Starting phenix.real_space_refine (version: 1.21rc1) on Sun Oct 8 19:37:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1t_34431/10_2023/8h1t_34431.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1t_34431/10_2023/8h1t_34431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1t_34431/10_2023/8h1t_34431.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1t_34431/10_2023/8h1t_34431.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1t_34431/10_2023/8h1t_34431.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1t_34431/10_2023/8h1t_34431.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 9.37, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.44 Conformation dependent library (CDL) restraints added in 1.9 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: 8.34 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.982A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 48 through 76 removed outlier: 4.078A pdb=" N GLU B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.538A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 38 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.471A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 58 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.925A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.516A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.651A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.512A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.347A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.526A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.559A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.658A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 49 removed outlier: 4.154A pdb=" N LEU K 42 " --> pdb=" O PRO K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 69 Processing helix chain 'K' and resid 75 through 85 Processing helix chain 'L' and resid 11 through 23 Processing helix chain 'L' and resid 54 through 60 Processing helix chain 'L' and resid 74 through 80 Processing helix chain 'L' and resid 90 through 102 Processing helix chain 'L' and resid 109 through 120 Processing helix chain 'L' and resid 123 through 133 Processing helix chain 'L' and resid 134 through 144 removed outlier: 3.616A pdb=" N HIS L 144 " --> pdb=" O ALA L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 152 Processing helix chain 'L' and resid 202 through 218 Processing helix chain 'L' and resid 236 through 243 removed outlier: 3.990A pdb=" N LYS L 240 " --> pdb=" O ASP L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 648 through 668 removed outlier: 3.545A pdb=" N THR L 668 " --> pdb=" O ASP L 664 " (cutoff:3.500A) Processing helix chain 'L' and resid 671 through 686 Processing helix chain 'L' and resid 687 through 695 removed outlier: 3.625A pdb=" N LEU L 691 " --> pdb=" O MET L 687 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU L 693 " --> pdb=" O ALA L 689 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 removed outlier: 3.548A pdb=" N VAL M 26 " --> pdb=" O THR M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'M' and resid 55 through 59 Processing helix chain 'N' and resid 263 through 268 Processing helix chain 'N' and resid 269 through 275 Processing helix chain 'N' and resid 277 through 286 removed outlier: 3.732A pdb=" N PHE N 286 " --> pdb=" O GLN N 282 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 327 Processing helix chain 'N' and resid 330 through 352 removed outlier: 4.396A pdb=" N ARG N 336 " --> pdb=" O GLU N 332 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU N 344 " --> pdb=" O GLU N 340 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS N 345 " --> pdb=" O MET N 341 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS N 346 " --> pdb=" O GLU N 342 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL N 347 " --> pdb=" O LYS N 343 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN N 349 " --> pdb=" O LYS N 345 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N TRP N 350 " --> pdb=" O LYS N 346 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS N 351 " --> pdb=" O VAL N 347 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.038A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.450A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.464A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.577A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.026A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.223A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 56 through 57 Processing sheet with id=AB2, first strand: chain 'L' and resid 8 through 9 removed outlier: 3.770A pdb=" N LEU L 8 " --> pdb=" O GLY M 75 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 28 through 30 removed outlier: 4.375A pdb=" N ALA L 167 " --> pdb=" O TRP L 52 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE L 191 " --> pdb=" O GLU L 182 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 12 through 15 Processing sheet with id=AB5, first strand: chain 'N' and resid 293 through 295 598 hydrogen bonds defined for protein. 1749 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 429 hydrogen bonds 858 hydrogen bond angles 0 basepair planarities 166 basepair parallelities 273 stacking parallelities Total time for adding SS restraints: 7.66 Time building geometry restraints manager: 9.85 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: 98.36 - 105.48: 1592 105.48 - 112.60: 10177 112.60 - 119.72: 5950 119.72 - 126.84: 7556 126.84 - 133.96: 934 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: 8029 27.39 - 54.78: 1575 54.78 - 82.17: 308 82.17 - 109.56: 4 109.56 - 136.96: 2 Dihedral angle restraints: 9918 sinusoidal: 6101 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 9915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2194 0.034 - 0.068: 558 0.068 - 0.103: 144 0.103 - 0.137: 54 0.137 - 0.171: 10 Chirality restraints: 2960 Sorted by residual: chirality pdb=" C3' DG J 159 " pdb=" C4' DG J 159 " pdb=" O3' DG J 159 " pdb=" C2' DG J 159 " both_signs ideal model delta sigma weight residual False -2.66 -2.83 0.17 2.00e-01 2.50e+01 7.32e-01 chirality pdb=" C3' DC J 7 " pdb=" C4' DC J 7 " pdb=" O3' DC J 7 " pdb=" C2' DC J 7 " both_signs ideal model delta sigma weight residual False -2.66 -2.50 -0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" C3' DG J 10 " pdb=" C4' DG J 10 " pdb=" O3' DG J 10 " pdb=" C2' DG J 10 " both_signs ideal model delta sigma weight residual False -2.66 -2.82 0.16 2.00e-01 2.50e+01 6.28e-01 ... (remaining 2957 not shown) Planarity restraints: 2176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS L 659 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.79e+00 pdb=" C LYS L 659 " -0.034 2.00e-02 2.50e+03 pdb=" O LYS L 659 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE L 660 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL L 234 " -0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO L 235 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO L 235 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 235 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 165 " 0.013 2.00e-02 2.50e+03 9.02e-03 1.83e+00 pdb=" N1 DC I 165 " -0.020 2.00e-02 2.50e+03 pdb=" C2 DC I 165 " 0.011 2.00e-02 2.50e+03 pdb=" O2 DC I 165 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DC I 165 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DC I 165 " 0.002 2.00e-02 2.50e+03 pdb=" N4 DC I 165 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DC I 165 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DC I 165 " -0.001 2.00e-02 2.50e+03 ... (remaining 2173 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 1 2.05 - 2.76: 2413 2.76 - 3.47: 24272 3.47 - 4.19: 47582 4.19 - 4.90: 72594 Nonbonded interactions: 146862 Sorted by model distance: nonbonded pdb=" NZ LYS C 119 " pdb=" C GLY M 76 " model vdw 1.336 3.350 nonbonded pdb=" CD1 LEU M 73 " pdb=" O ARG M 74 " model vdw 2.164 3.460 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.247 2.440 nonbonded pdb=" NZ LYS C 119 " pdb=" O GLY M 76 " model vdw 2.259 2.520 nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.278 2.440 ... (remaining 146857 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 10.440 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 56.120 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18360 Z= 0.149 Angle : 0.532 11.575 26209 Z= 0.325 Chirality : 0.037 0.171 2960 Planarity : 0.003 0.041 2176 Dihedral : 24.665 136.956 7450 Min Nonbonded Distance : 1.336 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.24), residues: 1295 helix: 2.55 (0.19), residues: 759 sheet: -0.00 (0.61), residues: 70 loop : -0.02 (0.29), residues: 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 351 average time/residue: 1.4617 time to fit residues: 563.8104 Evaluate side-chains 221 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 220 time to evaluate : 1.574 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.3090 time to fit residues: 2.3270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 chunk 124 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 E 39 HIS E 93 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 84 HIS ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 193 HIS M 62 GLN ** N 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18360 Z= 0.209 Angle : 0.589 14.133 26209 Z= 0.331 Chirality : 0.035 0.186 2960 Planarity : 0.004 0.038 2176 Dihedral : 29.429 136.412 4806 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.74 % Allowed : 16.30 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.24), residues: 1295 helix: 2.43 (0.19), residues: 784 sheet: -0.15 (0.61), residues: 71 loop : -0.07 (0.29), residues: 440 *********************** 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 273 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 231 time to evaluate : 1.485 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 20 residues processed: 253 average time/residue: 1.3184 time to fit residues: 370.5581 Evaluate side-chains 220 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 200 time to evaluate : 1.414 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 11 residues processed: 9 average time/residue: 0.3493 time to fit residues: 6.2989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 156 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 D 47 GLN D 109 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 84 HIS L 133 ASN ** N 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18360 Z= 0.234 Angle : 0.596 24.301 26209 Z= 0.329 Chirality : 0.036 0.282 2960 Planarity : 0.004 0.065 2176 Dihedral : 29.593 136.049 4806 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.36 % Allowed : 18.70 % Favored : 76.94 % 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: 1.93 (0.23), residues: 1295 helix: 2.22 (0.19), residues: 795 sheet: -0.24 (0.62), residues: 71 loop : -0.23 (0.29), residues: 429 *********************** 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 265 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 216 time to evaluate : 1.632 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 20 residues processed: 245 average time/residue: 1.2207 time to fit residues: 335.2859 Evaluate side-chains 213 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 193 time to evaluate : 1.380 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 12 residues processed: 9 average time/residue: 0.3554 time to fit residues: 6.1679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 153 optimal weight: 0.0040 chunk 137 optimal weight: 0.9980 chunk 41 optimal weight: 0.0470 chunk 127 optimal weight: 0.9990 overall best weight: 0.5290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN C 24 GLN C 94 ASN D 47 GLN E 76 GLN E 125 GLN H 95 GLN ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 84 HIS L 702 GLN M 62 GLN ** N 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18360 Z= 0.180 Angle : 0.592 28.387 26209 Z= 0.321 Chirality : 0.034 0.235 2960 Planarity : 0.004 0.048 2176 Dihedral : 29.579 136.181 4806 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.10 % Allowed : 19.95 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.24), residues: 1295 helix: 2.28 (0.19), residues: 792 sheet: -0.14 (0.64), residues: 69 loop : -0.22 (0.29), residues: 434 *********************** 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 264 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 218 time to evaluate : 1.483 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 27 residues processed: 249 average time/residue: 1.2813 time to fit residues: 355.8547 Evaluate side-chains 222 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 195 time to evaluate : 1.318 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 21 residues processed: 7 average time/residue: 0.1884 time to fit residues: 3.9333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 114 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 131 optimal weight: 0.4980 chunk 106 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 E 39 HIS ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 702 GLN M 62 GLN N 281 GLN ** N 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18360 Z= 0.284 Angle : 0.633 30.036 26209 Z= 0.343 Chirality : 0.036 0.246 2960 Planarity : 0.004 0.057 2176 Dihedral : 29.747 134.828 4806 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.54 % Allowed : 20.21 % Favored : 75.24 % 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: 1.71 (0.23), residues: 1295 helix: 2.10 (0.18), residues: 791 sheet: -0.33 (0.59), residues: 81 loop : -0.40 (0.29), residues: 423 *********************** 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 269 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 218 time to evaluate : 1.404 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 30 residues processed: 251 average time/residue: 1.2850 time to fit residues: 359.2293 Evaluate side-chains 227 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 197 time to evaluate : 1.400 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 18 residues processed: 12 average time/residue: 0.3240 time to fit residues: 7.4402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 27 GLN D 49 HIS D 63 ASN ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 229 ASN M 62 GLN N 281 GLN ** N 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18360 Z= 0.213 Angle : 0.607 25.757 26209 Z= 0.331 Chirality : 0.035 0.187 2960 Planarity : 0.004 0.052 2176 Dihedral : 29.738 135.684 4806 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.19 % Allowed : 22.08 % Favored : 73.73 % 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: 1.80 (0.23), residues: 1295 helix: 2.17 (0.18), residues: 785 sheet: -0.41 (0.58), residues: 81 loop : -0.29 (0.29), residues: 429 *********************** 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 263 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 216 time to evaluate : 1.554 Fit side-chains revert: symmetry clash outliers start: 47 outliers final: 30 residues processed: 243 average time/residue: 1.2483 time to fit residues: 339.5493 Evaluate side-chains 233 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 203 time to evaluate : 1.455 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 19 residues processed: 11 average time/residue: 0.6468 time to fit residues: 10.3515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 229 ASN L 710 HIS M 62 GLN ** N 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 18360 Z= 0.335 Angle : 0.663 25.291 26209 Z= 0.360 Chirality : 0.037 0.183 2960 Planarity : 0.005 0.059 2176 Dihedral : 29.875 134.097 4806 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.81 % Allowed : 21.82 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.23), residues: 1295 helix: 1.86 (0.18), residues: 794 sheet: -0.43 (0.58), residues: 81 loop : -0.52 (0.28), residues: 420 *********************** 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 263 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 209 time to evaluate : 1.512 Fit side-chains outliers start: 54 outliers final: 33 residues processed: 245 average time/residue: 1.2019 time to fit residues: 331.2627 Evaluate side-chains 232 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 199 time to evaluate : 1.398 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 25 residues processed: 8 average time/residue: 0.3597 time to fit residues: 5.7114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 7.9990 chunk 46 optimal weight: 0.0040 chunk 30 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 120 optimal weight: 0.0870 chunk 139 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 overall best weight: 0.5370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 93 GLN ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 229 ASN ** L 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 695 ASN L 702 GLN L 710 HIS N 281 GLN ** N 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18360 Z= 0.196 Angle : 0.637 19.710 26209 Z= 0.343 Chirality : 0.035 0.217 2960 Planarity : 0.004 0.040 2176 Dihedral : 29.805 135.796 4806 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.56 % Allowed : 24.13 % Favored : 72.31 % 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: 1.68 (0.23), residues: 1295 helix: 2.04 (0.18), residues: 788 sheet: -0.49 (0.58), residues: 81 loop : -0.26 (0.29), residues: 426 *********************** 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 262 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 222 time to evaluate : 1.458 Fit side-chains outliers start: 40 outliers final: 29 residues processed: 249 average time/residue: 1.2052 time to fit residues: 337.8260 Evaluate side-chains 235 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 206 time to evaluate : 1.339 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 21 residues processed: 8 average time/residue: 0.4270 time to fit residues: 6.3421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 0.6980 chunk 142 optimal weight: 0.6980 chunk 146 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 151 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN G 73 ASN H 67 ASN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 710 HIS M 62 GLN N 281 GLN ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 18360 Z= 0.206 Angle : 0.636 21.033 26209 Z= 0.345 Chirality : 0.036 0.228 2960 Planarity : 0.004 0.039 2176 Dihedral : 29.732 135.492 4806 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.38 % Allowed : 24.31 % Favored : 72.31 % 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: 1.74 (0.23), residues: 1295 helix: 2.09 (0.18), residues: 785 sheet: -0.40 (0.62), residues: 73 loop : -0.26 (0.29), residues: 437 *********************** 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 251 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 213 time to evaluate : 1.483 Fit side-chains outliers start: 38 outliers final: 27 residues processed: 241 average time/residue: 1.2080 time to fit residues: 327.4506 Evaluate side-chains 230 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 203 time to evaluate : 1.460 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 23 residues processed: 4 average time/residue: 0.1988 time to fit residues: 3.1252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 145 optimal weight: 0.0370 chunk 126 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 overall best weight: 1.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 710 HIS M 62 GLN ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 18360 Z= 0.318 Angle : 0.688 22.735 26209 Z= 0.369 Chirality : 0.038 0.221 2960 Planarity : 0.005 0.043 2176 Dihedral : 29.850 134.606 4806 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.29 % Allowed : 25.02 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.23), residues: 1295 helix: 1.80 (0.18), residues: 793 sheet: -0.43 (0.62), residues: 73 loop : -0.48 (0.28), residues: 429 ********************** 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 241 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 204 time to evaluate : 1.482 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 25 residues processed: 233 average time/residue: 1.3084 time to fit residues: 340.6564 Evaluate side-chains 222 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 197 time to evaluate : 1.447 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 23 residues processed: 2 average time/residue: 0.1807 time to fit residues: 2.3779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 0.5980 chunk 116 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 129 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 110 optimal weight: 0.2980 chunk 7 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 27 GLN ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 281 GLN ** N 294 GLN ** 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 = 0.4107 r_free = 0.4107 target = 0.158723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.134904 restraints weight = 43087.810| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.44 r_work: 0.3671 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 495 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 556 | |-----------------------------------------------------------------------------| r_final: 0.3643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 18360 Z= 0.211 Angle : 0.659 20.173 26209 Z= 0.354 Chirality : 0.036 0.200 2960 Planarity : 0.004 0.061 2176 Dihedral : 29.829 135.474 4806 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.94 % Allowed : 25.65 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.23), residues: 1295 helix: 1.88 (0.18), residues: 785 sheet: -0.51 (0.62), residues: 73 loop : -0.29 (0.29), residues: 437 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6036.39 seconds wall clock time: 107 minutes 54.58 seconds (6474.58 seconds total)