Starting phenix.real_space_refine on Wed Mar 4 05:39:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6seg_10155/03_2026/6seg_10155.cif Found real_map, /net/cci-nas-00/data/ceres_data/6seg_10155/03_2026/6seg_10155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6seg_10155/03_2026/6seg_10155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6seg_10155/03_2026/6seg_10155.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6seg_10155/03_2026/6seg_10155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6seg_10155/03_2026/6seg_10155.map" } resolution = 3.1 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 10 5.16 5 C 6471 2.51 5 N 2175 2.21 5 O 2745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11689 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "B" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 618 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 739 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "F" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 618 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 799 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "H" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 2.70, per 1000 atoms: 0.23 Number of scatterers: 11689 At special positions: 0 Unit cell: (74.24, 120.32, 113.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 288 15.00 O 2745 8.00 N 2175 7.00 C 6471 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 394.4 milliseconds 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1344 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 8 sheets defined 72.9% alpha, 2.7% beta 127 base pairs and 265 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.819A pdb=" N LYS A 49 " --> pdb=" O GLN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.082A pdb=" N LYS A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.531A pdb=" N LEU A 91 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 removed outlier: 3.869A pdb=" N VAL A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.890A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.780A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.164A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.613A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 56 through 84 removed outlier: 3.586A pdb=" N ASN D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.507A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.792A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 removed outlier: 3.504A pdb=" N SER E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.077A pdb=" N LYS E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 116 removed outlier: 3.766A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 134 removed outlier: 3.501A pdb=" N VAL E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.746A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.556A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.616A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.656A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.259A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.599A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.570A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 122 removed outlier: 3.617A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL H 111 " --> pdb=" O ALA H 107 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR H 119 " --> pdb=" O THR H 115 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.700A pdb=" N ASN A 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.490A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.455A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.754A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 85 through 86 removed outlier: 6.871A pdb=" N ASN E 85 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.583A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 357 hydrogen bonds defined for protein. 1062 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 329 hydrogen bonds 654 hydrogen bond angles 0 basepair planarities 127 basepair parallelities 265 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1875 1.33 - 1.45: 4394 1.45 - 1.57: 5633 1.57 - 1.68: 576 1.68 - 1.80: 18 Bond restraints: 12496 Sorted by residual: bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.494 -0.072 3.00e-02 1.11e+03 5.70e+00 bond pdb=" C LEU A 121 " pdb=" N PHE A 122 " ideal model delta sigma weight residual 1.335 1.277 0.058 3.04e-02 1.08e+03 3.64e+00 bond pdb=" CB MET G 51 " pdb=" CG MET G 51 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.13e+00 bond pdb=" CG LEU D 101 " pdb=" CD1 LEU D 101 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.58e+00 bond pdb=" CG GLU C 92 " pdb=" CD GLU C 92 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.42e+00 ... (remaining 12491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 17895 2.75 - 5.49: 210 5.49 - 8.24: 16 8.24 - 10.98: 3 10.98 - 13.73: 1 Bond angle restraints: 18125 Sorted by residual: angle pdb=" CA ARG A 80 " pdb=" CB ARG A 80 " pdb=" CG ARG A 80 " ideal model delta sigma weight residual 114.10 122.82 -8.72 2.00e+00 2.50e-01 1.90e+01 angle pdb=" CA LEU A 121 " pdb=" CB LEU A 121 " pdb=" CG LEU A 121 " ideal model delta sigma weight residual 116.30 130.03 -13.73 3.50e+00 8.16e-02 1.54e+01 angle pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sigma weight residual 120.20 125.69 -5.49 1.50e+00 4.44e-01 1.34e+01 angle pdb=" CB MET G 51 " pdb=" CG MET G 51 " pdb=" SD MET G 51 " ideal model delta sigma weight residual 112.70 101.94 10.76 3.00e+00 1.11e-01 1.29e+01 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 112.50 116.53 -4.03 1.16e+00 7.43e-01 1.21e+01 ... (remaining 18120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 5311 34.97 - 69.95: 1378 69.95 - 104.92: 18 104.92 - 139.89: 0 139.89 - 174.87: 1 Dihedral angle restraints: 6708 sinusoidal: 4618 harmonic: 2090 Sorted by residual: dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 45.13 174.87 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA ARG A 63 " pdb=" C ARG A 63 " pdb=" N LYS A 64 " pdb=" CA LYS A 64 " ideal model delta harmonic sigma weight residual -180.00 -161.09 -18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual -180.00 -162.53 -17.47 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 6705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1944 0.099 - 0.198: 106 0.198 - 0.298: 7 0.298 - 0.397: 1 0.397 - 0.496: 1 Chirality restraints: 2059 Sorted by residual: chirality pdb=" CG LEU D 45 " pdb=" CB LEU D 45 " pdb=" CD1 LEU D 45 " pdb=" CD2 LEU D 45 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.15e+00 chirality pdb=" CB ILE G 111 " pdb=" CA ILE G 111 " pdb=" CG1 ILE G 111 " pdb=" CG2 ILE G 111 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CG LEU E 112 " pdb=" CB LEU E 112 " pdb=" CD1 LEU E 112 " pdb=" CD2 LEU E 112 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 2056 not shown) Planarity restraints: 1283 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 69 " 0.035 2.00e-02 2.50e+03 2.01e-02 9.09e+00 pdb=" N1 DC I 69 " -0.044 2.00e-02 2.50e+03 pdb=" C2 DC I 69 " 0.011 2.00e-02 2.50e+03 pdb=" O2 DC I 69 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DC I 69 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 69 " 0.005 2.00e-02 2.50e+03 pdb=" N4 DC I 69 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DC I 69 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DC I 69 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 35 " 0.038 2.00e-02 2.50e+03 1.97e-02 8.70e+00 pdb=" N1 DC I 35 " -0.040 2.00e-02 2.50e+03 pdb=" C2 DC I 35 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DC I 35 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DC I 35 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC I 35 " 0.008 2.00e-02 2.50e+03 pdb=" N4 DC I 35 " 0.012 2.00e-02 2.50e+03 pdb=" C5 DC I 35 " -0.008 2.00e-02 2.50e+03 pdb=" C6 DC I 35 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 5 " -0.037 2.00e-02 2.50e+03 1.91e-02 8.24e+00 pdb=" N1 DC I 5 " 0.039 2.00e-02 2.50e+03 pdb=" C2 DC I 5 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DC I 5 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DC I 5 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 5 " -0.007 2.00e-02 2.50e+03 pdb=" N4 DC I 5 " -0.013 2.00e-02 2.50e+03 pdb=" C5 DC I 5 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DC I 5 " 0.005 2.00e-02 2.50e+03 ... (remaining 1280 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2588 2.81 - 3.33: 9223 3.33 - 3.85: 23485 3.85 - 4.38: 27726 4.38 - 4.90: 38845 Nonbonded interactions: 101867 Sorted by model distance: nonbonded pdb=" OG1 THR E 113 " pdb=" OD2 ASP E 125 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR A 113 " pdb=" OD2 ASP A 125 " model vdw 2.284 3.040 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.321 3.040 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.338 3.040 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.345 2.496 ... (remaining 101862 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 111) } ncs_group { reference = (chain 'D' and resid 35 through 124) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.470 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 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 : 0.006 0.072 12496 Z= 0.279 Angle : 0.857 13.727 18125 Z= 0.510 Chirality : 0.054 0.496 2059 Planarity : 0.007 0.063 1283 Dihedral : 27.752 174.868 5364 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % 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: -3.47 (0.23), residues: 712 helix: -2.21 (0.17), residues: 515 sheet: None (None), residues: 0 loop : -1.95 (0.34), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 42 TYR 0.022 0.003 TYR F 98 PHE 0.015 0.003 PHE A 84 TRP 0.005 0.001 TRP E 47 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00631 (12496) covalent geometry : angle 0.85651 (18125) hydrogen bonds : bond 0.10465 ( 686) hydrogen bonds : angle 4.48599 ( 1716) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.285 Fit side-chains REVERT: A 53 LYS cc_start: 0.8330 (tmmt) cc_final: 0.8125 (tmmt) REVERT: B 44 LYS cc_start: 0.8659 (tttt) cc_final: 0.8038 (mptt) REVERT: B 79 LYS cc_start: 0.8126 (mtmt) cc_final: 0.7482 (mtpp) REVERT: C 73 ASN cc_start: 0.8222 (t0) cc_final: 0.7834 (t0) REVERT: C 74 LYS cc_start: 0.7714 (mtmt) cc_final: 0.7453 (mttp) REVERT: C 95 LYS cc_start: 0.7845 (mtmt) cc_final: 0.7535 (ttmm) REVERT: D 37 TYR cc_start: 0.8839 (m-80) cc_final: 0.8451 (m-80) REVERT: D 59 MET cc_start: 0.7932 (tpp) cc_final: 0.7607 (tpt) REVERT: E 62 ILE cc_start: 0.8163 (mt) cc_final: 0.7951 (mt) REVERT: G 36 LYS cc_start: 0.8438 (mptt) cc_final: 0.8158 (mptt) REVERT: G 90 ASP cc_start: 0.7445 (t0) cc_final: 0.7199 (t0) REVERT: H 99 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.7767 (mtm110) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1780 time to fit residues: 25.2581 Evaluate side-chains 91 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN G 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.179815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.134292 restraints weight = 13574.982| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.00 r_work: 0.3420 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12496 Z= 0.194 Angle : 0.634 5.844 18125 Z= 0.378 Chirality : 0.036 0.154 2059 Planarity : 0.005 0.056 1283 Dihedral : 30.816 169.786 3964 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.17 % Allowed : 8.54 % Favored : 90.28 % 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: -0.96 (0.28), residues: 712 helix: -0.16 (0.21), residues: 521 sheet: None (None), residues: 0 loop : -1.69 (0.36), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 40 TYR 0.016 0.002 TYR F 98 PHE 0.012 0.001 PHE A 67 TRP 0.005 0.001 TRP E 86 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00422 (12496) covalent geometry : angle 0.63432 (18125) hydrogen bonds : bond 0.05328 ( 686) hydrogen bonds : angle 3.29894 ( 1716) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.251 Fit side-chains REVERT: A 53 LYS cc_start: 0.8593 (tmmt) cc_final: 0.8343 (tmmt) REVERT: B 44 LYS cc_start: 0.8905 (tttt) cc_final: 0.8191 (mptt) REVERT: B 79 LYS cc_start: 0.8262 (mtmt) cc_final: 0.7658 (mtpp) REVERT: C 74 LYS cc_start: 0.7725 (mtmt) cc_final: 0.7484 (mttp) REVERT: C 95 LYS cc_start: 0.8002 (mtmt) cc_final: 0.7695 (ttmm) REVERT: E 62 ILE cc_start: 0.8543 (mt) cc_final: 0.8310 (mt) REVERT: G 36 LYS cc_start: 0.8576 (mptt) cc_final: 0.8345 (mptt) outliers start: 7 outliers final: 5 residues processed: 101 average time/residue: 0.1604 time to fit residues: 20.8023 Evaluate side-chains 93 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 8 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN G 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.180638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.135541 restraints weight = 13637.814| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 0.91 r_work: 0.3314 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12496 Z= 0.221 Angle : 0.621 7.002 18125 Z= 0.370 Chirality : 0.037 0.146 2059 Planarity : 0.005 0.047 1283 Dihedral : 30.899 168.622 3964 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.51 % Allowed : 10.05 % Favored : 88.44 % 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: -0.12 (0.30), residues: 712 helix: 0.51 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.57 (0.38), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 86 TYR 0.010 0.002 TYR D 40 PHE 0.007 0.001 PHE A 78 TRP 0.004 0.001 TRP A 47 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00504 (12496) covalent geometry : angle 0.62093 (18125) hydrogen bonds : bond 0.05146 ( 686) hydrogen bonds : angle 3.06544 ( 1716) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.297 Fit side-chains REVERT: B 44 LYS cc_start: 0.8885 (tttt) cc_final: 0.8009 (mptt) REVERT: C 74 LYS cc_start: 0.7701 (mtmt) cc_final: 0.7420 (mttp) REVERT: D 59 MET cc_start: 0.8819 (tpp) cc_final: 0.8498 (tpt) REVERT: E 62 ILE cc_start: 0.8570 (mt) cc_final: 0.8303 (mt) REVERT: G 36 LYS cc_start: 0.8629 (mptt) cc_final: 0.8351 (mptt) REVERT: G 74 LYS cc_start: 0.7689 (mmtt) cc_final: 0.7394 (mmtt) outliers start: 9 outliers final: 7 residues processed: 96 average time/residue: 0.1512 time to fit residues: 19.0059 Evaluate side-chains 95 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 32 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.182268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.137438 restraints weight = 13667.128| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 0.91 r_work: 0.3362 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12496 Z= 0.159 Angle : 0.542 5.828 18125 Z= 0.330 Chirality : 0.033 0.139 2059 Planarity : 0.004 0.040 1283 Dihedral : 30.769 172.118 3964 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.01 % Allowed : 11.22 % Favored : 86.77 % 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: 0.77 (0.30), residues: 712 helix: 1.20 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.39 (0.38), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 86 TYR 0.013 0.001 TYR D 40 PHE 0.010 0.001 PHE E 67 TRP 0.002 0.001 TRP E 86 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00345 (12496) covalent geometry : angle 0.54230 (18125) hydrogen bonds : bond 0.04050 ( 686) hydrogen bonds : angle 2.72512 ( 1716) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.290 Fit side-chains REVERT: A 114 LEU cc_start: 0.8249 (mt) cc_final: 0.7924 (mp) REVERT: B 44 LYS cc_start: 0.8917 (tttt) cc_final: 0.7970 (mptt) REVERT: B 79 LYS cc_start: 0.8143 (mttp) cc_final: 0.7373 (mtpp) REVERT: B 91 LYS cc_start: 0.8777 (ttmm) cc_final: 0.8507 (ttmm) REVERT: C 92 GLU cc_start: 0.7792 (pm20) cc_final: 0.7581 (pm20) REVERT: E 62 ILE cc_start: 0.8506 (mt) cc_final: 0.8176 (mt) REVERT: F 91 LYS cc_start: 0.8727 (ttpt) cc_final: 0.8491 (ttpp) REVERT: G 23 LEU cc_start: 0.8306 (mt) cc_final: 0.8053 (mt) REVERT: G 74 LYS cc_start: 0.8004 (mmtt) cc_final: 0.7738 (mmtt) REVERT: G 112 GLN cc_start: 0.5927 (OUTLIER) cc_final: 0.5245 (pt0) outliers start: 12 outliers final: 9 residues processed: 104 average time/residue: 0.1483 time to fit residues: 20.3172 Evaluate side-chains 99 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.181962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.136812 restraints weight = 13590.243| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 0.88 r_work: 0.3316 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12496 Z= 0.225 Angle : 0.587 6.186 18125 Z= 0.350 Chirality : 0.037 0.139 2059 Planarity : 0.004 0.043 1283 Dihedral : 31.118 170.381 3964 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.84 % Allowed : 12.06 % Favored : 86.10 % 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: 0.76 (0.30), residues: 712 helix: 1.20 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.43 (0.37), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 42 TYR 0.010 0.002 TYR H 121 PHE 0.011 0.001 PHE A 78 TRP 0.007 0.001 TRP A 86 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00514 (12496) covalent geometry : angle 0.58720 (18125) hydrogen bonds : bond 0.04439 ( 686) hydrogen bonds : angle 2.84630 ( 1716) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.261 Fit side-chains REVERT: A 114 LEU cc_start: 0.8348 (mt) cc_final: 0.8060 (mp) REVERT: B 44 LYS cc_start: 0.8924 (tttt) cc_final: 0.7954 (mptt) REVERT: B 79 LYS cc_start: 0.8124 (mttp) cc_final: 0.7363 (mtpp) REVERT: C 35 ARG cc_start: 0.8222 (mtm-85) cc_final: 0.7646 (mtm-85) REVERT: C 92 GLU cc_start: 0.7818 (pm20) cc_final: 0.7586 (pm20) REVERT: F 91 LYS cc_start: 0.8744 (ttpt) cc_final: 0.8501 (ttpp) REVERT: G 74 LYS cc_start: 0.7890 (mmtt) cc_final: 0.7673 (mmtt) REVERT: G 112 GLN cc_start: 0.6135 (OUTLIER) cc_final: 0.5543 (pt0) outliers start: 11 outliers final: 8 residues processed: 101 average time/residue: 0.1732 time to fit residues: 22.3401 Evaluate side-chains 98 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 30 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 70 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN G 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.183546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.138493 restraints weight = 13584.956| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 0.87 r_work: 0.3336 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12496 Z= 0.183 Angle : 0.555 5.865 18125 Z= 0.334 Chirality : 0.034 0.137 2059 Planarity : 0.004 0.040 1283 Dihedral : 30.984 171.784 3964 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.84 % Allowed : 12.73 % Favored : 85.43 % 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: 1.09 (0.30), residues: 712 helix: 1.45 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.31 (0.37), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 11 TYR 0.009 0.001 TYR D 40 PHE 0.009 0.001 PHE E 67 TRP 0.005 0.001 TRP A 86 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00409 (12496) covalent geometry : angle 0.55480 (18125) hydrogen bonds : bond 0.04082 ( 686) hydrogen bonds : angle 2.72663 ( 1716) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.297 Fit side-chains REVERT: A 79 THR cc_start: 0.7911 (p) cc_final: 0.7553 (p) REVERT: A 114 LEU cc_start: 0.8318 (mt) cc_final: 0.8029 (mp) REVERT: B 44 LYS cc_start: 0.8927 (tttt) cc_final: 0.7968 (mttt) REVERT: C 35 ARG cc_start: 0.8220 (mtm-85) cc_final: 0.7625 (mtm-85) REVERT: C 92 GLU cc_start: 0.7824 (pm20) cc_final: 0.7595 (pm20) REVERT: F 91 LYS cc_start: 0.8752 (ttpt) cc_final: 0.8501 (ttpp) REVERT: G 23 LEU cc_start: 0.8285 (mt) cc_final: 0.8052 (mt) REVERT: G 74 LYS cc_start: 0.7899 (mmtt) cc_final: 0.7606 (mmtt) REVERT: G 112 GLN cc_start: 0.6043 (OUTLIER) cc_final: 0.5454 (pt0) outliers start: 11 outliers final: 9 residues processed: 94 average time/residue: 0.1591 time to fit residues: 19.4115 Evaluate side-chains 96 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 2 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN G 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.182995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.137981 restraints weight = 13591.050| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 0.86 r_work: 0.3430 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12496 Z= 0.161 Angle : 0.539 5.798 18125 Z= 0.327 Chirality : 0.033 0.136 2059 Planarity : 0.004 0.039 1283 Dihedral : 30.937 171.942 3964 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.01 % Allowed : 12.90 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.35 (0.30), residues: 712 helix: 1.64 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.22 (0.38), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 11 TYR 0.011 0.001 TYR D 40 PHE 0.008 0.001 PHE E 67 TRP 0.005 0.001 TRP A 86 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00353 (12496) covalent geometry : angle 0.53903 (18125) hydrogen bonds : bond 0.03971 ( 686) hydrogen bonds : angle 2.66019 ( 1716) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.282 Fit side-chains REVERT: A 79 THR cc_start: 0.7713 (p) cc_final: 0.7391 (p) REVERT: A 114 LEU cc_start: 0.8353 (mt) cc_final: 0.8070 (mp) REVERT: B 44 LYS cc_start: 0.8925 (tttt) cc_final: 0.8099 (mptt) REVERT: C 35 ARG cc_start: 0.8213 (mtm-85) cc_final: 0.7662 (mtm-85) REVERT: F 91 LYS cc_start: 0.8788 (ttpt) cc_final: 0.8548 (ttpp) REVERT: G 74 LYS cc_start: 0.7982 (mmtt) cc_final: 0.7709 (mmtt) REVERT: G 112 GLN cc_start: 0.6068 (OUTLIER) cc_final: 0.5515 (pt0) outliers start: 12 outliers final: 9 residues processed: 97 average time/residue: 0.1535 time to fit residues: 19.4746 Evaluate side-chains 99 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 66 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 0.0050 chunk 60 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.184733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.140055 restraints weight = 13515.259| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 0.85 r_work: 0.3459 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12496 Z= 0.153 Angle : 0.530 5.771 18125 Z= 0.323 Chirality : 0.033 0.136 2059 Planarity : 0.004 0.038 1283 Dihedral : 30.861 172.098 3964 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.84 % Allowed : 12.73 % Favored : 85.43 % 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: 1.54 (0.31), residues: 712 helix: 1.77 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.15 (0.38), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.011 0.001 TYR D 40 PHE 0.008 0.001 PHE E 67 TRP 0.005 0.001 TRP A 86 HIS 0.003 0.000 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00332 (12496) covalent geometry : angle 0.53018 (18125) hydrogen bonds : bond 0.03889 ( 686) hydrogen bonds : angle 2.60384 ( 1716) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.277 Fit side-chains REVERT: A 79 THR cc_start: 0.7645 (p) cc_final: 0.7340 (p) REVERT: A 114 LEU cc_start: 0.8340 (mt) cc_final: 0.8057 (mp) REVERT: B 44 LYS cc_start: 0.8913 (tttt) cc_final: 0.8082 (mptt) REVERT: B 91 LYS cc_start: 0.8677 (ttmm) cc_final: 0.7980 (mtpp) REVERT: C 35 ARG cc_start: 0.8215 (mtm-85) cc_final: 0.7675 (mtm-85) REVERT: F 91 LYS cc_start: 0.8758 (ttpt) cc_final: 0.8541 (ttpp) REVERT: G 74 LYS cc_start: 0.7978 (mmtt) cc_final: 0.7721 (mmtt) REVERT: G 112 GLN cc_start: 0.6030 (OUTLIER) cc_final: 0.5515 (pt0) outliers start: 11 outliers final: 9 residues processed: 93 average time/residue: 0.1433 time to fit residues: 17.5553 Evaluate side-chains 93 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 51 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.180487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.135274 restraints weight = 13408.833| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 0.88 r_work: 0.3365 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12496 Z= 0.244 Angle : 0.604 5.901 18125 Z= 0.356 Chirality : 0.038 0.154 2059 Planarity : 0.005 0.047 1283 Dihedral : 31.282 169.583 3964 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.01 % Allowed : 12.23 % Favored : 85.76 % 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: 1.13 (0.30), residues: 712 helix: 1.46 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.24 (0.38), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 11 TYR 0.011 0.002 TYR H 121 PHE 0.011 0.002 PHE A 67 TRP 0.005 0.001 TRP A 86 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00559 (12496) covalent geometry : angle 0.60372 (18125) hydrogen bonds : bond 0.04568 ( 686) hydrogen bonds : angle 2.83343 ( 1716) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.269 Fit side-chains REVERT: A 79 THR cc_start: 0.8052 (p) cc_final: 0.7728 (p) REVERT: A 114 LEU cc_start: 0.8447 (mt) cc_final: 0.8185 (mp) REVERT: B 44 LYS cc_start: 0.8902 (tttt) cc_final: 0.8012 (mttt) REVERT: B 91 LYS cc_start: 0.8754 (ttmm) cc_final: 0.8044 (mtpp) REVERT: C 35 ARG cc_start: 0.8267 (mtm-85) cc_final: 0.7835 (mtm-85) REVERT: D 120 LYS cc_start: 0.8373 (tttt) cc_final: 0.7996 (ttmm) REVERT: E 53 LYS cc_start: 0.8707 (ttpt) cc_final: 0.8344 (tttt) REVERT: F 91 LYS cc_start: 0.8814 (ttpt) cc_final: 0.8561 (ttpp) REVERT: G 74 LYS cc_start: 0.7987 (mmtt) cc_final: 0.7720 (mmtt) REVERT: G 75 LYS cc_start: 0.7984 (mmtm) cc_final: 0.7706 (mmtt) REVERT: G 107 VAL cc_start: 0.8717 (p) cc_final: 0.8337 (m) REVERT: G 112 GLN cc_start: 0.6205 (OUTLIER) cc_final: 0.5675 (pt0) outliers start: 12 outliers final: 8 residues processed: 101 average time/residue: 0.1561 time to fit residues: 20.1401 Evaluate side-chains 97 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 47 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 50 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN G 110 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 = 0.185225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.140367 restraints weight = 13484.832| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 0.87 r_work: 0.3329 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12496 Z= 0.156 Angle : 0.558 5.769 18125 Z= 0.337 Chirality : 0.035 0.138 2059 Planarity : 0.004 0.045 1283 Dihedral : 31.192 171.493 3964 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.01 % Allowed : 13.23 % Favored : 84.76 % 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: 1.35 (0.30), residues: 712 helix: 1.65 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.26 (0.37), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 86 TYR 0.010 0.002 TYR D 40 PHE 0.007 0.001 PHE A 84 TRP 0.005 0.001 TRP A 86 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00334 (12496) covalent geometry : angle 0.55824 (18125) hydrogen bonds : bond 0.04122 ( 686) hydrogen bonds : angle 2.69253 ( 1716) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.272 Fit side-chains REVERT: A 79 THR cc_start: 0.7849 (p) cc_final: 0.7487 (p) REVERT: A 114 LEU cc_start: 0.8273 (mt) cc_final: 0.8014 (mp) REVERT: B 44 LYS cc_start: 0.8911 (tttt) cc_final: 0.7882 (mttt) REVERT: B 91 LYS cc_start: 0.8601 (ttmm) cc_final: 0.7912 (mtpp) REVERT: C 35 ARG cc_start: 0.8205 (mtm-85) cc_final: 0.7746 (mtm-85) REVERT: D 120 LYS cc_start: 0.8323 (tttt) cc_final: 0.7941 (ttmm) REVERT: F 91 LYS cc_start: 0.8763 (ttpt) cc_final: 0.8498 (ttpp) REVERT: G 74 LYS cc_start: 0.7962 (mmtt) cc_final: 0.7698 (mmtt) REVERT: G 75 LYS cc_start: 0.7881 (mmtm) cc_final: 0.7595 (mmtt) REVERT: G 107 VAL cc_start: 0.8578 (p) cc_final: 0.8197 (m) REVERT: G 112 GLN cc_start: 0.6103 (OUTLIER) cc_final: 0.5515 (pt0) outliers start: 12 outliers final: 8 residues processed: 96 average time/residue: 0.1647 time to fit residues: 20.3395 Evaluate side-chains 96 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 68 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 43 optimal weight: 0.0870 chunk 65 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 30 optimal weight: 0.0060 chunk 55 optimal weight: 1.9990 overall best weight: 0.4574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.177688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.130749 restraints weight = 13500.079| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.14 r_work: 0.3294 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 12496 Z= 0.191 Angle : 0.801 59.183 18125 Z= 0.488 Chirality : 0.041 1.031 2059 Planarity : 0.004 0.067 1283 Dihedral : 31.192 171.454 3964 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.68 % Allowed : 13.23 % Favored : 85.09 % Cbeta Deviations : 0.15 % 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: 1.39 (0.30), residues: 712 helix: 1.68 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.26 (0.37), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 86 TYR 0.010 0.002 TYR D 40 PHE 0.007 0.001 PHE E 67 TRP 0.006 0.001 TRP A 86 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00400 (12496) covalent geometry : angle 0.80104 (18125) hydrogen bonds : bond 0.04110 ( 686) hydrogen bonds : angle 2.69391 ( 1716) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2817.08 seconds wall clock time: 48 minutes 38.24 seconds (2918.24 seconds total)