Starting phenix.real_space_refine on Thu Aug 6 22:27:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwh_47246/08_2026/9dwh_47246.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwh_47246/08_2026/9dwh_47246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dwh_47246/08_2026/9dwh_47246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwh_47246/08_2026/9dwh_47246.map" model { file = "/net/cci-nas-00/data/ceres_data/9dwh_47246/08_2026/9dwh_47246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwh_47246/08_2026/9dwh_47246.cif" } resolution = 3.3 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= 0.002 sd= 1.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4192 atoms to isotropic. 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 293 5.49 5 S 19 5.16 5 C 8308 2.51 5 N 2718 2.21 5 O 3315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14653 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 813 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 98, 805 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Conformer: "B" Number of residues, atoms: 98, 805 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} bond proxies already assigned to first conformer: 808 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 846 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 732 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 727 Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2383 Classifications: {'DNA': 117} Link IDs: {'rna3p': 116} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 595 Classifications: {'DNA': 29} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 28} Chain: "L" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2591 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 308} Chain breaks: 1 Time building chain proxies: 3.35, per 1000 atoms: 0.23 Number of scatterers: 14653 At special positions: 0 Unit cell: (97.468, 152.397, 136.29, 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 19 16.00 P 293 15.00 O 3315 8.00 N 2718 7.00 C 8308 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: 0.87 Conformation dependent library (CDL) restraints added in 481.2 milliseconds 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2030 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 11 sheets defined 67.9% alpha, 4.6% beta 144 base pairs and 241 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 4.139A pdb=" N GLU A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.645A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.574A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.534A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.500A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 57 removed outlier: 4.835A pdb=" N GLU E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ARG E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.659A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.163A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.394A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.543A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 124 Processing helix chain 'L' and resid 12 through 29 removed outlier: 4.188A pdb=" N GLU L 21 " --> pdb=" O ASP L 17 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU L 22 " --> pdb=" O MET L 18 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA L 23 " --> pdb=" O LEU L 19 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN L 24 " --> pdb=" O THR L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 48 removed outlier: 4.419A pdb=" N ALA L 38 " --> pdb=" O HIS L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 60 Processing helix chain 'L' and resid 66 through 80 removed outlier: 3.692A pdb=" N ALA L 70 " --> pdb=" O GLY L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 90 Processing helix chain 'L' and resid 91 through 102 removed outlier: 3.526A pdb=" N ARG L 102 " --> pdb=" O ASN L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 117 Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 129 through 132 Processing helix chain 'L' and resid 133 through 142 Processing helix chain 'L' and resid 142 through 147 removed outlier: 3.576A pdb=" N GLU L 147 " --> pdb=" O PHE L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 170 Processing helix chain 'L' and resid 209 through 221 removed outlier: 3.608A pdb=" N VAL L 214 " --> pdb=" O LEU L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 274 removed outlier: 4.640A pdb=" N TYR L 266 " --> pdb=" O LYS L 262 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N CYS L 267 " --> pdb=" O ASP L 263 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY L 274 " --> pdb=" O LEU L 270 " (cutoff:3.500A) Processing helix chain 'L' and resid 275 through 289 Processing helix chain 'L' and resid 315 through 323 removed outlier: 3.519A pdb=" N ILE L 323 " --> pdb=" O ILE L 319 " (cutoff:3.500A) Processing helix chain 'L' and resid 329 through 333 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.087A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.518A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.447A 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: 7.150A 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 77 through 78 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.185A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.697A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'L' and resid 150 through 151 removed outlier: 3.593A pdb=" N SER L 188 " --> pdb=" O ILE L 150 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 174 through 178 removed outlier: 3.611A pdb=" N ILE L 174 " --> pdb=" O THR L 196 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASP L 192 " --> pdb=" O CYS L 178 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL L 238 " --> pdb=" O THR L 227 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N THR L 227 " --> pdb=" O VAL L 238 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 291 through 293 530 hydrogen bonds defined for protein. 1558 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 369 hydrogen bonds 738 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 241 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 1.22 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: 2777 1.33 - 1.45: 4862 1.45 - 1.57: 7256 1.57 - 1.69: 584 1.69 - 1.81: 35 Bond restraints: 15514 Sorted by residual: bond pdb=" P DC K 119 " pdb=" OP3 DC K 119 " ideal model delta sigma weight residual 1.480 1.611 -0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" C3' DT I 117 " pdb=" C2' DT I 117 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" CA LYS L 35 " pdb=" C LYS L 35 " ideal model delta sigma weight residual 1.522 1.491 0.031 9.30e-03 1.16e+04 1.11e+01 bond pdb=" N ARG A 49 " pdb=" CA ARG A 49 " ideal model delta sigma weight residual 1.459 1.501 -0.043 1.28e-02 6.10e+03 1.10e+01 bond pdb=" C3' DA J 12 " pdb=" C2' DA J 12 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 ... (remaining 15509 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 21492 2.19 - 4.38: 647 4.38 - 6.57: 39 6.57 - 8.77: 8 8.77 - 10.96: 3 Bond angle restraints: 22189 Sorted by residual: angle pdb=" C GLY L 64 " pdb=" N VAL L 65 " pdb=" CA VAL L 65 " ideal model delta sigma weight residual 121.65 113.27 8.38 9.40e-01 1.13e+00 7.95e+01 angle pdb=" N LYS L 35 " pdb=" CA LYS L 35 " pdb=" C LYS L 35 " ideal model delta sigma weight residual 112.12 102.49 9.63 1.34e+00 5.57e-01 5.17e+01 angle pdb=" N PRO L 63 " pdb=" CA PRO L 63 " pdb=" C PRO L 63 " ideal model delta sigma weight residual 111.21 100.25 10.96 1.59e+00 3.96e-01 4.75e+01 angle pdb=" N VAL L 65 " pdb=" CA VAL L 65 " pdb=" CB VAL L 65 " ideal model delta sigma weight residual 112.28 118.38 -6.10 1.00e+00 1.00e+00 3.72e+01 angle pdb=" N VAL L 65 " pdb=" CA VAL L 65 " pdb=" C VAL L 65 " ideal model delta sigma weight residual 106.21 99.71 6.50 1.07e+00 8.73e-01 3.69e+01 ... (remaining 22184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.26: 7146 33.26 - 66.52: 1429 66.52 - 99.79: 38 99.79 - 133.05: 1 133.05 - 166.31: 5 Dihedral angle restraints: 8619 sinusoidal: 5468 harmonic: 3151 Sorted by residual: dihedral pdb=" CD ARG G 71 " pdb=" NE ARG G 71 " pdb=" CZ ARG G 71 " pdb=" NH1 ARG G 71 " ideal model delta sinusoidal sigma weight residual 0.00 72.24 -72.24 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" C ASP G 72 " pdb=" N ASP G 72 " pdb=" CA ASP G 72 " pdb=" CB ASP G 72 " ideal model delta harmonic sigma weight residual -122.60 -133.91 11.31 0 2.50e+00 1.60e-01 2.05e+01 dihedral pdb=" CA GLU E 50 " pdb=" C GLU E 50 " pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta harmonic sigma weight residual 180.00 157.89 22.11 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 8616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 2482 0.127 - 0.254: 23 0.254 - 0.380: 1 0.380 - 0.507: 1 0.507 - 0.634: 1 Chirality restraints: 2508 Sorted by residual: chirality pdb=" P DC K 119 " pdb=" OP1 DC K 119 " pdb=" OP2 DC K 119 " pdb=" O5' DC K 119 " both_signs ideal model delta sigma weight residual True 2.34 2.97 -0.63 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CA ASP G 72 " pdb=" N ASP G 72 " pdb=" C ASP G 72 " pdb=" CB ASP G 72 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" CA LYS L 35 " pdb=" N LYS L 35 " pdb=" C LYS L 35 " pdb=" CB LYS L 35 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 2505 not shown) Planarity restraints: 1800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 71 " -1.055 9.50e-02 1.11e+02 4.73e-01 1.35e+02 pdb=" NE ARG G 71 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG G 71 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG G 71 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG G 71 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS L 34 " 0.017 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C HIS L 34 " -0.062 2.00e-02 2.50e+03 pdb=" O HIS L 34 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS L 35 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 68 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C ASN G 68 " 0.059 2.00e-02 2.50e+03 pdb=" O ASN G 68 " -0.022 2.00e-02 2.50e+03 pdb=" N ALA G 69 " -0.020 2.00e-02 2.50e+03 ... (remaining 1797 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2432 2.78 - 3.31: 13006 3.31 - 3.84: 28608 3.84 - 4.37: 31837 4.37 - 4.90: 47177 Nonbonded interactions: 123060 Sorted by model distance: nonbonded pdb=" OP1 DC J 34 " pdb=" OG1 THR L 233 " model vdw 2.246 3.040 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.297 3.040 nonbonded pdb=" OG SER C 18 " pdb=" O LEU C 23 " model vdw 2.299 3.040 nonbonded pdb=" OG SER G 18 " pdb=" O LEU G 23 " model vdw 2.309 3.040 nonbonded pdb=" OG SER L 275 " pdb=" O SER L 334 " model vdw 2.311 3.040 ... (remaining 123055 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' and (resid 38 through 128 or resid 130 through 134)) selection = (chain 'E' and (resid 38 through 128 or resid 130 through 134)) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 14 through 119) selection = (chain 'G' and resid 14 through 119) } ncs_group { reference = (chain 'D' and (resid 32 through 81 or resid 83 through 124)) selection = (chain 'H' and (resid 32 through 81 or resid 83 through 124)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 16.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.920 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.490 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 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 : 0.005 0.131 15514 Z= 0.480 Angle : 0.797 10.956 22189 Z= 0.666 Chirality : 0.049 0.634 2508 Planarity : 0.012 0.473 1800 Dihedral : 26.100 166.309 6589 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.22 % Allowed : 0.33 % Favored : 99.46 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 1.85 (0.26), residues: 1067 helix: 1.91 (0.20), residues: 714 sheet: 1.19 (0.82), residues: 29 loop : -0.26 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 23 TYR 0.023 0.002 TYR H 83 PHE 0.015 0.001 PHE L 25 TRP 0.004 0.001 TRP L 325 HIS 0.009 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.48 (15514) covalent geometry : angle 0.79651 / 0.67 (22189) hydrogen bonds : bond 0.11342 / 7.79 ( 899) hydrogen bonds : angle 4.16907 / 3.12 ( 2296) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8329 (m-10) cc_final: 0.7940 (m-10) REVERT: E 60 LEU cc_start: 0.8042 (mm) cc_final: 0.7782 (mm) REVERT: L 11 LEU cc_start: 0.7427 (mp) cc_final: 0.7030 (tp) REVERT: L 236 MET cc_start: 0.8834 (mmp) cc_final: 0.8597 (mmp) outliers start: 2 outliers final: 0 residues processed: 161 average time/residue: 0.1481 time to fit residues: 33.0296 Evaluate side-chains 116 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 50.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN C 38 ASN C 112 GLN E 108 ASN F 75 HIS L 207 GLN L 285 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.094613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.055383 restraints weight = 108589.729| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.55 r_work: 0.2752 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 15514 Z= 0.322 Angle : 0.724 7.040 22189 Z= 0.407 Chirality : 0.046 0.254 2508 Planarity : 0.005 0.072 1800 Dihedral : 29.647 169.988 4405 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.74 % Allowed : 7.29 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 1.74 (0.26), residues: 1067 helix: 1.88 (0.19), residues: 725 sheet: 0.40 (0.68), residues: 29 loop : -0.45 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 79 TYR 0.028 0.003 TYR H 83 PHE 0.015 0.002 PHE L 25 TRP 0.001 0.000 TRP L 325 HIS 0.006 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00701 / 0.32 (15514) covalent geometry : angle 0.72424 / 0.41 (22189) hydrogen bonds : bond 0.05394 / 3.74 ( 899) hydrogen bonds : angle 3.70689 / 2.72 ( 2296) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8097 (tm-30) REVERT: E 59 GLU cc_start: 0.8578 (pm20) cc_final: 0.8314 (pm20) REVERT: L 11 LEU cc_start: 0.7898 (mp) cc_final: 0.7407 (tp) REVERT: L 18 MET cc_start: 0.5753 (ppp) cc_final: 0.5088 (ppp) REVERT: L 191 MET cc_start: 0.3528 (mmt) cc_final: 0.3178 (mmt) REVERT: L 236 MET cc_start: 0.8832 (mmp) cc_final: 0.8561 (mmp) outliers start: 16 outliers final: 12 residues processed: 126 average time/residue: 0.1366 time to fit residues: 24.5363 Evaluate side-chains 123 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 86 GLU Chi-restraints excluded: chain L residue 158 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 21 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 104 optimal weight: 0.0040 chunk 9 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.096668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.057852 restraints weight = 95038.644| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.36 r_work: 0.2823 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15514 Z= 0.136 Angle : 0.562 7.555 22189 Z= 0.336 Chirality : 0.041 0.284 2508 Planarity : 0.004 0.047 1800 Dihedral : 29.574 168.622 4405 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.65 % Allowed : 8.60 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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 (0.26), residues: 1067 helix: 2.15 (0.20), residues: 729 sheet: 0.04 (0.71), residues: 30 loop : -0.22 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 79 TYR 0.041 0.002 TYR H 83 PHE 0.007 0.001 PHE H 70 TRP 0.003 0.001 TRP L 325 HIS 0.004 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.14 (15514) covalent geometry : angle 0.56243 / 0.34 (22189) hydrogen bonds : bond 0.04038 / 2.80 ( 899) hydrogen bonds : angle 3.26697 / 2.43 ( 2296) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7910 (tm-30) REVERT: B 88 TYR cc_start: 0.8887 (m-10) cc_final: 0.8655 (m-10) REVERT: E 59 GLU cc_start: 0.8426 (pm20) cc_final: 0.8130 (pm20) REVERT: E 107 THR cc_start: 0.9366 (m) cc_final: 0.9137 (t) REVERT: L 11 LEU cc_start: 0.7894 (mp) cc_final: 0.7407 (tp) REVERT: L 18 MET cc_start: 0.5622 (ppp) cc_final: 0.5088 (ppp) REVERT: L 236 MET cc_start: 0.8833 (mmp) cc_final: 0.8545 (mmp) REVERT: L 282 MET cc_start: 0.5166 (mmm) cc_final: 0.4827 (mmm) outliers start: 6 outliers final: 2 residues processed: 127 average time/residue: 0.1352 time to fit residues: 24.7975 Evaluate side-chains 118 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain L residue 135 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 85 optimal weight: 40.0000 chunk 58 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 98 optimal weight: 30.0000 chunk 64 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.0770 overall best weight: 1.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.096170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.057171 restraints weight = 122457.636| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.83 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15514 Z= 0.141 Angle : 0.555 7.122 22189 Z= 0.329 Chirality : 0.041 0.271 2508 Planarity : 0.004 0.048 1800 Dihedral : 29.602 170.015 4405 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.98 % Allowed : 9.25 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.23 (0.27), residues: 1067 helix: 2.21 (0.20), residues: 734 sheet: 0.08 (0.74), residues: 30 loop : -0.19 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 79 TYR 0.024 0.002 TYR D 40 PHE 0.008 0.001 PHE E 67 TRP 0.003 0.001 TRP L 325 HIS 0.003 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 (15514) covalent geometry : angle 0.55486 / 0.33 (22189) hydrogen bonds : bond 0.03913 / 2.74 ( 899) hydrogen bonds : angle 3.17329 / 2.35 ( 2296) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7341 (tm-30) cc_final: 0.7108 (tm-30) REVERT: B 84 MET cc_start: 0.8567 (mmm) cc_final: 0.7888 (mmm) REVERT: B 88 TYR cc_start: 0.8552 (m-10) cc_final: 0.8208 (m-10) REVERT: F 84 MET cc_start: 0.8528 (tpp) cc_final: 0.8277 (tpp) REVERT: G 91 GLU cc_start: 0.8366 (tp30) cc_final: 0.8152 (tp30) REVERT: L 11 LEU cc_start: 0.7965 (mp) cc_final: 0.7472 (tp) REVERT: L 18 MET cc_start: 0.5744 (ppp) cc_final: 0.5291 (ppp) REVERT: L 155 MET cc_start: 0.8204 (mpp) cc_final: 0.7994 (mpp) REVERT: L 236 MET cc_start: 0.8699 (mmp) cc_final: 0.8401 (mmp) REVERT: L 282 MET cc_start: 0.5074 (mmm) cc_final: 0.4742 (mmm) outliers start: 9 outliers final: 7 residues processed: 128 average time/residue: 0.1353 time to fit residues: 24.7247 Evaluate side-chains 122 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain L residue 135 HIS Chi-restraints excluded: chain L residue 292 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 93 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.096058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.057293 restraints weight = 105601.700| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.52 r_work: 0.2805 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15514 Z= 0.143 Angle : 0.551 7.771 22189 Z= 0.327 Chirality : 0.040 0.264 2508 Planarity : 0.004 0.046 1800 Dihedral : 29.630 170.816 4405 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.41 % Allowed : 9.14 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.33 (0.27), residues: 1067 helix: 2.30 (0.20), residues: 732 sheet: 0.16 (0.73), residues: 30 loop : -0.16 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 79 TYR 0.031 0.002 TYR H 40 PHE 0.007 0.001 PHE E 67 TRP 0.003 0.001 TRP L 325 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 (15514) covalent geometry : angle 0.55075 / 0.33 (22189) hydrogen bonds : bond 0.03821 / 2.67 ( 899) hydrogen bonds : angle 3.10394 / 2.30 ( 2296) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7896 (tm-30) REVERT: B 88 TYR cc_start: 0.8897 (m-10) cc_final: 0.8632 (m-10) REVERT: G 91 GLU cc_start: 0.8707 (tp30) cc_final: 0.8476 (tp30) REVERT: L 11 LEU cc_start: 0.7936 (mp) cc_final: 0.7455 (tp) REVERT: L 18 MET cc_start: 0.5568 (ppp) cc_final: 0.5196 (ppp) REVERT: L 155 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7924 (mpp) REVERT: L 191 MET cc_start: 0.3952 (mmt) cc_final: 0.3432 (mmt) REVERT: L 236 MET cc_start: 0.8828 (mmp) cc_final: 0.8514 (mmp) REVERT: L 282 MET cc_start: 0.5346 (mmm) cc_final: 0.5009 (mmm) outliers start: 13 outliers final: 11 residues processed: 133 average time/residue: 0.1287 time to fit residues: 24.8174 Evaluate side-chains 128 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain L residue 135 HIS Chi-restraints excluded: chain L residue 155 MET Chi-restraints excluded: chain L residue 292 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 27 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 104 optimal weight: 30.0000 chunk 86 optimal weight: 40.0000 chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.096285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.058311 restraints weight = 73747.599| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.96 r_work: 0.2843 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15514 Z= 0.150 Angle : 0.557 8.587 22189 Z= 0.328 Chirality : 0.040 0.262 2508 Planarity : 0.004 0.046 1800 Dihedral : 29.645 171.158 4405 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.63 % Allowed : 9.79 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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 (0.27), residues: 1067 helix: 2.30 (0.20), residues: 732 sheet: 0.28 (0.73), residues: 30 loop : -0.14 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 71 TYR 0.032 0.002 TYR H 83 PHE 0.007 0.001 PHE E 67 TRP 0.002 0.000 TRP L 325 HIS 0.003 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 (15514) covalent geometry : angle 0.55723 / 0.33 (22189) hydrogen bonds : bond 0.03829 / 2.67 ( 899) hydrogen bonds : angle 3.09455 / 2.29 ( 2296) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7771 (tm-30) REVERT: B 84 MET cc_start: 0.8855 (mmm) cc_final: 0.8192 (mmm) REVERT: B 88 TYR cc_start: 0.8856 (m-10) cc_final: 0.8543 (m-10) REVERT: G 91 GLU cc_start: 0.8674 (tp30) cc_final: 0.8425 (tp30) REVERT: L 11 LEU cc_start: 0.7930 (mp) cc_final: 0.7457 (tp) REVERT: L 18 MET cc_start: 0.5514 (ppp) cc_final: 0.5196 (ppp) REVERT: L 155 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7944 (mpp) REVERT: L 236 MET cc_start: 0.8798 (mmp) cc_final: 0.8477 (mmp) outliers start: 15 outliers final: 12 residues processed: 129 average time/residue: 0.1108 time to fit residues: 20.8184 Evaluate side-chains 130 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain L residue 135 HIS Chi-restraints excluded: chain L residue 155 MET Chi-restraints excluded: chain L residue 292 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 30 optimal weight: 0.0370 chunk 17 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 54 optimal weight: 0.0470 chunk 13 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 73 optimal weight: 50.0000 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.096835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.058286 restraints weight = 122433.488| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.88 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15514 Z= 0.124 Angle : 0.540 10.575 22189 Z= 0.321 Chirality : 0.040 0.260 2508 Planarity : 0.003 0.042 1800 Dihedral : 29.595 171.751 4405 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.31 % Allowed : 10.34 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 1067 helix: 2.34 (0.20), residues: 734 sheet: 0.51 (0.67), residues: 36 loop : -0.08 (0.39), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 71 TYR 0.027 0.001 TYR H 40 PHE 0.017 0.001 PHE L 278 TRP 0.001 0.000 TRP L 325 HIS 0.003 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.12 (15514) covalent geometry : angle 0.53980 / 0.32 (22189) hydrogen bonds : bond 0.03626 / 2.51 ( 899) hydrogen bonds : angle 2.97780 / 2.22 ( 2296) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7324 (tm-30) cc_final: 0.7027 (tm-30) REVERT: B 84 MET cc_start: 0.8537 (mmm) cc_final: 0.7932 (mmm) REVERT: B 88 TYR cc_start: 0.8524 (m-10) cc_final: 0.8225 (m-10) REVERT: G 91 GLU cc_start: 0.8348 (tp30) cc_final: 0.8099 (tp30) REVERT: L 11 LEU cc_start: 0.8053 (mp) cc_final: 0.7565 (tp) REVERT: L 18 MET cc_start: 0.5654 (ppp) cc_final: 0.5336 (ppp) REVERT: L 155 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7931 (mpp) REVERT: L 236 MET cc_start: 0.8706 (mmp) cc_final: 0.8381 (mmp) outliers start: 12 outliers final: 10 residues processed: 132 average time/residue: 0.1174 time to fit residues: 22.7686 Evaluate side-chains 131 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain L residue 135 HIS Chi-restraints excluded: chain L residue 155 MET Chi-restraints excluded: chain L residue 292 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 70 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 131 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 95 optimal weight: 20.0000 chunk 98 optimal weight: 30.0000 chunk 128 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.095224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.056837 restraints weight = 64762.685| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.83 r_work: 0.2806 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15514 Z= 0.189 Angle : 0.592 9.306 22189 Z= 0.342 Chirality : 0.041 0.253 2508 Planarity : 0.004 0.038 1800 Dihedral : 29.763 173.638 4405 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.74 % Allowed : 10.66 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.48 (0.27), residues: 1067 helix: 2.37 (0.19), residues: 730 sheet: 0.65 (0.67), residues: 36 loop : -0.04 (0.39), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 71 TYR 0.030 0.002 TYR H 40 PHE 0.010 0.001 PHE E 67 TRP 0.002 0.000 TRP L 325 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 (15514) covalent geometry : angle 0.59229 / 0.34 (22189) hydrogen bonds : bond 0.04300 / 2.99 ( 899) hydrogen bonds : angle 3.14935 / 2.32 ( 2296) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7826 (tm-30) REVERT: B 88 TYR cc_start: 0.8875 (m-10) cc_final: 0.8623 (m-10) REVERT: G 91 GLU cc_start: 0.8706 (tp30) cc_final: 0.8476 (tp30) REVERT: L 18 MET cc_start: 0.5622 (ppp) cc_final: 0.5342 (ppp) REVERT: L 155 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7861 (mpp) REVERT: L 236 MET cc_start: 0.8793 (mmp) cc_final: 0.8538 (mmp) outliers start: 16 outliers final: 15 residues processed: 129 average time/residue: 0.1281 time to fit residues: 23.8581 Evaluate side-chains 129 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain L residue 135 HIS Chi-restraints excluded: chain L residue 155 MET Chi-restraints excluded: chain L residue 292 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 124 optimal weight: 20.0000 chunk 123 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 97 optimal weight: 30.0000 chunk 28 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.096278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.057771 restraints weight = 89695.940| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.36 r_work: 0.2820 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15514 Z= 0.127 Angle : 0.550 9.133 22189 Z= 0.325 Chirality : 0.040 0.257 2508 Planarity : 0.003 0.037 1800 Dihedral : 29.669 173.157 4405 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.41 % Allowed : 10.99 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.58 (0.27), residues: 1067 helix: 2.46 (0.20), residues: 732 sheet: 0.60 (0.67), residues: 36 loop : -0.04 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 71 TYR 0.028 0.001 TYR H 40 PHE 0.006 0.001 PHE L 235 TRP 0.001 0.000 TRP L 325 HIS 0.002 0.000 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.13 (15514) covalent geometry : angle 0.55048 / 0.33 (22189) hydrogen bonds : bond 0.03672 / 2.55 ( 899) hydrogen bonds : angle 2.98628 / 2.21 ( 2296) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7814 (tm-30) REVERT: B 84 MET cc_start: 0.8821 (mmm) cc_final: 0.8188 (mmm) REVERT: B 88 TYR cc_start: 0.8880 (m-10) cc_final: 0.7958 (m-10) REVERT: D 71 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8738 (tp30) REVERT: D 83 TYR cc_start: 0.8508 (m-10) cc_final: 0.8119 (m-10) REVERT: G 91 GLU cc_start: 0.8691 (tp30) cc_final: 0.8455 (tp30) REVERT: L 11 LEU cc_start: 0.8155 (mp) cc_final: 0.7491 (tt) REVERT: L 18 MET cc_start: 0.5639 (ppp) cc_final: 0.5355 (ppp) REVERT: L 155 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7845 (mpp) REVERT: L 236 MET cc_start: 0.8795 (mmp) cc_final: 0.8462 (mmp) outliers start: 13 outliers final: 10 residues processed: 133 average time/residue: 0.1331 time to fit residues: 25.9336 Evaluate side-chains 133 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain L residue 135 HIS Chi-restraints excluded: chain L residue 155 MET Chi-restraints excluded: chain L residue 292 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 20 optimal weight: 0.0270 chunk 125 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 123 optimal weight: 20.0000 chunk 106 optimal weight: 8.9990 chunk 99 optimal weight: 40.0000 chunk 113 optimal weight: 0.0470 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.096644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.058193 restraints weight = 92633.813| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.44 r_work: 0.2827 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15514 Z= 0.126 Angle : 0.556 9.201 22189 Z= 0.327 Chirality : 0.040 0.251 2508 Planarity : 0.003 0.039 1800 Dihedral : 29.637 174.459 4405 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.09 % Allowed : 11.32 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.57 (0.27), residues: 1067 helix: 2.43 (0.20), residues: 734 sheet: 0.60 (0.68), residues: 36 loop : 0.00 (0.39), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 71 TYR 0.046 0.002 TYR L 39 PHE 0.007 0.001 PHE E 67 TRP 0.001 0.000 TRP L 325 HIS 0.006 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.13 (15514) covalent geometry : angle 0.55633 / 0.33 (22189) hydrogen bonds : bond 0.03663 / 2.55 ( 899) hydrogen bonds : angle 3.00375 / 2.21 ( 2296) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7791 (tm-30) REVERT: B 84 MET cc_start: 0.8845 (mmm) cc_final: 0.8217 (mmm) REVERT: B 88 TYR cc_start: 0.8878 (m-10) cc_final: 0.7952 (m-10) REVERT: D 71 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8725 (tp30) REVERT: D 83 TYR cc_start: 0.8497 (m-10) cc_final: 0.8060 (m-10) REVERT: G 91 GLU cc_start: 0.8718 (tp30) cc_final: 0.8475 (tp30) REVERT: L 11 LEU cc_start: 0.8207 (mp) cc_final: 0.7553 (tp) REVERT: L 18 MET cc_start: 0.5646 (ppp) cc_final: 0.5357 (ppp) REVERT: L 155 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7817 (mpp) REVERT: L 236 MET cc_start: 0.8811 (mmp) cc_final: 0.8474 (mmp) outliers start: 10 outliers final: 9 residues processed: 130 average time/residue: 0.1227 time to fit residues: 23.4054 Evaluate side-chains 129 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain L residue 135 HIS Chi-restraints excluded: chain L residue 155 MET Chi-restraints excluded: chain L residue 292 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 120 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 79 optimal weight: 20.0000 chunk 71 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 59 optimal weight: 0.0570 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 75 HIS H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.096583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.057881 restraints weight = 98646.732| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.50 r_work: 0.2828 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15514 Z= 0.133 Angle : 0.566 9.674 22189 Z= 0.328 Chirality : 0.040 0.247 2508 Planarity : 0.003 0.039 1800 Dihedral : 29.651 175.484 4405 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.20 % Allowed : 11.64 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.56 (0.27), residues: 1067 helix: 2.42 (0.20), residues: 734 sheet: 0.63 (0.68), residues: 36 loop : 0.00 (0.39), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 71 TYR 0.035 0.002 TYR L 39 PHE 0.007 0.001 PHE E 67 TRP 0.001 0.000 TRP L 325 HIS 0.003 0.001 HIS L 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.13 (15514) covalent geometry : angle 0.56556 / 0.33 (22189) hydrogen bonds : bond 0.03699 / 2.57 ( 899) hydrogen bonds : angle 3.04261 / 2.23 ( 2296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4789.81 seconds wall clock time: 82 minutes 12.97 seconds (4932.97 seconds total)