Starting phenix.real_space_refine on Sun Jun 15 07:28:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h1t_34431/06_2025/8h1t_34431.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h1t_34431/06_2025/8h1t_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/cci-nas-00/data/ceres_data/8h1t_34431/06_2025/8h1t_34431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h1t_34431/06_2025/8h1t_34431.map" model { file = "/net/cci-nas-00/data/ceres_data/8h1t_34431/06_2025/8h1t_34431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h1t_34431/06_2025/8h1t_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-5710/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: 13.61, per 1000 atoms: 0.78 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.23 Conformation dependent library (CDL) restraints added in 1.7 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: 8.95 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: 10.06 Time building geometry restraints manager: 6.18 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: 2.16 - 2.71: 769 2.71 - 3.26: 16082 3.26 - 3.81: 32948 3.81 - 4.35: 39282 4.35 - 4.90: 57777 Nonbonded interactions: 146858 Sorted by model distance: 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=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.278 3.040 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.290 3.040 nonbonded pdb=" NE2 GLN E 55 " pdb=" O ARG F 40 " model vdw 2.294 3.120 ... (remaining 146853 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: 425.300 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: 0.020 Extract box with map and model: 9.530 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 57.450 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.150 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:49.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 542.540 ------------------------------------------------------------------------------- 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 0.094 18361 Z= 0.157 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 : 2.164 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 Details of bonding type rmsd hydrogen bonds : bond 0.10243 ( 1027) hydrogen bonds : angle 3.98155 ( 2607) covalent geometry : bond 0.00277 (18360) covalent geometry : angle 0.53199 (26209) Misc. bond : bond 0.09441 ( 1) *********************** 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 to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 1.503 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: 1.6640 time to fit residues: 642.2655 Evaluate side-chains 230 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 1.609 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.3980 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: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.165473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.143346 restraints weight = 44256.718| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.59 r_work: 0.3781 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3785 r_free = 0.3785 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 495 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 570 | |-----------------------------------------------------------------------------| r_final: 0.3778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18361 Z= 0.162 Angle : 0.591 15.143 26209 Z= 0.332 Chirality : 0.035 0.157 2960 Planarity : 0.004 0.038 2176 Dihedral : 29.001 136.149 5084 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.03 % Allowed : 15.32 % Favored : 81.66 % 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: 2.14 (0.24), residues: 1295 helix: 2.41 (0.19), residues: 785 sheet: -0.23 (0.60), residues: 71 loop : -0.11 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP L 202 HIS 0.007 0.001 HIS D 109 PHE 0.026 0.002 PHE L 118 TYR 0.012 0.001 TYR A 54 ARG 0.009 0.001 ARG M 54 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 1027) hydrogen bonds : angle 3.25575 ( 2607) covalent geometry : bond 0.00361 (18360) covalent geometry : angle 0.59113 (26209) Misc. bond : bond 0.00229 ( 1) *********************** 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 286 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 252 time to evaluate : 1.903 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8452 (mm) cc_final: 0.8218 (mt) REVERT: B 35 ARG cc_start: 0.8312 (mtp85) cc_final: 0.7839 (mtp85) REVERT: B 74 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7576 (tm-30) REVERT: C 90 ASP cc_start: 0.8540 (t0) cc_final: 0.7555 (t70) REVERT: C 116 LEU cc_start: 0.8494 (mp) cc_final: 0.8292 (mp) REVERT: D 34 LYS cc_start: 0.8118 (mppt) cc_final: 0.7861 (mppt) REVERT: D 57 LYS cc_start: 0.8256 (tppp) cc_final: 0.7741 (tptt) REVERT: E 59 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6658 (pm20) REVERT: F 77 LYS cc_start: 0.8640 (mmtm) cc_final: 0.8254 (mmmm) REVERT: G 73 ASN cc_start: 0.8584 (t0) cc_final: 0.8157 (t0) REVERT: H 34 LYS cc_start: 0.8012 (tptm) cc_final: 0.7567 (mmtm) REVERT: H 47 GLN cc_start: 0.8773 (tt0) cc_final: 0.8483 (tt0) REVERT: L 694 GLN cc_start: 0.8058 (mt0) cc_final: 0.7714 (mt0) REVERT: L 710 HIS cc_start: 0.6367 (OUTLIER) cc_final: 0.5886 (m-70) REVERT: N 337 ILE cc_start: 0.8100 (mt) cc_final: 0.7102 (mt) outliers start: 34 outliers final: 15 residues processed: 268 average time/residue: 1.3235 time to fit residues: 393.3807 Evaluate side-chains 224 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 1.355 ------------------------------------------------------------------------------- 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 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 710 HIS Chi-restraints excluded: chain M residue 4 PHE 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 37 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 153 optimal weight: 0.0060 chunk 148 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 44 optimal weight: 0.0970 chunk 98 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 157 optimal weight: 0.1980 chunk 136 optimal weight: 0.7980 overall best weight: 0.3794 ------------------------------------------------------------------------------- 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 D 47 GLN D 109 HIS ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS E 125 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 ASN L 84 HIS L 133 ASN L 695 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.164239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.141849 restraints weight = 43677.038| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.54 r_work: 0.3781 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3796 r_free = 0.3796 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 570 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3796 r_free = 0.3796 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 594 | |-----------------------------------------------------------------------------| r_final: 0.3796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18361 Z= 0.141 Angle : 0.575 17.391 26209 Z= 0.322 Chirality : 0.035 0.245 2960 Planarity : 0.004 0.034 2176 Dihedral : 29.029 136.401 5082 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.47 % Allowed : 18.43 % Favored : 78.09 % 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: 2.45 (0.19), residues: 785 sheet: -0.29 (0.60), residues: 71 loop : -0.11 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 202 HIS 0.004 0.001 HIS F 75 PHE 0.019 0.001 PHE L 118 TYR 0.009 0.001 TYR H 83 ARG 0.006 0.000 ARG L 146 Details of bonding type rmsd hydrogen bonds : bond 0.03241 ( 1027) hydrogen bonds : angle 3.14903 ( 2607) covalent geometry : bond 0.00309 (18360) covalent geometry : angle 0.57508 (26209) Misc. bond : bond 0.00092 ( 1) *********************** 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 261 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 222 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8407 (mtp85) cc_final: 0.8142 (mtp85) REVERT: B 74 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: C 90 ASP cc_start: 0.8477 (t0) cc_final: 0.7940 (t70) REVERT: C 92 GLU cc_start: 0.8168 (pm20) cc_final: 0.7840 (pm20) REVERT: D 34 LYS cc_start: 0.8143 (mppt) cc_final: 0.7884 (mppt) REVERT: E 59 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6635 (pm20) REVERT: F 35 ARG cc_start: 0.8499 (ttm-80) cc_final: 0.8020 (mtp85) REVERT: F 77 LYS cc_start: 0.8608 (mmtm) cc_final: 0.8202 (mmmm) REVERT: F 80 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8633 (p) REVERT: G 73 ASN cc_start: 0.8623 (t0) cc_final: 0.8189 (t0) REVERT: G 92 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7906 (mt-10) REVERT: H 34 LYS cc_start: 0.8028 (tptm) cc_final: 0.7593 (mmtm) REVERT: H 47 GLN cc_start: 0.8810 (tt0) cc_final: 0.8502 (tt0) REVERT: H 86 ARG cc_start: 0.7724 (mmt90) cc_final: 0.7349 (mmt90) outliers start: 39 outliers final: 14 residues processed: 239 average time/residue: 1.2850 time to fit residues: 341.8422 Evaluate side-chains 220 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 203 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU 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 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 44 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 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 92 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 17 optimal weight: 9.9990 chunk 19 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 C 24 GLN C 94 ASN D 47 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN E 125 GLN H 95 GLN L 78 ASN ** L 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 94 HIS N 282 GLN ** N 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.159101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.135357 restraints weight = 43282.530| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.53 r_work: 0.3662 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 594 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 605 | |-----------------------------------------------------------------------------| r_final: 0.3667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18361 Z= 0.196 Angle : 0.618 27.461 26209 Z= 0.337 Chirality : 0.036 0.149 2960 Planarity : 0.004 0.033 2176 Dihedral : 29.217 135.129 5082 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.63 % Allowed : 17.81 % 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: 1.86 (0.23), residues: 1295 helix: 2.15 (0.18), residues: 794 sheet: -0.12 (0.63), residues: 71 loop : -0.23 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 196 HIS 0.004 0.001 HIS L 193 PHE 0.027 0.002 PHE L 122 TYR 0.013 0.002 TYR A 54 ARG 0.011 0.001 ARG M 74 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 1027) hydrogen bonds : angle 3.22449 ( 2607) covalent geometry : bond 0.00440 (18360) covalent geometry : angle 0.61823 (26209) Misc. bond : bond 0.00125 ( 1) *********************** 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 286 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 234 time to evaluate : 1.541 Fit side-chains REVERT: A 79 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.6853 (tttt) REVERT: B 35 ARG cc_start: 0.8525 (mtp85) cc_final: 0.8259 (mtp85) REVERT: B 74 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7933 (tm-30) REVERT: C 41 GLU cc_start: 0.8318 (tt0) cc_final: 0.8063 (tt0) REVERT: C 90 ASP cc_start: 0.8541 (t0) cc_final: 0.7617 (t70) REVERT: C 92 GLU cc_start: 0.8177 (pm20) cc_final: 0.7728 (pm20) REVERT: D 34 LYS cc_start: 0.8090 (mppt) cc_final: 0.7803 (mppt) REVERT: D 57 LYS cc_start: 0.8028 (tptm) cc_final: 0.7744 (tppp) REVERT: D 68 ASP cc_start: 0.8964 (t70) cc_final: 0.8749 (t0) REVERT: E 42 ARG cc_start: 0.8023 (mtm-85) cc_final: 0.7234 (mtt180) REVERT: E 59 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.6773 (pm20) REVERT: E 73 GLU cc_start: 0.8433 (tt0) cc_final: 0.8083 (tt0) REVERT: F 77 LYS cc_start: 0.8640 (mmtm) cc_final: 0.8308 (mmmm) REVERT: F 80 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8686 (p) REVERT: G 73 ASN cc_start: 0.8546 (t0) cc_final: 0.8063 (t0) REVERT: G 92 GLU cc_start: 0.8414 (mt-10) cc_final: 0.7958 (mt-10) REVERT: H 34 LYS cc_start: 0.7838 (tptm) cc_final: 0.7441 (mmtm) REVERT: H 47 GLN cc_start: 0.8765 (tt0) cc_final: 0.8464 (tt0) REVERT: L 710 HIS cc_start: 0.6636 (OUTLIER) cc_final: 0.6163 (m-70) outliers start: 52 outliers final: 29 residues processed: 255 average time/residue: 1.2340 time to fit residues: 350.6073 Evaluate side-chains 233 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 64 LYS 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 117 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 64 GLU 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 65 LEU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 80 THR 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 71 VAL Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 129 TYR Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 202 TRP 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 305 SER 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 54 optimal weight: 8.9990 chunk 126 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 145 optimal weight: 0.0970 chunk 51 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 110 optimal weight: 0.0370 chunk 119 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 89 ASN C 94 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN L 84 HIS 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.160859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.136996 restraints weight = 43680.811| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.58 r_work: 0.3687 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 605 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 608 | |-----------------------------------------------------------------------------| r_final: 0.3692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18361 Z= 0.145 Angle : 0.600 26.945 26209 Z= 0.326 Chirality : 0.035 0.174 2960 Planarity : 0.004 0.041 2176 Dihedral : 29.184 135.801 5082 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.65 % Allowed : 20.57 % Favored : 75.78 % 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: 1.98 (0.24), residues: 1295 helix: 2.24 (0.18), residues: 788 sheet: -0.23 (0.62), residues: 71 loop : -0.12 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 202 HIS 0.005 0.001 HIS F 75 PHE 0.015 0.001 PHE L 122 TYR 0.012 0.001 TYR L 223 ARG 0.008 0.000 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.03154 ( 1027) hydrogen bonds : angle 3.14710 ( 2607) covalent geometry : bond 0.00319 (18360) covalent geometry : angle 0.59988 (26209) Misc. bond : bond 0.00070 ( 1) *********************** 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 270 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 229 time to evaluate : 1.385 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.6784 (tttt) REVERT: B 63 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8049 (mt-10) REVERT: B 74 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.8022 (tm-30) REVERT: B 84 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7978 (tpp) REVERT: B 88 TYR cc_start: 0.8479 (m-10) cc_final: 0.8273 (m-10) REVERT: C 41 GLU cc_start: 0.8353 (tt0) cc_final: 0.8110 (tt0) REVERT: C 90 ASP cc_start: 0.8536 (t0) cc_final: 0.7535 (t70) REVERT: C 92 GLU cc_start: 0.8257 (pm20) cc_final: 0.7728 (pm20) REVERT: D 34 LYS cc_start: 0.8079 (mppt) cc_final: 0.7815 (mppt) REVERT: D 57 LYS cc_start: 0.7973 (tptm) cc_final: 0.7687 (tppp) REVERT: D 68 ASP cc_start: 0.8928 (t70) cc_final: 0.8726 (t0) REVERT: E 42 ARG cc_start: 0.7965 (mtm-85) cc_final: 0.7192 (mtt180) REVERT: E 59 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6728 (pm20) REVERT: E 73 GLU cc_start: 0.8332 (tt0) cc_final: 0.7827 (tt0) REVERT: E 125 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8208 (mp10) REVERT: F 35 ARG cc_start: 0.8472 (ttm-80) cc_final: 0.7918 (mtp85) REVERT: F 44 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8529 (ptmm) REVERT: F 77 LYS cc_start: 0.8615 (mmtm) cc_final: 0.8307 (mmmm) REVERT: G 73 ASN cc_start: 0.8591 (t0) cc_final: 0.8113 (t0) REVERT: G 92 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7890 (mt-10) REVERT: H 34 LYS cc_start: 0.7815 (tptm) cc_final: 0.7341 (mmtm) REVERT: H 47 GLN cc_start: 0.8829 (tt0) cc_final: 0.8542 (tt0) outliers start: 41 outliers final: 26 residues processed: 248 average time/residue: 1.3070 time to fit residues: 361.5270 Evaluate side-chains 234 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 202 time to evaluate : 1.523 ------------------------------------------------------------------------------- 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 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 64 GLU 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 44 LYS 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 165 MET Chi-restraints excluded: chain L residue 202 TRP Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 34 GLU Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 312 PHE 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 126 optimal weight: 0.7980 chunk 154 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 140 optimal weight: 0.0170 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 0.0040 chunk 157 optimal weight: 3.9990 overall best weight: 0.5630 ------------------------------------------------------------------------------- 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 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN ** N 310 ASN ** 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 = 0.4146 r_free = 0.4146 target = 0.160517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.136908 restraints weight = 43745.191| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.52 r_work: 0.3697 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 608 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 614 | |-----------------------------------------------------------------------------| r_final: 0.3700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18361 Z= 0.147 Angle : 0.606 26.799 26209 Z= 0.328 Chirality : 0.034 0.155 2960 Planarity : 0.004 0.047 2176 Dihedral : 29.142 135.404 5082 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.54 % Allowed : 20.84 % 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: 2.00 (0.23), residues: 1295 helix: 2.24 (0.18), residues: 787 sheet: -0.18 (0.62), residues: 71 loop : -0.07 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 202 HIS 0.004 0.001 HIS F 75 PHE 0.026 0.001 PHE L 118 TYR 0.013 0.001 TYR H 42 ARG 0.010 0.000 ARG M 72 Details of bonding type rmsd hydrogen bonds : bond 0.03148 ( 1027) hydrogen bonds : angle 3.13063 ( 2607) covalent geometry : bond 0.00326 (18360) covalent geometry : angle 0.60578 (26209) Misc. bond : bond 0.00078 ( 1) *********************** 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 to be fit. rotamer outliers: 51 poor density : 219 time to evaluate : 1.540 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7592 (tttm) REVERT: A 123 ASP cc_start: 0.8665 (m-30) cc_final: 0.8273 (m-30) REVERT: B 35 ARG cc_start: 0.8621 (mtp85) cc_final: 0.8222 (mtp85) REVERT: B 74 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8059 (tm-30) REVERT: B 79 LYS cc_start: 0.7913 (mttm) cc_final: 0.7493 (mttt) REVERT: B 84 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.8002 (tpp) REVERT: C 41 GLU cc_start: 0.8399 (tt0) cc_final: 0.8155 (tt0) REVERT: C 90 ASP cc_start: 0.8565 (t0) cc_final: 0.7561 (t70) REVERT: C 92 GLU cc_start: 0.8237 (pm20) cc_final: 0.7719 (pm20) REVERT: D 34 LYS cc_start: 0.8073 (mppt) cc_final: 0.7804 (mppt) REVERT: D 57 LYS cc_start: 0.7984 (tptm) cc_final: 0.7679 (tppp) REVERT: D 68 ASP cc_start: 0.8931 (t70) cc_final: 0.8696 (t0) REVERT: E 42 ARG cc_start: 0.7967 (mtm-85) cc_final: 0.7183 (mtt180) REVERT: E 59 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.6671 (pm20) REVERT: E 73 GLU cc_start: 0.8387 (tt0) cc_final: 0.7811 (tt0) REVERT: F 35 ARG cc_start: 0.8517 (ttm-80) cc_final: 0.8054 (mtp85) REVERT: F 44 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8539 (ptmm) REVERT: F 77 LYS cc_start: 0.8635 (mmtm) cc_final: 0.8329 (mmmm) REVERT: F 84 MET cc_start: 0.8483 (mmm) cc_final: 0.8267 (mmm) REVERT: G 92 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7901 (mt-10) REVERT: H 34 LYS cc_start: 0.7858 (tptm) cc_final: 0.7385 (mmtm) REVERT: H 47 GLN cc_start: 0.8829 (tt0) cc_final: 0.8543 (tt0) REVERT: M 63 LYS cc_start: 0.8105 (mmpt) cc_final: 0.7742 (mtmm) outliers start: 51 outliers final: 29 residues processed: 246 average time/residue: 1.3341 time to fit residues: 365.4505 Evaluate side-chains 240 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 1.507 ------------------------------------------------------------------------------- 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 74 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 118 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 44 LYS 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 24 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 71 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 4 PHE Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 34 GLU 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 312 PHE 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 114 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN D 84 ASN D 95 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 694 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.156264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.131697 restraints weight = 42819.556| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.48 r_work: 0.3605 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 614 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 617 | |-----------------------------------------------------------------------------| r_final: 0.3603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18361 Z= 0.227 Angle : 0.663 25.977 26209 Z= 0.358 Chirality : 0.037 0.153 2960 Planarity : 0.005 0.051 2176 Dihedral : 29.313 134.574 5082 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.36 % Allowed : 21.02 % 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: 1.54 (0.23), residues: 1295 helix: 1.89 (0.18), residues: 796 sheet: -0.31 (0.59), residues: 81 loop : -0.36 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 196 HIS 0.004 0.001 HIS F 75 PHE 0.022 0.002 PHE L 118 TYR 0.013 0.002 TYR H 83 ARG 0.011 0.001 ARG M 72 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 1027) hydrogen bonds : angle 3.35118 ( 2607) covalent geometry : bond 0.00511 (18360) covalent geometry : angle 0.66316 (26209) Misc. bond : bond 0.00159 ( 1) *********************** 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 276 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 227 time to evaluate : 1.406 Fit side-chains REVERT: A 73 GLU cc_start: 0.8643 (tt0) cc_final: 0.8271 (pt0) REVERT: A 79 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7636 (tttm) REVERT: A 123 ASP cc_start: 0.8770 (m-30) cc_final: 0.8352 (m-30) REVERT: B 35 ARG cc_start: 0.8657 (mtp85) cc_final: 0.8397 (mtp85) REVERT: B 79 LYS cc_start: 0.7917 (mttm) cc_final: 0.7660 (mttp) REVERT: B 88 TYR cc_start: 0.8472 (m-10) cc_final: 0.8267 (m-10) REVERT: C 41 GLU cc_start: 0.8441 (tt0) cc_final: 0.8179 (tt0) REVERT: C 90 ASP cc_start: 0.8561 (t0) cc_final: 0.7599 (t70) REVERT: C 92 GLU cc_start: 0.8202 (pm20) cc_final: 0.7658 (pm20) REVERT: C 104 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7863 (mm110) REVERT: D 34 LYS cc_start: 0.8046 (mppt) cc_final: 0.7770 (mppt) REVERT: D 57 LYS cc_start: 0.8182 (tptm) cc_final: 0.7487 (tppt) REVERT: D 68 ASP cc_start: 0.8988 (t70) cc_final: 0.8770 (t0) REVERT: E 42 ARG cc_start: 0.8044 (mtm-85) cc_final: 0.7196 (mtt180) REVERT: E 59 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.6853 (pm20) REVERT: E 73 GLU cc_start: 0.8475 (tt0) cc_final: 0.7876 (tt0) REVERT: F 44 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8560 (ptmm) REVERT: F 77 LYS cc_start: 0.8654 (mmtm) cc_final: 0.8344 (mmmm) REVERT: F 92 ARG cc_start: 0.8947 (ptm-80) cc_final: 0.8551 (ptm160) REVERT: G 19 SER cc_start: 0.8618 (t) cc_final: 0.8221 (p) REVERT: G 92 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7877 (mt-10) REVERT: H 34 LYS cc_start: 0.7980 (tptm) cc_final: 0.7472 (mmtm) REVERT: H 47 GLN cc_start: 0.8814 (tt0) cc_final: 0.8537 (tt0) REVERT: L 652 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6830 (pt0) REVERT: L 672 ASP cc_start: 0.7944 (p0) cc_final: 0.7696 (p0) outliers start: 49 outliers final: 28 residues processed: 253 average time/residue: 1.3629 time to fit residues: 382.0586 Evaluate side-chains 248 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 1.398 ------------------------------------------------------------------------------- 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 64 GLU 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 F residue 44 LYS 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 33 TYR 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 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 308 LEU Chi-restraints excluded: chain N residue 312 PHE 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 9 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 E 125 GLN F 75 HIS H 84 ASN L 702 GLN L 710 HIS ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.156536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.131912 restraints weight = 43063.064| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.47 r_work: 0.3630 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 617 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 618 | |-----------------------------------------------------------------------------| r_final: 0.3629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18361 Z= 0.207 Angle : 0.650 23.482 26209 Z= 0.351 Chirality : 0.037 0.267 2960 Planarity : 0.004 0.044 2176 Dihedral : 29.366 134.743 5082 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.92 % Allowed : 21.82 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.23), residues: 1295 helix: 1.85 (0.18), residues: 796 sheet: -0.40 (0.58), residues: 81 loop : -0.40 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 202 HIS 0.005 0.001 HIS L 144 PHE 0.022 0.002 PHE L 118 TYR 0.017 0.002 TYR H 83 ARG 0.011 0.001 ARG M 72 Details of bonding type rmsd hydrogen bonds : bond 0.03455 ( 1027) hydrogen bonds : angle 3.33599 ( 2607) covalent geometry : bond 0.00466 (18360) covalent geometry : angle 0.64972 (26209) Misc. bond : bond 0.00133 ( 1) *********************** 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 273 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 229 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.6767 (tttt) REVERT: B 79 LYS cc_start: 0.7885 (mttm) cc_final: 0.7627 (mttp) REVERT: B 88 TYR cc_start: 0.8468 (m-10) cc_final: 0.8260 (m-10) REVERT: C 18 SER cc_start: 0.8124 (p) cc_final: 0.7862 (m) REVERT: C 41 GLU cc_start: 0.8463 (tt0) cc_final: 0.8205 (tt0) REVERT: C 90 ASP cc_start: 0.8534 (t0) cc_final: 0.7570 (t70) REVERT: C 92 GLU cc_start: 0.8207 (pm20) cc_final: 0.7659 (pm20) REVERT: C 104 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7890 (mm-40) REVERT: D 57 LYS cc_start: 0.8161 (tptm) cc_final: 0.7476 (tppt) REVERT: D 68 ASP cc_start: 0.8966 (t70) cc_final: 0.8765 (t0) REVERT: E 42 ARG cc_start: 0.8058 (mtm-85) cc_final: 0.7198 (mtt180) REVERT: E 59 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.6943 (pm20) REVERT: E 73 GLU cc_start: 0.8469 (tt0) cc_final: 0.7834 (tt0) REVERT: F 35 ARG cc_start: 0.8525 (ttm-80) cc_final: 0.8107 (mtp85) REVERT: F 44 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8541 (ptmm) REVERT: F 77 LYS cc_start: 0.8645 (mmtm) cc_final: 0.8383 (mmmm) REVERT: F 92 ARG cc_start: 0.8942 (ptm-80) cc_final: 0.8598 (ptm160) REVERT: G 19 SER cc_start: 0.8615 (t) cc_final: 0.8237 (p) REVERT: G 73 ASN cc_start: 0.8462 (t0) cc_final: 0.7949 (t0) REVERT: G 92 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7857 (mt-10) REVERT: H 34 LYS cc_start: 0.7899 (tptm) cc_final: 0.7468 (mmtm) REVERT: H 47 GLN cc_start: 0.8774 (tt0) cc_final: 0.8471 (tt0) REVERT: H 101 LEU cc_start: 0.9185 (mt) cc_final: 0.8976 (mt) REVERT: L 652 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7018 (pt0) REVERT: L 690 ASN cc_start: 0.7967 (t0) cc_final: 0.7608 (t0) REVERT: L 694 GLN cc_start: 0.8258 (mt0) cc_final: 0.8046 (mp10) outliers start: 44 outliers final: 30 residues processed: 255 average time/residue: 1.3071 time to fit residues: 371.3642 Evaluate side-chains 254 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 B residue 97 LEU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 64 GLU 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 125 GLN Chi-restraints excluded: chain F residue 44 LYS 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 18 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 131 ILE 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 672 ASP Chi-restraints excluded: chain L residue 698 VAL 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 305 SER Chi-restraints excluded: chain N residue 312 PHE Chi-restraints excluded: chain N residue 324 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 19 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN D 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 125 GLN G 110 ASN H 67 ASN L 710 HIS ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.157485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.133033 restraints weight = 43235.866| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.47 r_work: 0.3636 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 618 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 614 | |-----------------------------------------------------------------------------| r_final: 0.3626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 18361 Z= 0.169 Angle : 0.653 23.177 26209 Z= 0.349 Chirality : 0.036 0.257 2960 Planarity : 0.004 0.044 2176 Dihedral : 29.331 134.826 5082 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.47 % Allowed : 23.42 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.23), residues: 1295 helix: 1.90 (0.18), residues: 790 sheet: -0.40 (0.61), residues: 73 loop : -0.30 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 202 HIS 0.004 0.001 HIS L 144 PHE 0.022 0.002 PHE L 118 TYR 0.030 0.002 TYR H 83 ARG 0.009 0.001 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.03321 ( 1027) hydrogen bonds : angle 3.32720 ( 2607) covalent geometry : bond 0.00383 (18360) covalent geometry : angle 0.65336 (26209) Misc. bond : bond 0.00106 ( 1) *********************** 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 268 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 229 time to evaluate : 1.373 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7599 (tttm) REVERT: A 123 ASP cc_start: 0.8679 (m-30) cc_final: 0.8110 (m-30) REVERT: B 79 LYS cc_start: 0.7875 (mttm) cc_final: 0.7610 (mttp) REVERT: C 18 SER cc_start: 0.8126 (p) cc_final: 0.7891 (m) REVERT: C 41 GLU cc_start: 0.8459 (tt0) cc_final: 0.8200 (tt0) REVERT: C 90 ASP cc_start: 0.8543 (t0) cc_final: 0.7566 (t70) REVERT: C 92 GLU cc_start: 0.8191 (pm20) cc_final: 0.7635 (pm20) REVERT: C 104 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7863 (mm-40) REVERT: D 57 LYS cc_start: 0.8160 (tptm) cc_final: 0.7913 (tppp) REVERT: D 68 ASP cc_start: 0.8954 (t70) cc_final: 0.8731 (t0) REVERT: E 42 ARG cc_start: 0.8062 (mtm-85) cc_final: 0.7192 (mtt180) REVERT: E 73 GLU cc_start: 0.8483 (tt0) cc_final: 0.7830 (tt0) REVERT: F 35 ARG cc_start: 0.8514 (ttm-80) cc_final: 0.8115 (mtp85) REVERT: F 44 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8531 (ptmm) REVERT: F 77 LYS cc_start: 0.8616 (mmtm) cc_final: 0.8377 (mmmm) REVERT: F 92 ARG cc_start: 0.8910 (ptm-80) cc_final: 0.8580 (ptm160) REVERT: G 19 SER cc_start: 0.8598 (t) cc_final: 0.8220 (p) REVERT: G 73 ASN cc_start: 0.8520 (t0) cc_final: 0.8256 (t0) REVERT: G 92 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: H 34 LYS cc_start: 0.7805 (tptm) cc_final: 0.7337 (mmtm) REVERT: H 42 TYR cc_start: 0.8248 (t80) cc_final: 0.8047 (t80) REVERT: H 47 GLN cc_start: 0.8770 (tt0) cc_final: 0.8462 (tt0) REVERT: H 101 LEU cc_start: 0.9173 (mt) cc_final: 0.8959 (mt) REVERT: L 672 ASP cc_start: 0.7775 (p0) cc_final: 0.7539 (p0) outliers start: 39 outliers final: 26 residues processed: 251 average time/residue: 1.3306 time to fit residues: 371.0828 Evaluate side-chains 246 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 217 time to evaluate : 1.489 ------------------------------------------------------------------------------- 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 97 LEU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 64 GLU 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 F residue 44 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 33 TYR 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 698 VAL 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 312 PHE 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 30 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 138 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 130 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 125 GLN G 110 ASN L 710 HIS ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4109 r_free = 0.4109 target = 0.158040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.133808 restraints weight = 42770.293| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.45 r_work: 0.3651 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 614 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 619 | |-----------------------------------------------------------------------------| r_final: 0.3649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 18361 Z= 0.161 Angle : 0.645 20.931 26209 Z= 0.347 Chirality : 0.036 0.264 2960 Planarity : 0.004 0.042 2176 Dihedral : 29.259 135.074 5082 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.03 % Allowed : 23.69 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.23), residues: 1295 helix: 1.93 (0.18), residues: 790 sheet: -0.38 (0.61), residues: 73 loop : -0.21 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 202 HIS 0.004 0.001 HIS L 144 PHE 0.018 0.002 PHE L 118 TYR 0.014 0.002 TYR D 83 ARG 0.009 0.001 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.03317 ( 1027) hydrogen bonds : angle 3.32636 ( 2607) covalent geometry : bond 0.00363 (18360) covalent geometry : angle 0.64501 (26209) Misc. bond : bond 0.00064 ( 1) ********************** 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 261 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 227 time to evaluate : 1.499 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7552 (tttm) REVERT: A 123 ASP cc_start: 0.8639 (m-30) cc_final: 0.8112 (m-30) REVERT: A 129 ARG cc_start: 0.8491 (tpt90) cc_final: 0.8129 (tpp80) REVERT: B 79 LYS cc_start: 0.7835 (mttm) cc_final: 0.7567 (mttp) REVERT: C 18 SER cc_start: 0.8073 (p) cc_final: 0.7865 (m) REVERT: C 41 GLU cc_start: 0.8462 (tt0) cc_final: 0.8214 (tt0) REVERT: C 90 ASP cc_start: 0.8580 (t0) cc_final: 0.7539 (t70) REVERT: C 92 GLU cc_start: 0.8199 (pm20) cc_final: 0.7597 (pm20) REVERT: C 104 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7840 (mm-40) REVERT: D 57 LYS cc_start: 0.8164 (tptm) cc_final: 0.7909 (tppp) REVERT: D 68 ASP cc_start: 0.8922 (t70) cc_final: 0.8686 (t0) REVERT: D 83 TYR cc_start: 0.7965 (m-10) cc_final: 0.7720 (m-10) REVERT: E 42 ARG cc_start: 0.8024 (mtm-85) cc_final: 0.7161 (mtt180) REVERT: E 59 GLU cc_start: 0.7782 (pm20) cc_final: 0.6879 (pm20) REVERT: E 73 GLU cc_start: 0.8421 (tt0) cc_final: 0.7532 (tt0) REVERT: F 25 ASN cc_start: 0.7845 (p0) cc_final: 0.7575 (p0) REVERT: F 35 ARG cc_start: 0.8510 (ttm-80) cc_final: 0.8142 (mtp85) REVERT: F 44 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8544 (ptmm) REVERT: F 77 LYS cc_start: 0.8616 (mmtm) cc_final: 0.8373 (mmmm) REVERT: F 92 ARG cc_start: 0.8864 (ptm-80) cc_final: 0.8531 (ptm160) REVERT: G 19 SER cc_start: 0.8596 (t) cc_final: 0.8225 (p) REVERT: G 73 ASN cc_start: 0.8417 (t0) cc_final: 0.8173 (t0) REVERT: G 92 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7835 (mt-10) REVERT: H 34 LYS cc_start: 0.7836 (tptm) cc_final: 0.7339 (mmtm) REVERT: H 47 GLN cc_start: 0.8799 (tt0) cc_final: 0.8478 (tt0) REVERT: H 101 LEU cc_start: 0.9164 (mt) cc_final: 0.8949 (mt) REVERT: L 672 ASP cc_start: 0.7841 (p0) cc_final: 0.7639 (p0) REVERT: L 691 LEU cc_start: 0.8456 (pt) cc_final: 0.8193 (pp) REVERT: L 708 ARG cc_start: 0.6872 (mmt180) cc_final: 0.6546 (tpt-90) outliers start: 34 outliers final: 21 residues processed: 246 average time/residue: 1.3429 time to fit residues: 366.3223 Evaluate side-chains 243 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 219 time to evaluate : 1.398 ------------------------------------------------------------------------------- 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 64 GLU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL 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 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 694 GLN 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 305 SER Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 312 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 51 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 39 optimal weight: 0.4980 chunk 73 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 125 GLN ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.156981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.132469 restraints weight = 42754.724| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.45 r_work: 0.3629 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 619 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 626 | |-----------------------------------------------------------------------------| r_final: 0.3635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 18361 Z= 0.198 Angle : 0.665 21.047 26209 Z= 0.356 Chirality : 0.037 0.271 2960 Planarity : 0.004 0.042 2176 Dihedral : 29.281 134.870 5082 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.94 % Allowed : 24.40 % Favored : 72.66 % 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: 1.48 (0.23), residues: 1295 helix: 1.83 (0.18), residues: 790 sheet: -0.37 (0.61), residues: 73 loop : -0.31 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 202 HIS 0.010 0.001 HIS L 710 PHE 0.037 0.002 PHE L 122 TYR 0.017 0.002 TYR D 83 ARG 0.009 0.001 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 1027) hydrogen bonds : angle 3.39292 ( 2607) covalent geometry : bond 0.00449 (18360) covalent geometry : angle 0.66475 (26209) Misc. bond : bond 0.00043 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13293.44 seconds wall clock time: 229 minutes 43.67 seconds (13783.67 seconds total)