 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.74 % Allowed : 20.39 % Favored : 75.87 % 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: 2.00 (0.23), residues: 1295 helix: 2.22 (0.18), residues: 788 sheet: -0.15 (0.64), residues: 71 loop : -0.03 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 202 HIS 0.004 0.001 HIS F 75 PHE 0.020 0.001 PHE L 118 TYR 0.016 0.001 TYR D 83 ARG 0.009 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 228 time to evaluate : 1.360 Fit side-chains REVERT: A 59 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7543 (pm20) REVERT: A 79 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.6911 (tttt) REVERT: A 129 ARG cc_start: 0.8575 (tpt90) cc_final: 0.8283 (tpp80) REVERT: B 79 LYS cc_start: 0.8248 (mttt) cc_final: 0.7947 (mttt) REVERT: C 41 GLU cc_start: 0.8193 (tt0) cc_final: 0.7917 (tt0) REVERT: C 90 ASP cc_start: 0.8379 (t0) cc_final: 0.7491 (t70) REVERT: C 92 GLU cc_start: 0.7858 (pm20) cc_final: 0.7565 (pm20) REVERT: D 57 LYS cc_start: 0.8386 (tppp) cc_final: 0.7994 (tptp) REVERT: D 84 ASN cc_start: 0.8948 (m110) cc_final: 0.8735 (m-40) REVERT: E 42 ARG cc_start: 0.7899 (mtm-85) cc_final: 0.7154 (mtt180) REVERT: E 59 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.6925 (pm20) REVERT: E 73 GLU cc_start: 0.7836 (tt0) cc_final: 0.7337 (tt0) REVERT: F 35 ARG cc_start: 0.8624 (ttm-80) cc_final: 0.8234 (mtp85) REVERT: F 77 LYS cc_start: 0.8656 (mmtm) cc_final: 0.8375 (mmmm) REVERT: F 92 ARG cc_start: 0.8808 (ptm-80) cc_final: 0.8459 (ptm160) REVERT: G 92 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7772 (mt-10) REVERT: H 34 LYS cc_start: 0.7503 (tptm) cc_final: 0.7035 (mmtm) REVERT: H 35 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8115 (mm-30) REVERT: H 47 GLN cc_start: 0.8622 (tt0) cc_final: 0.8314 (tt0) REVERT: L 51 LYS cc_start: 0.8746 (tttt) cc_final: 0.8329 (tptm) REVERT: L 90 SER cc_start: 0.6817 (m) cc_final: 0.6284 (p) REVERT: L 204 ASP cc_start: 0.8601 (t0) cc_final: 0.8249 (t70) REVERT: L 659 LYS cc_start: 0.9053 (pttt) cc_final: 0.8609 (mmtm) REVERT: L 665 GLN cc_start: 0.9259 (tp-100) cc_final: 0.8991 (tp40) REVERT: L 685 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7833 (tm-30) REVERT: N 305 SER cc_start: 0.8720 (m) cc_final: 0.8387 (p) REVERT: N 322 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8537 (mm-30) outliers start: 42 outliers final: 24 residues processed: 250 average time/residue: 1.2539 time to fit residues: 349.1220 Evaluate side-chains 239 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 211 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 63 LYS Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 129 TYR Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 202 TRP Chi-restraints excluded: chain L residue 685 GLU Chi-restraints excluded: chain M residue 4 PHE Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 41 GLN Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 324 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN D 109 HIS ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 2 GLN ** N 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18360 Z= 0.295 Angle : 0.629 23.137 26209 Z= 0.344 Chirality : 0.037 0.192 2960 Planarity : 0.004 0.045 2176 Dihedral : 29.301 134.626 5082 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.10 % Allowed : 20.21 % Favored : 75.69 % 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 (0.23), residues: 1295 helix: 1.97 (0.18), residues: 796 sheet: -0.40 (0.59), residues: 81 loop : -0.29 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 202 HIS 0.006 0.001 HIS L 144 PHE 0.015 0.002 PHE L 660 TYR 0.015 0.002 TYR D 83 ARG 0.008 0.001 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 219 time to evaluate : 1.387 Fit side-chains REVERT: A 73 GLU cc_start: 0.8603 (tt0) cc_final: 0.8242 (pt0) REVERT: A 79 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.6942 (tttt) REVERT: A 123 ASP cc_start: 0.8740 (m-30) cc_final: 0.8301 (m-30) REVERT: B 79 LYS cc_start: 0.8305 (mttt) cc_final: 0.8007 (mttt) REVERT: C 41 GLU cc_start: 0.8263 (tt0) cc_final: 0.7974 (tt0) REVERT: C 90 ASP cc_start: 0.8369 (t0) cc_final: 0.7448 (t70) REVERT: C 92 GLU cc_start: 0.7834 (pm20) cc_final: 0.7514 (pm20) REVERT: C 104 GLN cc_start: 0.8367 (mm-40) cc_final: 0.8067 (mm110) REVERT: D 57 LYS cc_start: 0.8535 (tppp) cc_final: 0.8116 (tptp) REVERT: D 84 ASN cc_start: 0.8927 (m110) cc_final: 0.8703 (m-40) REVERT: E 42 ARG cc_start: 0.7936 (mtm-85) cc_final: 0.7139 (mtt180) REVERT: E 59 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7016 (pm20) REVERT: E 73 GLU cc_start: 0.7900 (tt0) cc_final: 0.7452 (tt0) REVERT: E 125 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8465 (mp10) REVERT: F 77 LYS cc_start: 0.8645 (mmtm) cc_final: 0.8351 (mmmm) REVERT: F 92 ARG cc_start: 0.8830 (ptm-80) cc_final: 0.8555 (ptm160) REVERT: G 19 SER cc_start: 0.8589 (t) cc_final: 0.8212 (p) REVERT: G 92 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7789 (mt-10) REVERT: H 34 LYS cc_start: 0.7561 (tptm) cc_final: 0.7060 (mmtm) REVERT: H 35 GLU cc_start: 0.8247 (mm-30) cc_final: 0.8036 (mm-30) REVERT: H 47 GLN cc_start: 0.8571 (tt0) cc_final: 0.8268 (tt0) REVERT: H 95 GLN cc_start: 0.8554 (tt0) cc_final: 0.8338 (tt0) REVERT: L 115 MET cc_start: 0.8846 (tpp) cc_final: 0.8556 (tmm) REVERT: L 204 ASP cc_start: 0.8715 (t0) cc_final: 0.8412 (t70) REVERT: L 652 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7448 (pt0) REVERT: L 659 LYS cc_start: 0.9032 (pttt) cc_final: 0.8695 (mmtm) REVERT: M 2 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7579 (tm130) REVERT: N 305 SER cc_start: 0.8941 (m) cc_final: 0.8517 (p) REVERT: N 322 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8661 (mm-30) outliers start: 46 outliers final: 27 residues processed: 248 average time/residue: 1.2960 time to fit residues: 358.4319 Evaluate side-chains 248 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 216 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 63 LYS Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 129 TYR Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 202 TRP Chi-restraints excluded: chain L residue 652 GLU Chi-restraints excluded: chain L residue 698 VAL Chi-restraints excluded: chain M residue 2 GLN Chi-restraints excluded: chain M residue 4 PHE Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 41 GLN Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 306 SER Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 324 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 7.9990 chunk 46 optimal weight: 0.0770 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 139 optimal weight: 0.5980 chunk 146 optimal weight: 0.9980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN D 49 HIS D 63 ASN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 125 GLN F 75 HIS L 702 GLN L 710 HIS ** N 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18360 Z= 0.197 Angle : 0.627 24.751 26209 Z= 0.337 Chirality : 0.035 0.179 2960 Planarity : 0.004 0.037 2176 Dihedral : 29.257 135.389 5082 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.29 % Allowed : 22.08 % Favored : 74.62 % 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: 1.88 (0.23), residues: 1295 helix: 2.16 (0.18), residues: 788 sheet: -0.57 (0.60), residues: 73 loop : -0.08 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 202 HIS 0.005 0.001 HIS D 49 PHE 0.018 0.002 PHE L 122 TYR 0.018 0.002 TYR H 83 ARG 0.009 0.000 ARG M 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 233 time to evaluate : 1.512 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8575 (tt0) cc_final: 0.8224 (pt0) REVERT: A 79 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7784 (tttm) REVERT: A 123 ASP cc_start: 0.8698 (m-30) cc_final: 0.8298 (m-30) REVERT: B 79 LYS cc_start: 0.8276 (mttt) cc_final: 0.7971 (mttt) REVERT: C 41 GLU cc_start: 0.8262 (tt0) cc_final: 0.7978 (tt0) REVERT: C 90 ASP cc_start: 0.8358 (t0) cc_final: 0.7413 (t70) REVERT: C 92 GLU cc_start: 0.7919 (pm20) cc_final: 0.7578 (pm20) REVERT: D 57 LYS cc_start: 0.8485 (tppp) cc_final: 0.8072 (tptp) REVERT: E 42 ARG cc_start: 0.7936 (mtm-85) cc_final: 0.7120 (mtt180) REVERT: E 59 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.6872 (pm20) REVERT: E 73 GLU cc_start: 0.7830 (tt0) cc_final: 0.7277 (tt0) REVERT: F 35 ARG cc_start: 0.8616 (ttm-80) cc_final: 0.8237 (mtp85) REVERT: F 77 LYS cc_start: 0.8584 (mmtm) cc_final: 0.8365 (mmmm) REVERT: F 92 ARG cc_start: 0.8863 (ptm-80) cc_final: 0.8655 (ptm160) REVERT: G 62 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8459 (tt) REVERT: G 73 ASN cc_start: 0.8613 (t0) cc_final: 0.8103 (t0) REVERT: G 92 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7728 (mt-10) REVERT: H 34 LYS cc_start: 0.7554 (tptm) cc_final: 0.7029 (mmtm) REVERT: H 35 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7988 (mm-30) REVERT: H 47 GLN cc_start: 0.8582 (tt0) cc_final: 0.8270 (tt0) REVERT: L 51 LYS cc_start: 0.8755 (tttt) cc_final: 0.8357 (tptm) REVERT: L 115 MET cc_start: 0.8884 (tpp) cc_final: 0.8617 (tmm) REVERT: L 204 ASP cc_start: 0.8694 (t0) cc_final: 0.8350 (t70) REVERT: L 212 GLU cc_start: 0.8228 (pt0) cc_final: 0.7604 (pm20) REVERT: L 665 GLN cc_start: 0.9241 (tp-100) cc_final: 0.8949 (tp40) REVERT: L 685 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.8016 (tm-30) REVERT: N 305 SER cc_start: 0.8831 (m) cc_final: 0.8453 (p) REVERT: N 322 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8533 (mm-30) outliers start: 37 outliers final: 20 residues processed: 254 average time/residue: 1.3325 time to fit residues: 376.6272 Evaluate side-chains 242 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 218 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 63 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 129 TYR Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 202 TRP Chi-restraints excluded: chain L residue 685 GLU Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 41 GLN Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain N residue 347 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 0.1980 chunk 142 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN D 49 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN L 710 HIS ** N 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18360 Z= 0.213 Angle : 0.640 23.669 26209 Z= 0.341 Chirality : 0.036 0.278 2960 Planarity : 0.004 0.066 2176 Dihedral : 29.231 135.151 5082 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.76 % Allowed : 22.71 % Favored : 74.53 % 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: 1.82 (0.23), residues: 1295 helix: 2.10 (0.18), residues: 788 sheet: -0.59 (0.60), residues: 73 loop : -0.07 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 202 HIS 0.004 0.001 HIS L 144 PHE 0.017 0.002 PHE L 118 TYR 0.021 0.002 TYR D 83 ARG 0.009 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 224 time to evaluate : 1.604 Fit side-chains REVERT: A 73 GLU cc_start: 0.8572 (tt0) cc_final: 0.8209 (pt0) REVERT: A 79 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7779 (tttm) REVERT: B 79 LYS cc_start: 0.8280 (mttt) cc_final: 0.7972 (mttt) REVERT: C 18 SER cc_start: 0.8908 (m) cc_final: 0.8580 (m) REVERT: C 41 GLU cc_start: 0.8267 (tt0) cc_final: 0.8035 (tt0) REVERT: C 90 ASP cc_start: 0.8363 (t0) cc_final: 0.7406 (t70) REVERT: C 92 GLU cc_start: 0.7912 (pm20) cc_final: 0.7570 (pm20) REVERT: D 57 LYS cc_start: 0.8519 (tppp) cc_final: 0.8103 (tptp) REVERT: E 42 ARG cc_start: 0.7920 (mtm-85) cc_final: 0.7097 (mtt180) REVERT: E 59 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.6925 (pm20) REVERT: E 73 GLU cc_start: 0.7759 (tt0) cc_final: 0.7265 (tt0) REVERT: F 35 ARG cc_start: 0.8610 (ttm-80) cc_final: 0.8317 (mtp85) REVERT: F 77 LYS cc_start: 0.8581 (mmtm) cc_final: 0.8363 (mmmm) REVERT: F 92 ARG cc_start: 0.8923 (ptm-80) cc_final: 0.8642 (ptm160) REVERT: G 73 ASN cc_start: 0.8620 (t0) cc_final: 0.8088 (t0) REVERT: G 92 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7727 (mt-10) REVERT: H 34 LYS cc_start: 0.7583 (tptm) cc_final: 0.7068 (mmtm) REVERT: H 95 GLN cc_start: 0.8662 (tt0) cc_final: 0.8318 (tt0) REVERT: L 51 LYS cc_start: 0.8752 (tttt) cc_final: 0.8351 (tptm) REVERT: L 115 MET cc_start: 0.8886 (tpp) cc_final: 0.8612 (tmm) REVERT: L 204 ASP cc_start: 0.8716 (t0) cc_final: 0.8369 (t70) REVERT: N 302 ARG cc_start: 0.8254 (mmm160) cc_final: 0.7881 (tmm-80) REVERT: N 305 SER cc_start: 0.8839 (m) cc_final: 0.8465 (p) REVERT: N 322 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8568 (mm-30) outliers start: 31 outliers final: 20 residues processed: 242 average time/residue: 1.3072 time to fit residues: 350.9312 Evaluate side-chains 239 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 217 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 63 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 129 TYR Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 202 TRP Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 41 GLN Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 306 SER Chi-restraints excluded: chain N residue 324 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 145 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 134 optimal weight: 0.0270 overall best weight: 1.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN D 84 ASN E 39 HIS E 68 GLN E 125 GLN G 110 ASN L 710 HIS M 2 GLN ** N 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 18360 Z= 0.340 Angle : 0.681 24.710 26209 Z= 0.368 Chirality : 0.038 0.258 2960 Planarity : 0.005 0.045 2176 Dihedral : 29.404 134.104 5082 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.47 % Allowed : 22.53 % Favored : 74.00 % 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: 1.32 (0.23), residues: 1295 helix: 1.75 (0.18), residues: 794 sheet: -0.64 (0.62), residues: 73 loop : -0.44 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 202 HIS 0.006 0.001 HIS L 144 PHE 0.016 0.002 PHE G 25 TYR 0.029 0.002 TYR H 83 ARG 0.009 0.001 ARG H 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 228 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.6930 (tttt) REVERT: B 96 THR cc_start: 0.9277 (m) cc_final: 0.9055 (m) REVERT: C 41 GLU cc_start: 0.8259 (tt0) cc_final: 0.7997 (tt0) REVERT: C 90 ASP cc_start: 0.8383 (t0) cc_final: 0.7869 (t70) REVERT: C 92 GLU cc_start: 0.7909 (pm20) cc_final: 0.7662 (pm20) REVERT: C 104 GLN cc_start: 0.8369 (mm-40) cc_final: 0.7995 (mm110) REVERT: D 57 LYS cc_start: 0.8584 (tppp) cc_final: 0.8333 (tppp) REVERT: E 42 ARG cc_start: 0.7948 (mtm-85) cc_final: 0.7092 (mtt180) REVERT: E 73 GLU cc_start: 0.7868 (tt0) cc_final: 0.7399 (tt0) REVERT: F 35 ARG cc_start: 0.8651 (ttm-80) cc_final: 0.8356 (mtp85) REVERT: F 77 LYS cc_start: 0.8606 (mmtm) cc_final: 0.8400 (mmmm) REVERT: F 92 ARG cc_start: 0.8869 (ptm-80) cc_final: 0.8641 (ptm160) REVERT: G 19 SER cc_start: 0.8662 (t) cc_final: 0.8280 (p) REVERT: G 62 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8543 (tt) REVERT: G 73 ASN cc_start: 0.8603 (t0) cc_final: 0.8347 (t0) REVERT: G 92 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7698 (mt-10) REVERT: H 34 LYS cc_start: 0.7573 (tptm) cc_final: 0.7078 (mmtm) REVERT: H 35 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8151 (mm-30) REVERT: H 42 TYR cc_start: 0.7901 (t80) cc_final: 0.7686 (t80) REVERT: H 95 GLN cc_start: 0.8668 (tt0) cc_final: 0.8345 (tt0) REVERT: L 51 LYS cc_start: 0.8755 (tttt) cc_final: 0.8408 (tptm) REVERT: L 115 MET cc_start: 0.8964 (tpp) cc_final: 0.8633 (tmm) REVERT: L 204 ASP cc_start: 0.8782 (t0) cc_final: 0.8451 (t70) REVERT: L 710 HIS cc_start: 0.7170 (OUTLIER) cc_final: 0.6964 (t-90) REVERT: M 2 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8142 (tm130) REVERT: N 305 SER cc_start: 0.9061 (m) cc_final: 0.8623 (p) REVERT: N 322 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8718 (mm-30) outliers start: 39 outliers final: 27 residues processed: 254 average time/residue: 1.3090 time to fit residues: 369.4408 Evaluate side-chains 253 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 222 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 129 TYR Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 202 TRP Chi-restraints excluded: chain L residue 664 ASP Chi-restraints excluded: chain L residue 672 ASP Chi-restraints excluded: chain L residue 710 HIS Chi-restraints excluded: chain M residue 2 GLN Chi-restraints excluded: chain M residue 4 PHE Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 41 GLN Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 306 SER Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain N residue 347 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 126 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN D 49 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 125 GLN G 110 ASN ** N 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.157279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.133428 restraints weight = 43031.526| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.45 r_work: 0.3623 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 495 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 555 | |-----------------------------------------------------------------------------| r_final: 0.3613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 18360 Z= 0.250 Angle : 0.670 22.603 26209 Z= 0.360 Chirality : 0.037 0.280 2960 Planarity : 0.005 0.070 2176 Dihedral : 29.406 134.640 5082 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.85 % Allowed : 23.78 % Favored : 73.37 % 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: 1.35 (0.23), residues: 1295 helix: 1.77 (0.18), residues: 788 sheet: -0.70 (0.62), residues: 73 loop : -0.39 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 202 HIS 0.007 0.001 HIS E 39 PHE 0.017 0.002 PHE L 118 TYR 0.023 0.002 TYR D 83 ARG 0.009 0.001 ARG H 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6243.64 seconds wall clock time: 109 minutes 42.76 seconds (6582.76 seconds total)