Starting phenix.real_space_refine on Thu Jul 2 07:20:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9coo_45787/07_2026/9coo_45787.cif Found real_map, /net/cci-nas-00/data/ceres_data/9coo_45787/07_2026/9coo_45787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9coo_45787/07_2026/9coo_45787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9coo_45787/07_2026/9coo_45787.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9coo_45787/07_2026/9coo_45787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9coo_45787/07_2026/9coo_45787.map" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 Ca 3 9.91 5 S 36 5.16 5 C 4685 2.51 5 N 1266 2.21 5 O 1503 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7493 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3170 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 11, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 155 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 2, 'ARG:plan': 3, 'PHE:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 101 Chain: "B" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 926 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 923 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "L" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 769 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "N" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 859 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 3, 'TRANS': 120} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 3, 'ASP:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "R" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 801 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 94 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 7, 'ASN:plan1': 2, 'GLN:plan1': 5, 'GLU:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 91 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Time building chain proxies: 1.67, per 1000 atoms: 0.22 Number of scatterers: 7493 At special positions: 0 Unit cell: (104.58, 117.86, 126.16, 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) Ca 3 19.99 S 36 16.00 O 1503 8.00 N 1266 7.00 C 4685 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 68 " - pdb=" SG CYS R 82 " distance=2.03 Simple disulfide: pdb=" SG CYS R 75 " - pdb=" SG CYS R 95 " distance=2.03 Simple disulfide: pdb=" SG CYS R 89 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 121 " distance=2.04 Simple disulfide: pdb=" SG CYS R 116 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 128 " - pdb=" SG CYS R 143 " distance=2.03 Simple disulfide: pdb=" SG CYS R 148 " - pdb=" SG CYS R 160 " distance=2.03 Simple disulfide: pdb=" SG CYS R 155 " - pdb=" SG CYS R 173 " distance=2.03 Simple disulfide: pdb=" SG CYS R 167 " - pdb=" SG CYS R 184 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A4601 " - " ASN A3336 " " NAG A4602 " - " ASN A3101 " Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 269.1 milliseconds 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 11 sheets defined 13.0% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 335 through 353 removed outlier: 4.163A pdb=" N ALA B 339 " --> pdb=" O PRO B 335 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE B 349 " --> pdb=" O ARG B 345 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 370 removed outlier: 3.783A pdb=" N ALA B 365 " --> pdb=" O ALA B 361 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET B 370 " --> pdb=" O GLN B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 388 Processing helix chain 'B' and resid 391 through 406 removed outlier: 3.612A pdb=" N GLU B 398 " --> pdb=" O GLU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 428 removed outlier: 4.077A pdb=" N SER B 422 " --> pdb=" O GLY B 418 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU B 428 " --> pdb=" O PHE B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 448 Processing helix chain 'B' and resid 451 through 469 Processing helix chain 'L' and resid 85 through 89 removed outlier: 3.937A pdb=" N LEU L 89 " --> pdb=" O PRO L 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.756A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 88 No H-bonds generated for 'chain 'R' and resid 86 through 88' Processing helix chain 'R' and resid 137 through 142 removed outlier: 3.855A pdb=" N SER R 142 " --> pdb=" O SER R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 2825 through 2831 removed outlier: 3.570A pdb=" N VAL A2828 " --> pdb=" O HIS A2839 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HIS A2839 " --> pdb=" O VAL A2828 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A2846 " --> pdb=" O ALA A2849 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A2849 " --> pdb=" O PHE A2846 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A2858 " --> pdb=" O LEU A2869 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR A2866 " --> pdb=" O LYS A2892 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A2868 " --> pdb=" O PHE A2890 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE A2890 " --> pdb=" O GLU A2868 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A2906 " --> pdb=" O TYR A2889 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE A2895 " --> pdb=" O PHE A2900 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2918 through 2922 current: chain 'A' and resid 2939 through 2951 removed outlier: 3.649A pdb=" N ASN A2961 " --> pdb=" O GLN A2972 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2968 through 2975 current: chain 'A' and resid 3000 through 3009 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 3015 through 3023 current: chain 'A' and resid 3030 through 3031 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 3030 through 3031 current: chain 'A' and resid 3064 through 3074 removed outlier: 4.172A pdb=" N ASP A3069 " --> pdb=" O ARG A3092 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG A3092 " --> pdb=" O ASP A3069 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A3090 " --> pdb=" O LEU A3071 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR A3098 " --> pdb=" O ALA A3091 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A3096 " --> pdb=" O PHE A3093 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3337 through 3344 removed outlier: 3.669A pdb=" N ALA A3364 " --> pdb=" O THR A3385 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR A3385 " --> pdb=" O ALA A3364 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A3366 " --> pdb=" O GLY A3383 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY A3383 " --> pdb=" O LEU A3366 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'H' and resid 46 through 51 removed outlier: 4.836A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY H 33 " --> pdb=" O ARG H 99 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA6, first strand: chain 'L' and resid 39 through 44 removed outlier: 6.306A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 59 through 60 current: chain 'L' and resid 102 through 103 Processing sheet with id=AA7, first strand: chain 'N' and resid 6 through 7 removed outlier: 3.549A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.434A pdb=" N GLY N 10 " --> pdb=" O THR N 120 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N SER N 122 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL N 12 " --> pdb=" O SER N 122 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET N 34 " --> pdb=" O ILE N 51 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 72 through 74 Processing sheet with id=AB1, first strand: chain 'R' and resid 113 through 115 Processing sheet with id=AB2, first strand: chain 'R' and resid 152 through 154 removed outlier: 3.590A pdb=" N ILE R 161 " --> pdb=" O PHE R 153 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 759 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2471 1.34 - 1.46: 1309 1.46 - 1.57: 3811 1.57 - 1.69: 0 1.69 - 1.81: 47 Bond restraints: 7638 Sorted by residual: bond pdb=" CB ASP L 66 " pdb=" CG ASP L 66 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.30e+00 bond pdb=" CB ASN B 379 " pdb=" CG ASN B 379 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.14e+00 bond pdb=" CB GLU A2826 " pdb=" CG GLU A2826 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.73e-01 bond pdb=" CB CYS H 96 " pdb=" SG CYS H 96 " ideal model delta sigma weight residual 1.808 1.775 0.033 3.30e-02 9.18e+02 9.73e-01 bond pdb=" CA ASN H 77 " pdb=" CB ASN H 77 " ideal model delta sigma weight residual 1.527 1.543 -0.015 1.61e-02 3.86e+03 9.17e-01 ... (remaining 7633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 10183 1.92 - 3.84: 185 3.84 - 5.75: 25 5.75 - 7.67: 11 7.67 - 9.59: 4 Bond angle restraints: 10408 Sorted by residual: angle pdb=" CA ARG B 345 " pdb=" CB ARG B 345 " pdb=" CG ARG B 345 " ideal model delta sigma weight residual 114.10 121.08 -6.98 2.00e+00 2.50e-01 1.22e+01 angle pdb=" C2 NAG A4602 " pdb=" N2 NAG A4602 " pdb=" C7 NAG A4602 " ideal model delta sigma weight residual 124.56 133.57 -9.01 3.00e+00 1.11e-01 9.03e+00 angle pdb=" CB ARG B 345 " pdb=" CG ARG B 345 " pdb=" CD ARG B 345 " ideal model delta sigma weight residual 111.30 118.00 -6.70 2.30e+00 1.89e-01 8.49e+00 angle pdb=" CA LEU A2869 " pdb=" CB LEU A2869 " pdb=" CG LEU A2869 " ideal model delta sigma weight residual 116.30 125.89 -9.59 3.50e+00 8.16e-02 7.51e+00 angle pdb=" CB MET A3007 " pdb=" CG MET A3007 " pdb=" SD MET A3007 " ideal model delta sigma weight residual 112.70 120.87 -8.17 3.00e+00 1.11e-01 7.41e+00 ... (remaining 10403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 3870 16.47 - 32.93: 485 32.93 - 49.40: 145 49.40 - 65.87: 41 65.87 - 82.34: 5 Dihedral angle restraints: 4546 sinusoidal: 1606 harmonic: 2940 Sorted by residual: dihedral pdb=" CB CYS R 155 " pdb=" SG CYS R 155 " pdb=" SG CYS R 173 " pdb=" CB CYS R 173 " ideal model delta sinusoidal sigma weight residual -86.00 -143.19 57.19 1 1.00e+01 1.00e-02 4.40e+01 dihedral pdb=" CB CYS R 109 " pdb=" SG CYS R 109 " pdb=" SG CYS R 121 " pdb=" CB CYS R 121 " ideal model delta sinusoidal sigma weight residual -86.00 -142.47 56.47 1 1.00e+01 1.00e-02 4.30e+01 dihedral pdb=" CB CYS R 68 " pdb=" SG CYS R 68 " pdb=" SG CYS R 82 " pdb=" CB CYS R 82 " ideal model delta sinusoidal sigma weight residual 93.00 146.80 -53.80 1 1.00e+01 1.00e-02 3.93e+01 ... (remaining 4543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1017 0.056 - 0.112: 160 0.112 - 0.168: 25 0.168 - 0.224: 0 0.224 - 0.279: 2 Chirality restraints: 1204 Sorted by residual: chirality pdb=" C1 NAG A4602 " pdb=" ND2 ASN A3101 " pdb=" C2 NAG A4602 " pdb=" O5 NAG A4602 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CG LEU B 462 " pdb=" CB LEU B 462 " pdb=" CD1 LEU B 462 " pdb=" CD2 LEU B 462 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" C2 NAG A4602 " pdb=" C1 NAG A4602 " pdb=" C3 NAG A4602 " pdb=" N2 NAG A4602 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.17 2.00e-01 2.50e+01 6.90e-01 ... (remaining 1201 not shown) Planarity restraints: 1359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A2971 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C ASN A2971 " 0.055 2.00e-02 2.50e+03 pdb=" O ASN A2971 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN A2972 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 83 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO R 84 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO R 84 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 84 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A2895 " 0.024 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO A2896 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A2896 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A2896 " 0.021 5.00e-02 4.00e+02 ... (remaining 1356 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 577 2.73 - 3.27: 8002 3.27 - 3.81: 12364 3.81 - 4.36: 14118 4.36 - 4.90: 24213 Nonbonded interactions: 59274 Sorted by model distance: nonbonded pdb=" OD2 ASP B 448 " pdb=" ND2 ASN B 454 " model vdw 2.182 3.120 nonbonded pdb=" OD1 ASP R 170 " pdb="CA CA R 903 " model vdw 2.226 3.250 nonbonded pdb=" OE2 GLU R 101 " pdb="CA CA R 901 " model vdw 2.233 3.250 nonbonded pdb=" O SER R 130 " pdb=" OG SER R 130 " model vdw 2.235 3.040 nonbonded pdb=" O TYR A3379 " pdb=" NZ LYS A3380 " model vdw 2.236 3.120 ... (remaining 59269 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.360 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 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 0.043 7652 Z= 0.155 Angle : 0.677 11.241 10438 Z= 0.337 Chirality : 0.043 0.279 1204 Planarity : 0.004 0.051 1357 Dihedral : 16.582 82.337 2620 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.45 % Allowed : 32.36 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.26), residues: 1006 helix: -0.50 (0.46), residues: 123 sheet: -1.96 (0.24), residues: 441 loop : -1.69 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2836 TYR 0.016 0.001 TYR B 342 PHE 0.015 0.001 PHE A3038 TRP 0.011 0.001 TRP R 87 HIS 0.011 0.001 HIS N 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 7638) covalent geometry : angle 0.66309 / 0.33 (10408) SS BOND : bond 0.00229 / 0.13 ( 12) SS BOND : angle 1.03109 / 0.63 ( 24) hydrogen bonds : bond 0.14111 / 8.90 ( 278) hydrogen bonds : angle 8.13022 / 5.63 ( 759) link_NAG-ASN : bond 0.01162 / 0.61 ( 2) link_NAG-ASN : angle 5.55840 / 5.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 2843 MET cc_start: 0.7825 (tmm) cc_final: 0.6856 (tmm) REVERT: A 3174 LYS cc_start: 0.8036 (mmtm) cc_final: 0.7628 (mtpt) REVERT: A 3340 ASP cc_start: 0.7895 (p0) cc_final: 0.7523 (m-30) REVERT: B 456 LEU cc_start: 0.8882 (tp) cc_final: 0.8604 (tt) REVERT: H 29 PHE cc_start: 0.8251 (t80) cc_final: 0.7677 (t80) REVERT: H 108 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.7257 (m-80) REVERT: L 79 LEU cc_start: 0.7855 (tp) cc_final: 0.7255 (pp) outliers start: 11 outliers final: 7 residues processed: 109 average time/residue: 0.0684 time to fit residues: 10.6935 Evaluate side-chains 106 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2850 ILE Chi-restraints excluded: chain A residue 2963 ILE Chi-restraints excluded: chain A residue 2975 VAL Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 84 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3353 ASN ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.112824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.099228 restraints weight = 23270.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.100830 restraints weight = 14071.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.101867 restraints weight = 10010.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.102522 restraints weight = 7927.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.102756 restraints weight = 6811.165| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7652 Z= 0.194 Angle : 0.672 12.387 10438 Z= 0.337 Chirality : 0.044 0.328 1204 Planarity : 0.004 0.049 1357 Dihedral : 5.794 53.561 1146 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 4.49 % Allowed : 29.06 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.26), residues: 1006 helix: 0.36 (0.49), residues: 121 sheet: -1.92 (0.25), residues: 425 loop : -1.69 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 345 TYR 0.016 0.002 TYR A3177 PHE 0.019 0.002 PHE B 424 TRP 0.023 0.002 TRP R 165 HIS 0.010 0.001 HIS N 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 ( 7638) covalent geometry : angle 0.65462 / 0.33 (10408) SS BOND : bond 0.00202 / 0.11 ( 12) SS BOND : angle 0.77333 / 0.54 ( 24) hydrogen bonds : bond 0.03581 / 2.26 ( 278) hydrogen bonds : angle 6.36766 / 4.36 ( 759) link_NAG-ASN : bond 0.01187 / 0.62 ( 2) link_NAG-ASN : angle 6.23011 / 5.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.302 Fit side-chains REVERT: A 2843 MET cc_start: 0.7740 (tmm) cc_final: 0.7057 (tmm) REVERT: A 2933 CYS cc_start: 0.6492 (OUTLIER) cc_final: 0.5876 (m) REVERT: A 3106 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.7841 (m-40) REVERT: A 3126 LEU cc_start: 0.7690 (tp) cc_final: 0.7458 (tp) REVERT: A 3174 LYS cc_start: 0.7684 (mmtm) cc_final: 0.7439 (mtpt) REVERT: B 456 LEU cc_start: 0.8607 (tp) cc_final: 0.8187 (tt) REVERT: B 464 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: H 108 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.6925 (m-80) REVERT: R 126 PHE cc_start: 0.7349 (m-80) cc_final: 0.6864 (m-80) REVERT: R 163 GLN cc_start: 0.8370 (mp10) cc_final: 0.7766 (tp-100) outliers start: 34 outliers final: 18 residues processed: 125 average time/residue: 0.0710 time to fit residues: 12.7868 Evaluate side-chains 113 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2850 ILE Chi-restraints excluded: chain A residue 2933 CYS Chi-restraints excluded: chain A residue 2963 ILE Chi-restraints excluded: chain A residue 2975 VAL Chi-restraints excluded: chain A residue 3021 HIS Chi-restraints excluded: chain A residue 3106 ASN Chi-restraints excluded: chain A residue 3164 THR Chi-restraints excluded: chain A residue 3353 ASN Chi-restraints excluded: chain A residue 3385 THR Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain A residue 3402 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain R residue 131 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 63 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 0.3980 chunk 47 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2865 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3353 ASN ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.112486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.098827 restraints weight = 23207.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.100412 restraints weight = 14015.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.101398 restraints weight = 9954.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.102121 restraints weight = 7970.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.102480 restraints weight = 6806.754| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7652 Z= 0.190 Angle : 0.664 12.400 10438 Z= 0.331 Chirality : 0.044 0.315 1204 Planarity : 0.004 0.051 1357 Dihedral : 5.860 54.333 1146 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 6.08 % Allowed : 27.61 % Favored : 66.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.26), residues: 1006 helix: 0.57 (0.50), residues: 121 sheet: -1.97 (0.25), residues: 424 loop : -1.69 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A3092 TYR 0.015 0.002 TYR A3177 PHE 0.016 0.002 PHE B 424 TRP 0.014 0.002 TRP R 165 HIS 0.010 0.001 HIS N 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 ( 7638) covalent geometry : angle 0.64739 / 0.33 (10408) SS BOND : bond 0.00209 / 0.11 ( 12) SS BOND : angle 0.63980 / 0.43 ( 24) hydrogen bonds : bond 0.03332 / 2.16 ( 278) hydrogen bonds : angle 6.22246 / 4.25 ( 759) link_NAG-ASN : bond 0.01238 / 0.65 ( 2) link_NAG-ASN : angle 6.24757 / 5.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 96 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 2843 MET cc_start: 0.7967 (tmm) cc_final: 0.7244 (tmm) REVERT: A 2933 CYS cc_start: 0.6561 (OUTLIER) cc_final: 0.6160 (m) REVERT: A 3166 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8275 (tptp) REVERT: A 3353 ASN cc_start: 0.7838 (m110) cc_final: 0.7558 (m-40) REVERT: B 360 GLN cc_start: 0.6922 (OUTLIER) cc_final: 0.6441 (tt0) REVERT: B 426 GLU cc_start: 0.6730 (pp20) cc_final: 0.6447 (pp20) REVERT: B 456 LEU cc_start: 0.8635 (tp) cc_final: 0.8423 (mt) REVERT: B 464 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.7817 (mp0) REVERT: H 108 TYR cc_start: 0.7452 (OUTLIER) cc_final: 0.6915 (m-80) REVERT: R 126 PHE cc_start: 0.7319 (m-80) cc_final: 0.6800 (m-80) REVERT: R 163 GLN cc_start: 0.7908 (mp10) cc_final: 0.7529 (tp-100) outliers start: 46 outliers final: 29 residues processed: 134 average time/residue: 0.0750 time to fit residues: 14.1403 Evaluate side-chains 126 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2850 ILE Chi-restraints excluded: chain A residue 2933 CYS Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 2963 ILE Chi-restraints excluded: chain A residue 2974 LEU Chi-restraints excluded: chain A residue 2975 VAL Chi-restraints excluded: chain A residue 3106 ASN Chi-restraints excluded: chain A residue 3164 THR Chi-restraints excluded: chain A residue 3166 LYS Chi-restraints excluded: chain A residue 3355 GLU Chi-restraints excluded: chain A residue 3385 THR Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain A residue 3402 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 381 PHE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 155 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 0.7980 chunk 79 optimal weight: 0.1980 chunk 92 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2839 HIS ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.112596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.099007 restraints weight = 23483.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.100615 restraints weight = 14150.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.101626 restraints weight = 10015.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.102334 restraints weight = 7985.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.102630 restraints weight = 6819.555| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7652 Z= 0.185 Angle : 0.659 12.648 10438 Z= 0.327 Chirality : 0.043 0.289 1204 Planarity : 0.004 0.052 1357 Dihedral : 5.893 54.574 1146 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 5.94 % Allowed : 27.61 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.26), residues: 1006 helix: 0.65 (0.51), residues: 121 sheet: -1.92 (0.25), residues: 420 loop : -1.66 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 345 TYR 0.020 0.002 TYR B 342 PHE 0.017 0.002 PHE B 424 TRP 0.012 0.002 TRP R 87 HIS 0.010 0.001 HIS N 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 7638) covalent geometry : angle 0.64172 / 0.32 (10408) SS BOND : bond 0.00206 / 0.11 ( 12) SS BOND : angle 0.58013 / 0.39 ( 24) hydrogen bonds : bond 0.03176 / 2.05 ( 278) hydrogen bonds : angle 6.12599 / 4.17 ( 759) link_NAG-ASN : bond 0.01204 / 0.63 ( 2) link_NAG-ASN : angle 6.27468 / 5.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 100 time to evaluate : 0.191 Fit side-chains REVERT: A 2843 MET cc_start: 0.7958 (tmm) cc_final: 0.7348 (tmm) REVERT: A 2933 CYS cc_start: 0.6554 (OUTLIER) cc_final: 0.6089 (m) REVERT: A 3126 LEU cc_start: 0.7747 (tp) cc_final: 0.7444 (tp) REVERT: A 3166 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8239 (tptp) REVERT: A 3359 GLN cc_start: 0.6554 (OUTLIER) cc_final: 0.4573 (pm20) REVERT: B 360 GLN cc_start: 0.6891 (OUTLIER) cc_final: 0.6499 (tt0) REVERT: B 426 GLU cc_start: 0.6721 (pp20) cc_final: 0.6463 (pp20) REVERT: B 456 LEU cc_start: 0.8667 (tp) cc_final: 0.8457 (mt) REVERT: B 464 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.7906 (mp0) REVERT: H 108 TYR cc_start: 0.7496 (OUTLIER) cc_final: 0.6802 (m-80) REVERT: R 101 GLU cc_start: 0.7894 (mm-30) cc_final: 0.6628 (mm-30) REVERT: R 126 PHE cc_start: 0.7352 (m-80) cc_final: 0.6848 (m-80) outliers start: 45 outliers final: 34 residues processed: 137 average time/residue: 0.0658 time to fit residues: 12.6821 Evaluate side-chains 130 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 90 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2822 LEU Chi-restraints excluded: chain A residue 2850 ILE Chi-restraints excluded: chain A residue 2898 LEU Chi-restraints excluded: chain A residue 2933 CYS Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 2963 ILE Chi-restraints excluded: chain A residue 2974 LEU Chi-restraints excluded: chain A residue 2975 VAL Chi-restraints excluded: chain A residue 3021 HIS Chi-restraints excluded: chain A residue 3106 ASN Chi-restraints excluded: chain A residue 3164 THR Chi-restraints excluded: chain A residue 3166 LYS Chi-restraints excluded: chain A residue 3355 GLU Chi-restraints excluded: chain A residue 3359 GLN Chi-restraints excluded: chain A residue 3385 THR Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain A residue 3402 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 381 PHE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 155 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 64 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 75 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.111181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.097422 restraints weight = 23369.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.099066 restraints weight = 14009.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.100136 restraints weight = 9915.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.100816 restraints weight = 7850.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.101297 restraints weight = 6717.773| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 7652 Z= 0.229 Angle : 0.713 13.092 10438 Z= 0.354 Chirality : 0.044 0.292 1204 Planarity : 0.004 0.054 1357 Dihedral : 6.194 54.777 1145 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 7.40 % Allowed : 27.48 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.27), residues: 1006 helix: 0.61 (0.51), residues: 121 sheet: -2.07 (0.24), residues: 435 loop : -1.62 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 345 TYR 0.015 0.002 TYR L 92 PHE 0.012 0.002 PHE B 424 TRP 0.014 0.002 TRP N 113 HIS 0.010 0.001 HIS N 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.23 ( 7638) covalent geometry : angle 0.69707 / 0.35 (10408) SS BOND : bond 0.00238 / 0.13 ( 12) SS BOND : angle 0.61070 / 0.41 ( 24) hydrogen bonds : bond 0.03377 / 2.21 ( 278) hydrogen bonds : angle 6.27460 / 4.27 ( 759) link_NAG-ASN : bond 0.01024 / 0.54 ( 2) link_NAG-ASN : angle 6.28052 / 5.64 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 92 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 2843 MET cc_start: 0.8045 (tmm) cc_final: 0.7273 (tmm) REVERT: A 2933 CYS cc_start: 0.6447 (OUTLIER) cc_final: 0.5965 (m) REVERT: A 3126 LEU cc_start: 0.7809 (tp) cc_final: 0.7570 (tp) REVERT: A 3166 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8244 (tptp) REVERT: A 3359 GLN cc_start: 0.6580 (OUTLIER) cc_final: 0.4617 (pm20) REVERT: B 360 GLN cc_start: 0.6895 (OUTLIER) cc_final: 0.6519 (tt0) REVERT: B 464 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.7981 (mp0) REVERT: H 79 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8387 (tp) REVERT: H 108 TYR cc_start: 0.7568 (OUTLIER) cc_final: 0.6899 (m-80) REVERT: R 101 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7471 (mm-30) REVERT: R 126 PHE cc_start: 0.7492 (m-80) cc_final: 0.6933 (m-80) outliers start: 56 outliers final: 40 residues processed: 136 average time/residue: 0.0586 time to fit residues: 11.2838 Evaluate side-chains 134 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 87 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2822 LEU Chi-restraints excluded: chain A residue 2850 ILE Chi-restraints excluded: chain A residue 2933 CYS Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 2963 ILE Chi-restraints excluded: chain A residue 2974 LEU Chi-restraints excluded: chain A residue 2975 VAL Chi-restraints excluded: chain A residue 3021 HIS Chi-restraints excluded: chain A residue 3106 ASN Chi-restraints excluded: chain A residue 3164 THR Chi-restraints excluded: chain A residue 3166 LYS Chi-restraints excluded: chain A residue 3355 GLU Chi-restraints excluded: chain A residue 3359 GLN Chi-restraints excluded: chain A residue 3385 THR Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain A residue 3402 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 381 PHE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 97 TYR Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 155 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 41 optimal weight: 0.0470 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3094 ASN ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.112099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.098469 restraints weight = 23379.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.100108 restraints weight = 13955.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.101185 restraints weight = 9832.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.101882 restraints weight = 7747.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.102379 restraints weight = 6621.040| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7652 Z= 0.185 Angle : 0.680 12.578 10438 Z= 0.336 Chirality : 0.044 0.293 1204 Planarity : 0.004 0.054 1357 Dihedral : 6.065 54.602 1145 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 7.40 % Allowed : 28.01 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.27), residues: 1006 helix: 0.67 (0.51), residues: 122 sheet: -2.06 (0.24), residues: 437 loop : -1.53 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 345 TYR 0.024 0.002 TYR B 342 PHE 0.017 0.002 PHE A3038 TRP 0.013 0.002 TRP H 47 HIS 0.010 0.001 HIS N 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 7638) covalent geometry : angle 0.66304 / 0.33 (10408) SS BOND : bond 0.00219 / 0.12 ( 12) SS BOND : angle 0.54752 / 0.36 ( 24) hydrogen bonds : bond 0.03145 / 2.05 ( 278) hydrogen bonds : angle 6.13313 / 4.17 ( 759) link_NAG-ASN : bond 0.01172 / 0.62 ( 2) link_NAG-ASN : angle 6.33302 / 5.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 101 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 2843 MET cc_start: 0.8044 (tmm) cc_final: 0.7306 (tmm) REVERT: A 2933 CYS cc_start: 0.6961 (OUTLIER) cc_final: 0.6697 (m) REVERT: A 3126 LEU cc_start: 0.7817 (tp) cc_final: 0.7562 (tp) REVERT: A 3166 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8199 (tptp) REVERT: A 3359 GLN cc_start: 0.6547 (OUTLIER) cc_final: 0.4581 (pm20) REVERT: B 360 GLN cc_start: 0.6876 (OUTLIER) cc_final: 0.6437 (tm-30) REVERT: B 456 LEU cc_start: 0.8700 (tp) cc_final: 0.8490 (mt) REVERT: B 464 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: H 29 PHE cc_start: 0.8100 (t80) cc_final: 0.7718 (t80) REVERT: H 108 TYR cc_start: 0.7416 (OUTLIER) cc_final: 0.6745 (m-80) REVERT: R 101 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7343 (mm-30) REVERT: R 126 PHE cc_start: 0.7391 (m-80) cc_final: 0.6861 (m-80) outliers start: 56 outliers final: 45 residues processed: 147 average time/residue: 0.0668 time to fit residues: 13.9394 Evaluate side-chains 139 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 88 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2822 LEU Chi-restraints excluded: chain A residue 2850 ILE Chi-restraints excluded: chain A residue 2891 HIS Chi-restraints excluded: chain A residue 2928 SER Chi-restraints excluded: chain A residue 2933 CYS Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 2944 SER Chi-restraints excluded: chain A residue 2963 ILE Chi-restraints excluded: chain A residue 2974 LEU Chi-restraints excluded: chain A residue 2975 VAL Chi-restraints excluded: chain A residue 3077 PHE Chi-restraints excluded: chain A residue 3106 ASN Chi-restraints excluded: chain A residue 3164 THR Chi-restraints excluded: chain A residue 3166 LYS Chi-restraints excluded: chain A residue 3173 VAL Chi-restraints excluded: chain A residue 3355 GLU Chi-restraints excluded: chain A residue 3359 GLN Chi-restraints excluded: chain A residue 3384 THR Chi-restraints excluded: chain A residue 3385 THR Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain A residue 3402 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 381 PHE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 97 TYR Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 114 PHE Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 155 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 61 optimal weight: 0.0980 chunk 45 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.111827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.098135 restraints weight = 23426.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.099758 restraints weight = 13982.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.100852 restraints weight = 9872.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.101513 restraints weight = 7798.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.101993 restraints weight = 6690.812| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7652 Z= 0.189 Angle : 0.685 12.572 10438 Z= 0.340 Chirality : 0.043 0.287 1204 Planarity : 0.004 0.053 1357 Dihedral : 6.112 56.085 1145 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 7.13 % Allowed : 28.93 % Favored : 63.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.27), residues: 1006 helix: 0.67 (0.51), residues: 122 sheet: -2.05 (0.24), residues: 435 loop : -1.55 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG N 67 TYR 0.017 0.002 TYR A3177 PHE 0.012 0.002 PHE B 424 TRP 0.013 0.002 TRP H 47 HIS 0.009 0.001 HIS N 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 ( 7638) covalent geometry : angle 0.66786 / 0.34 (10408) SS BOND : bond 0.00223 / 0.12 ( 12) SS BOND : angle 0.58867 / 0.38 ( 24) hydrogen bonds : bond 0.03168 / 2.06 ( 278) hydrogen bonds : angle 6.12660 / 4.16 ( 759) link_NAG-ASN : bond 0.01113 / 0.59 ( 2) link_NAG-ASN : angle 6.33266 / 5.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 96 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 2843 MET cc_start: 0.8043 (tmm) cc_final: 0.7290 (tmm) REVERT: A 2844 LEU cc_start: 0.7450 (mm) cc_final: 0.7138 (mp) REVERT: A 2933 CYS cc_start: 0.6332 (OUTLIER) cc_final: 0.5879 (m) REVERT: A 3166 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8191 (tptp) REVERT: A 3359 GLN cc_start: 0.6549 (OUTLIER) cc_final: 0.4593 (pm20) REVERT: B 360 GLN cc_start: 0.6853 (OUTLIER) cc_final: 0.6582 (tt0) REVERT: B 464 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: H 79 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8288 (tp) REVERT: H 108 TYR cc_start: 0.7415 (OUTLIER) cc_final: 0.6735 (m-80) REVERT: R 101 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7354 (mm-30) REVERT: R 126 PHE cc_start: 0.7436 (m-80) cc_final: 0.6934 (m-80) outliers start: 54 outliers final: 45 residues processed: 140 average time/residue: 0.0681 time to fit residues: 13.6860 Evaluate side-chains 142 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 90 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2850 ILE Chi-restraints excluded: chain A residue 2891 HIS Chi-restraints excluded: chain A residue 2928 SER Chi-restraints excluded: chain A residue 2933 CYS Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 2944 SER Chi-restraints excluded: chain A residue 2963 ILE Chi-restraints excluded: chain A residue 2974 LEU Chi-restraints excluded: chain A residue 2975 VAL Chi-restraints excluded: chain A residue 3077 PHE Chi-restraints excluded: chain A residue 3106 ASN Chi-restraints excluded: chain A residue 3164 THR Chi-restraints excluded: chain A residue 3166 LYS Chi-restraints excluded: chain A residue 3173 VAL Chi-restraints excluded: chain A residue 3355 GLU Chi-restraints excluded: chain A residue 3359 GLN Chi-restraints excluded: chain A residue 3384 THR Chi-restraints excluded: chain A residue 3385 THR Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain A residue 3402 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 381 PHE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 97 TYR Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 155 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 23 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 98 optimal weight: 0.0070 chunk 79 optimal weight: 0.0070 chunk 24 optimal weight: 0.0870 chunk 54 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3114 HIS B 377 GLN B 406 GLN ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.113818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.100389 restraints weight = 23399.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.101986 restraints weight = 14104.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.102945 restraints weight = 10004.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.103642 restraints weight = 8000.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.103974 restraints weight = 6851.947| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7652 Z= 0.126 Angle : 0.653 12.638 10438 Z= 0.321 Chirality : 0.043 0.278 1204 Planarity : 0.004 0.051 1357 Dihedral : 5.687 54.803 1145 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 5.55 % Allowed : 31.18 % Favored : 63.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.27), residues: 1006 helix: 0.92 (0.52), residues: 122 sheet: -1.89 (0.25), residues: 426 loop : -1.43 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 99 TYR 0.025 0.001 TYR B 342 PHE 0.021 0.001 PHE B 340 TRP 0.010 0.001 TRP R 87 HIS 0.009 0.001 HIS N 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 7638) covalent geometry : angle 0.63562 / 0.32 (10408) SS BOND : bond 0.00188 / 0.11 ( 12) SS BOND : angle 0.56584 / 0.37 ( 24) hydrogen bonds : bond 0.02807 / 1.78 ( 278) hydrogen bonds : angle 5.78528 / 3.93 ( 759) link_NAG-ASN : bond 0.00977 / 0.51 ( 2) link_NAG-ASN : angle 6.31478 / 5.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 100 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 2822 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.6989 (mm) REVERT: A 2843 MET cc_start: 0.8025 (tmm) cc_final: 0.7321 (tmm) REVERT: A 2844 LEU cc_start: 0.7213 (mm) cc_final: 0.6947 (mp) REVERT: A 2933 CYS cc_start: 0.6894 (OUTLIER) cc_final: 0.6660 (m) REVERT: B 360 GLN cc_start: 0.6884 (OUTLIER) cc_final: 0.6501 (tt0) REVERT: B 456 LEU cc_start: 0.8517 (mt) cc_final: 0.8313 (mt) REVERT: B 464 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: H 79 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8255 (tp) REVERT: H 108 TYR cc_start: 0.7356 (OUTLIER) cc_final: 0.6742 (m-80) REVERT: L 3 MET cc_start: 0.7074 (OUTLIER) cc_final: 0.6496 (mmp) REVERT: N 5 GLN cc_start: 0.5510 (OUTLIER) cc_final: 0.4949 (pm20) REVERT: N 38 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8014 (ttp-170) REVERT: R 101 GLU cc_start: 0.7850 (mm-30) cc_final: 0.6614 (mm-30) REVERT: R 126 PHE cc_start: 0.7262 (m-80) cc_final: 0.6792 (m-80) REVERT: R 163 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7083 (mm-40) outliers start: 42 outliers final: 25 residues processed: 136 average time/residue: 0.0626 time to fit residues: 12.2754 Evaluate side-chains 130 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2822 LEU Chi-restraints excluded: chain A residue 2850 ILE Chi-restraints excluded: chain A residue 2891 HIS Chi-restraints excluded: chain A residue 2928 SER Chi-restraints excluded: chain A residue 2933 CYS Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 2963 ILE Chi-restraints excluded: chain A residue 2974 LEU Chi-restraints excluded: chain A residue 2975 VAL Chi-restraints excluded: chain A residue 3114 HIS Chi-restraints excluded: chain A residue 3164 THR Chi-restraints excluded: chain A residue 3173 VAL Chi-restraints excluded: chain A residue 3384 THR Chi-restraints excluded: chain A residue 3385 THR Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain A residue 3402 SER Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 155 CYS Chi-restraints excluded: chain R residue 163 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 87 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 95 optimal weight: 0.0170 chunk 81 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 98 optimal weight: 0.3980 chunk 43 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3114 HIS ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.113562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.100246 restraints weight = 23342.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.101836 restraints weight = 13902.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.102882 restraints weight = 9824.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.103405 restraints weight = 7787.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.103960 restraints weight = 6786.750| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7652 Z= 0.145 Angle : 0.687 12.970 10438 Z= 0.337 Chirality : 0.043 0.217 1204 Planarity : 0.004 0.053 1357 Dihedral : 5.692 55.364 1145 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 6.08 % Allowed : 30.25 % Favored : 63.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.27), residues: 1006 helix: 1.01 (0.53), residues: 121 sheet: -1.89 (0.25), residues: 426 loop : -1.41 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2836 TYR 0.022 0.001 TYR A2889 PHE 0.013 0.001 PHE B 424 TRP 0.010 0.001 TRP R 87 HIS 0.009 0.001 HIS N 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 7638) covalent geometry : angle 0.66878 / 0.33 (10408) SS BOND : bond 0.00261 / 0.14 ( 12) SS BOND : angle 0.72941 / 0.53 ( 24) hydrogen bonds : bond 0.02851 / 1.82 ( 278) hydrogen bonds : angle 5.77871 / 3.93 ( 759) link_NAG-ASN : bond 0.01354 / 0.71 ( 2) link_NAG-ASN : angle 6.60692 / 5.85 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 93 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 2822 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.6994 (mm) REVERT: A 2843 MET cc_start: 0.8019 (tmm) cc_final: 0.7289 (tmm) REVERT: A 2844 LEU cc_start: 0.7247 (mm) cc_final: 0.6994 (mp) REVERT: A 2933 CYS cc_start: 0.6851 (OUTLIER) cc_final: 0.6621 (m) REVERT: B 462 LEU cc_start: 0.9003 (tp) cc_final: 0.8697 (tp) REVERT: B 464 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: H 79 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8253 (tp) REVERT: H 108 TYR cc_start: 0.7356 (OUTLIER) cc_final: 0.6746 (m-80) REVERT: N 5 GLN cc_start: 0.5042 (OUTLIER) cc_final: 0.4541 (pm20) REVERT: N 38 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8040 (ttp-170) REVERT: R 101 GLU cc_start: 0.8036 (mm-30) cc_final: 0.6943 (mm-30) REVERT: R 126 PHE cc_start: 0.7294 (m-80) cc_final: 0.6780 (m-80) REVERT: R 163 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7073 (mm-40) outliers start: 46 outliers final: 34 residues processed: 132 average time/residue: 0.0601 time to fit residues: 11.4232 Evaluate side-chains 134 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 92 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2822 LEU Chi-restraints excluded: chain A residue 2850 ILE Chi-restraints excluded: chain A residue 2891 HIS Chi-restraints excluded: chain A residue 2928 SER Chi-restraints excluded: chain A residue 2933 CYS Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 2944 SER Chi-restraints excluded: chain A residue 2963 ILE Chi-restraints excluded: chain A residue 2974 LEU Chi-restraints excluded: chain A residue 2975 VAL Chi-restraints excluded: chain A residue 3077 PHE Chi-restraints excluded: chain A residue 3114 HIS Chi-restraints excluded: chain A residue 3164 THR Chi-restraints excluded: chain A residue 3173 VAL Chi-restraints excluded: chain A residue 3384 THR Chi-restraints excluded: chain A residue 3385 THR Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain A residue 3402 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 114 PHE Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 155 CYS Chi-restraints excluded: chain R residue 163 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 0.2980 chunk 26 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 50 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 0.1980 chunk 19 optimal weight: 3.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3114 HIS ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.113563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.100267 restraints weight = 23290.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.101795 restraints weight = 13912.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.102824 restraints weight = 9850.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.103356 restraints weight = 7853.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.103915 restraints weight = 6830.342| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7652 Z= 0.145 Angle : 0.683 12.629 10438 Z= 0.337 Chirality : 0.043 0.212 1204 Planarity : 0.004 0.053 1357 Dihedral : 5.711 55.626 1145 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 5.55 % Allowed : 30.91 % Favored : 63.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.27), residues: 1006 helix: 1.10 (0.53), residues: 116 sheet: -1.76 (0.25), residues: 419 loop : -1.44 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2836 TYR 0.029 0.002 TYR B 342 PHE 0.020 0.002 PHE A3038 TRP 0.010 0.001 TRP R 87 HIS 0.009 0.001 HIS N 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 7638) covalent geometry : angle 0.66492 / 0.33 (10408) SS BOND : bond 0.00220 / 0.13 ( 12) SS BOND : angle 0.87094 / 0.59 ( 24) hydrogen bonds : bond 0.02813 / 1.78 ( 278) hydrogen bonds : angle 5.76616 / 3.93 ( 759) link_NAG-ASN : bond 0.01182 / 0.62 ( 2) link_NAG-ASN : angle 6.48454 / 5.72 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 94 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 2822 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.6982 (mm) REVERT: A 2843 MET cc_start: 0.8018 (tmm) cc_final: 0.7287 (tmm) REVERT: A 2844 LEU cc_start: 0.7247 (mm) cc_final: 0.6997 (mp) REVERT: A 2933 CYS cc_start: 0.6920 (OUTLIER) cc_final: 0.6672 (m) REVERT: B 464 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: H 29 PHE cc_start: 0.8095 (t80) cc_final: 0.7845 (t80) REVERT: H 79 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8293 (tp) REVERT: H 108 TYR cc_start: 0.7354 (OUTLIER) cc_final: 0.6743 (m-80) REVERT: N 5 GLN cc_start: 0.5030 (OUTLIER) cc_final: 0.4538 (pm20) REVERT: N 38 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8037 (ttp-170) REVERT: R 101 GLU cc_start: 0.8086 (mm-30) cc_final: 0.6984 (mm-30) REVERT: R 126 PHE cc_start: 0.7287 (m-80) cc_final: 0.6795 (m-80) REVERT: R 163 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7314 (mm-40) outliers start: 42 outliers final: 33 residues processed: 130 average time/residue: 0.0548 time to fit residues: 10.3413 Evaluate side-chains 134 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 93 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2822 LEU Chi-restraints excluded: chain A residue 2850 ILE Chi-restraints excluded: chain A residue 2891 HIS Chi-restraints excluded: chain A residue 2928 SER Chi-restraints excluded: chain A residue 2933 CYS Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 2944 SER Chi-restraints excluded: chain A residue 2963 ILE Chi-restraints excluded: chain A residue 2974 LEU Chi-restraints excluded: chain A residue 2975 VAL Chi-restraints excluded: chain A residue 3077 PHE Chi-restraints excluded: chain A residue 3114 HIS Chi-restraints excluded: chain A residue 3164 THR Chi-restraints excluded: chain A residue 3173 VAL Chi-restraints excluded: chain A residue 3384 THR Chi-restraints excluded: chain A residue 3385 THR Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain A residue 3402 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 114 PHE Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 155 CYS Chi-restraints excluded: chain R residue 163 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 60 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 84 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3114 HIS ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.112742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.099215 restraints weight = 23277.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.100865 restraints weight = 13843.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.101888 restraints weight = 9722.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.102518 restraints weight = 7713.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.103036 restraints weight = 6652.718| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7652 Z= 0.168 Angle : 0.688 13.439 10438 Z= 0.340 Chirality : 0.043 0.223 1204 Planarity : 0.004 0.054 1357 Dihedral : 5.820 55.716 1145 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 6.08 % Allowed : 30.12 % Favored : 63.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.27), residues: 1006 helix: 1.03 (0.53), residues: 116 sheet: -1.79 (0.25), residues: 421 loop : -1.43 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2836 TYR 0.022 0.002 TYR A2889 PHE 0.015 0.001 PHE B 424 TRP 0.009 0.001 TRP R 87 HIS 0.016 0.002 HIS A3114 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 ( 7638) covalent geometry : angle 0.66955 / 0.34 (10408) SS BOND : bond 0.00239 / 0.15 ( 12) SS BOND : angle 0.81722 / 0.55 ( 24) hydrogen bonds : bond 0.02901 / 1.86 ( 278) hydrogen bonds : angle 5.81783 / 3.96 ( 759) link_NAG-ASN : bond 0.01009 / 0.53 ( 2) link_NAG-ASN : angle 6.51282 / 5.92 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1305.51 seconds wall clock time: 23 minutes 15.66 seconds (1395.66 seconds total)