Starting phenix.real_space_refine on Sat Jul 4 02:22:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwh_47246/07_2026/9dwh_47246.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwh_47246/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9dwh_47246/07_2026/9dwh_47246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwh_47246/07_2026/9dwh_47246.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dwh_47246/07_2026/9dwh_47246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwh_47246/07_2026/9dwh_47246.map" } 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-dev-6108/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: 4.10, per 1000 atoms: 0.28 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: 1.32 Conformation dependent library (CDL) restraints added in 604.3 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: 2.06 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: 3.10 Time building geometry restraints manager: 1.77 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: 21493 2.19 - 4.38: 646 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: 22.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 1.010 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.430 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.700 ------------------------------------------------------------------------------- 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 : 0.791 10.956 22189 Z= 0.661 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 0.79070 / 0.66 (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 : 0.571 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: 0.8598 (mmp) outliers start: 2 outliers final: 0 residues processed: 161 average time/residue: 0.1676 time to fit residues: 37.2147 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 : 0.460 ------------------------------------------------------------------------------- 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: 30.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 50.0000 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 overall best weight: 5.9992 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.094223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.055210 restraints weight = 107995.980| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.51 r_work: 0.2735 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 15514 Z= 0.340 Angle : 0.737 7.196 22189 Z= 0.411 Chirality : 0.047 0.241 2508 Planarity : 0.006 0.075 1800 Dihedral : 29.800 170.339 4405 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.63 % Allowed : 8.05 % Favored : 90.32 % 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: 1.59 (0.25), residues: 1067 helix: 1.76 (0.19), residues: 726 sheet: 0.40 (0.68), residues: 29 loop : -0.50 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 79 TYR 0.027 0.003 TYR H 83 PHE 0.017 0.002 PHE L 25 TRP 0.001 0.000 TRP L 325 HIS 0.007 0.002 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00754 / 0.34 (15514) covalent geometry : angle 0.73697 / 0.41 (22189) hydrogen bonds : bond 0.05850 / 4.06 ( 899) hydrogen bonds : angle 3.76687 / 2.75 ( 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: 15 poor density : 114 time to evaluate : 0.477 Fit side-chains REVERT: A 97 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8136 (tm-30) REVERT: B 88 TYR cc_start: 0.8969 (m-10) cc_final: 0.8512 (m-10) REVERT: C 56 GLU cc_start: 0.8834 (tt0) cc_final: 0.8579 (tt0) REVERT: D 71 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8711 (tm-30) REVERT: D 83 TYR cc_start: 0.8788 (m-10) cc_final: 0.8328 (m-10) REVERT: E 59 GLU cc_start: 0.8618 (pm20) cc_final: 0.8336 (pm20) REVERT: G 63 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9309 (mm) REVERT: L 11 LEU cc_start: 0.7905 (mp) cc_final: 0.7414 (tp) REVERT: L 18 MET cc_start: 0.5775 (ppp) cc_final: 0.5135 (ppp) REVERT: L 191 MET cc_start: 0.3583 (mmt) cc_final: 0.3240 (mmt) REVERT: L 236 MET cc_start: 0.8824 (mmp) cc_final: 0.8554 (mmp) outliers start: 15 outliers final: 12 residues processed: 127 average time/residue: 0.1557 time to fit residues: 27.9478 Evaluate side-chains 124 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 G residue 63 LEU 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: 0.9980 chunk 69 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 129 optimal weight: 0.0050 chunk 54 optimal weight: 0.0370 chunk 43 optimal weight: 0.9980 chunk 122 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 overall best weight: 0.6072 ------------------------------------------------------------------------------- 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 = 0.096374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.057597 restraints weight = 94726.850| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.36 r_work: 0.2833 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 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: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15514 Z= 0.135 Angle : 0.554 7.517 22189 Z= 0.333 Chirality : 0.041 0.260 2508 Planarity : 0.004 0.048 1800 Dihedral : 29.647 167.970 4405 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.76 % Allowed : 8.49 % 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: 2.16 (0.20), residues: 730 sheet: 0.07 (0.71), residues: 30 loop : -0.24 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 79 TYR 0.035 0.002 TYR H 83 PHE 0.009 0.001 PHE H 70 TRP 0.004 0.001 TRP L 325 HIS 0.004 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.13 (15514) covalent geometry : angle 0.55401 / 0.33 (22189) hydrogen bonds : bond 0.04079 / 2.83 ( 899) hydrogen bonds : angle 3.25328 / 2.41 ( 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 133 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7903 (tm-30) REVERT: E 59 GLU cc_start: 0.8394 (pm20) cc_final: 0.8086 (pm20) REVERT: E 107 THR cc_start: 0.9377 (m) cc_final: 0.9148 (t) REVERT: L 11 LEU cc_start: 0.7916 (mp) cc_final: 0.7424 (tp) REVERT: L 18 MET cc_start: 0.5650 (ppp) cc_final: 0.5140 (ppp) REVERT: L 236 MET cc_start: 0.8839 (mmp) cc_final: 0.8546 (mmp) REVERT: L 282 MET cc_start: 0.5126 (mmm) cc_final: 0.4772 (mmm) outliers start: 7 outliers final: 4 residues processed: 130 average time/residue: 0.1466 time to fit residues: 27.1731 Evaluate side-chains 121 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 88 THR 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: 6.9990 chunk 8 optimal weight: 5.9990 chunk 85 optimal weight: 40.0000 chunk 58 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 129 optimal weight: 0.7980 chunk 98 optimal weight: 40.0000 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 0.0170 chunk 48 optimal weight: 0.8980 overall best weight: 0.9220 ------------------------------------------------------------------------------- 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 = 0.096378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.057357 restraints weight = 122319.221| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.79 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1522 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= 0.132 Angle : 0.539 7.207 22189 Z= 0.324 Chirality : 0.040 0.252 2508 Planarity : 0.004 0.047 1800 Dihedral : 29.645 169.547 4405 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.09 % Allowed : 9.25 % Favored : 89.66 % 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: 2.26 (0.27), residues: 1067 helix: 2.24 (0.20), residues: 733 sheet: 0.08 (0.74), residues: 30 loop : -0.18 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 79 TYR 0.043 0.002 TYR H 83 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 0.00219 / 0.13 (15514) covalent geometry : angle 0.53891 / 0.32 (22189) hydrogen bonds : bond 0.03846 / 2.69 ( 899) hydrogen bonds : angle 3.14926 / 2.34 ( 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 135 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7291 (tm-30) cc_final: 0.7091 (tm-30) REVERT: B 88 TYR cc_start: 0.8499 (m-10) cc_final: 0.8167 (m-10) REVERT: L 11 LEU cc_start: 0.7891 (mp) cc_final: 0.7407 (tp) REVERT: L 18 MET cc_start: 0.5677 (ppp) cc_final: 0.5256 (ppp) REVERT: L 236 MET cc_start: 0.8684 (mmp) cc_final: 0.8384 (mmp) REVERT: L 282 MET cc_start: 0.5047 (mmm) cc_final: 0.4725 (mmm) outliers start: 10 outliers final: 8 residues processed: 133 average time/residue: 0.1411 time to fit residues: 26.9184 Evaluate side-chains 128 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 60 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 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: 0.5980 chunk 68 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.096499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.057918 restraints weight = 106091.689| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.64 r_work: 0.2805 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 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 = 0.2794 r_free = 0.2794 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: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15514 Z= 0.135 Angle : 0.541 7.726 22189 Z= 0.325 Chirality : 0.040 0.245 2508 Planarity : 0.004 0.045 1800 Dihedral : 29.665 170.408 4405 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.63 % Allowed : 9.68 % Favored : 88.68 % 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: 2.32 (0.27), residues: 1067 helix: 2.28 (0.20), residues: 733 sheet: 0.12 (0.74), residues: 30 loop : -0.14 (0.38), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 79 TYR 0.024 0.001 TYR H 83 PHE 0.007 0.001 PHE E 67 TRP 0.002 0.001 TRP L 325 HIS 0.003 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.14 (15514) covalent geometry : angle 0.54063 / 0.32 (22189) hydrogen bonds : bond 0.03766 / 2.63 ( 899) hydrogen bonds : angle 3.08724 / 2.29 ( 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 138 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7864 (tm-30) REVERT: B 88 TYR cc_start: 0.8864 (m-10) cc_final: 0.8570 (m-10) REVERT: L 11 LEU cc_start: 0.7967 (mp) cc_final: 0.7482 (tp) REVERT: L 18 MET cc_start: 0.5531 (ppp) cc_final: 0.5174 (ppp) REVERT: L 236 MET cc_start: 0.8821 (mmp) cc_final: 0.8511 (mmp) REVERT: L 282 MET cc_start: 0.5314 (mmm) cc_final: 0.4980 (mmm) outliers start: 15 outliers final: 14 residues processed: 134 average time/residue: 0.1417 time to fit residues: 27.3505 Evaluate side-chains 132 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 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 H residue 88 THR Chi-restraints excluded: chain L residue 135 HIS 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: 3.9990 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 30 optimal weight: 0.0370 chunk 23 optimal weight: 9.9990 chunk 104 optimal weight: 30.0000 chunk 86 optimal weight: 40.0000 chunk 25 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 overall best weight: 2.2064 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.095832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.057136 restraints weight = 74495.020| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.01 r_work: 0.2814 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 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 = 0.2796 r_free = 0.2796 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: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15514 Z= 0.165 Angle : 0.554 8.229 22189 Z= 0.328 Chirality : 0.040 0.240 2508 Planarity : 0.004 0.044 1800 Dihedral : 29.745 171.362 4405 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.63 % Allowed : 10.01 % 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: 2.41 (0.27), residues: 1067 helix: 2.37 (0.20), residues: 731 sheet: 0.25 (0.74), residues: 30 loop : -0.15 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 35 TYR 0.019 0.002 TYR H 40 PHE 0.007 0.001 PHE E 67 TRP 0.002 0.000 TRP L 325 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 (15514) covalent geometry : angle 0.55375 / 0.33 (22189) hydrogen bonds : bond 0.03948 / 2.76 ( 899) hydrogen bonds : angle 3.11272 / 2.30 ( 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 : 0.474 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7821 (tm-30) REVERT: B 84 MET cc_start: 0.8902 (mmm) cc_final: 0.8318 (mmm) REVERT: B 88 TYR cc_start: 0.8860 (m-10) cc_final: 0.8542 (m-10) REVERT: F 84 MET cc_start: 0.8842 (tpp) cc_final: 0.8540 (tpp) REVERT: G 91 GLU cc_start: 0.8705 (tp30) cc_final: 0.8484 (tp30) REVERT: L 11 LEU cc_start: 0.8014 (mp) cc_final: 0.7528 (tp) REVERT: L 18 MET cc_start: 0.5542 (ppp) cc_final: 0.5236 (ppp) REVERT: L 236 MET cc_start: 0.8826 (mmp) cc_final: 0.8498 (mmp) outliers start: 15 outliers final: 13 residues processed: 130 average time/residue: 0.1373 time to fit residues: 26.0463 Evaluate side-chains 129 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 60 LEU Chi-restraints excluded: chain E residue 96 SER 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 292 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 30 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 73 optimal weight: 40.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.096262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.057541 restraints weight = 122106.223| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.88 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15514 Z= 0.130 Angle : 0.538 8.326 22189 Z= 0.323 Chirality : 0.040 0.242 2508 Planarity : 0.003 0.040 1800 Dihedral : 29.705 171.371 4405 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.52 % Allowed : 10.23 % Favored : 88.25 % 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: 2.47 (0.27), residues: 1067 helix: 2.38 (0.20), residues: 733 sheet: 0.54 (0.67), residues: 36 loop : -0.10 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 35 TYR 0.026 0.001 TYR D 40 PHE 0.010 0.001 PHE L 278 TRP 0.000 0.000 TRP L 325 HIS 0.002 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.13 (15514) covalent geometry : angle 0.53767 / 0.32 (22189) hydrogen bonds : bond 0.03697 / 2.57 ( 899) hydrogen bonds : angle 3.01337 / 2.23 ( 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 138 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7378 (tm-30) cc_final: 0.7077 (tm-30) REVERT: B 84 MET cc_start: 0.8622 (mmm) cc_final: 0.7880 (mmm) REVERT: B 88 TYR cc_start: 0.8521 (m-10) cc_final: 0.8162 (m-10) REVERT: G 91 GLU cc_start: 0.8386 (tp30) cc_final: 0.8179 (tp30) REVERT: L 11 LEU cc_start: 0.8101 (mp) cc_final: 0.7610 (tp) REVERT: L 18 MET cc_start: 0.5738 (ppp) cc_final: 0.5430 (ppp) REVERT: L 236 MET cc_start: 0.8704 (mmp) cc_final: 0.8374 (mmp) outliers start: 14 outliers final: 12 residues processed: 136 average time/residue: 0.1397 time to fit residues: 27.0036 Evaluate side-chains 132 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 31 LYS 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 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 292 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 70 optimal weight: 2.9990 chunk 129 optimal weight: 40.0000 chunk 17 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 119 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 95 optimal weight: 20.0000 chunk 98 optimal weight: 30.0000 chunk 128 optimal weight: 9.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.095039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.056363 restraints weight = 65174.048| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.87 r_work: 0.2803 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15514 Z= 0.200 Angle : 0.587 9.313 22189 Z= 0.341 Chirality : 0.041 0.235 2508 Planarity : 0.004 0.038 1800 Dihedral : 29.839 172.761 4405 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.85 % Allowed : 10.45 % Favored : 87.70 % 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: 2.43 (0.27), residues: 1067 helix: 2.35 (0.19), residues: 729 sheet: 0.56 (0.68), residues: 36 loop : -0.08 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 71 TYR 0.024 0.002 TYR D 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 0.00410 / 0.20 (15514) covalent geometry : angle 0.58656 / 0.34 (22189) hydrogen bonds : bond 0.04350 / 3.03 ( 899) hydrogen bonds : angle 3.17986 / 2.34 ( 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 133 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7849 (tm-30) REVERT: B 88 TYR cc_start: 0.8857 (m-10) cc_final: 0.8579 (m-10) REVERT: G 91 GLU cc_start: 0.8750 (tp30) cc_final: 0.8529 (tp30) REVERT: L 18 MET cc_start: 0.5686 (ppp) cc_final: 0.5419 (ppp) REVERT: L 236 MET cc_start: 0.8805 (mmp) cc_final: 0.8544 (mmp) outliers start: 17 outliers final: 16 residues processed: 130 average time/residue: 0.1304 time to fit residues: 24.3351 Evaluate side-chains 130 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 60 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 97 GLU 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 292 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 124 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 97 optimal weight: 30.0000 chunk 28 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.096155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.057711 restraints weight = 89304.497| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.32 r_work: 0.2820 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 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 = 0.2802 r_free = 0.2802 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: 0.2802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15514 Z= 0.132 Angle : 0.561 11.529 22189 Z= 0.330 Chirality : 0.040 0.241 2508 Planarity : 0.003 0.039 1800 Dihedral : 29.759 172.052 4405 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.63 % Allowed : 11.10 % Favored : 87.27 % 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: 2.39 (0.20), residues: 731 sheet: 0.58 (0.68), residues: 36 loop : -0.07 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 71 TYR 0.030 0.002 TYR H 40 PHE 0.006 0.001 PHE H 65 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 0.00221 / 0.13 (15514) covalent geometry : angle 0.56052 / 0.33 (22189) hydrogen bonds : bond 0.03763 / 2.62 ( 899) hydrogen bonds : angle 3.04517 / 2.25 ( 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 134 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.368 Fit side-chains REVERT: A 97 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7828 (tm-30) REVERT: B 84 MET cc_start: 0.8880 (mmm) cc_final: 0.8199 (mmm) REVERT: B 88 TYR cc_start: 0.8852 (m-10) cc_final: 0.7926 (m-10) REVERT: D 71 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8735 (tp30) REVERT: D 83 TYR cc_start: 0.8442 (m-10) cc_final: 0.8029 (m-10) REVERT: G 91 GLU cc_start: 0.8726 (tp30) cc_final: 0.8499 (tp30) REVERT: L 11 LEU cc_start: 0.8162 (mp) cc_final: 0.7483 (tt) REVERT: L 18 MET cc_start: 0.5730 (ppp) cc_final: 0.5462 (ppp) REVERT: L 236 MET cc_start: 0.8801 (mmp) cc_final: 0.8467 (mmp) outliers start: 15 outliers final: 12 residues processed: 132 average time/residue: 0.1342 time to fit residues: 25.6133 Evaluate side-chains 131 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 31 LYS 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 292 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 20 optimal weight: 0.6980 chunk 125 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 17 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 123 optimal weight: 20.0000 chunk 106 optimal weight: 0.8980 chunk 99 optimal weight: 40.0000 chunk 113 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3973 r_free = 0.3973 target = 0.095743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.057240 restraints weight = 91952.406| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.37 r_work: 0.2800 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15514 Z= 0.156 Angle : 0.564 9.522 22189 Z= 0.332 Chirality : 0.040 0.234 2508 Planarity : 0.003 0.040 1800 Dihedral : 29.785 173.019 4405 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.63 % Allowed : 11.53 % Favored : 86.83 % 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: 2.51 (0.27), residues: 1067 helix: 2.41 (0.20), residues: 728 sheet: 0.61 (0.68), residues: 36 loop : -0.03 (0.38), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 71 TYR 0.030 0.002 TYR H 40 PHE 0.008 0.001 PHE E 67 TRP 0.000 0.000 TRP L 325 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.16 (15514) covalent geometry : angle 0.56371 / 0.33 (22189) hydrogen bonds : bond 0.03947 / 2.76 ( 899) hydrogen bonds : angle 3.12859 / 2.29 ( 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 135 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7867 (tm-30) REVERT: B 84 MET cc_start: 0.8935 (mmm) cc_final: 0.8280 (mmm) REVERT: B 88 TYR cc_start: 0.8870 (m-10) cc_final: 0.8592 (m-10) REVERT: D 71 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8727 (tp30) REVERT: G 91 GLU cc_start: 0.8779 (tp30) cc_final: 0.8559 (tp30) REVERT: H 84 ASN cc_start: 0.8845 (m110) cc_final: 0.8534 (m110) REVERT: L 11 LEU cc_start: 0.8231 (mp) cc_final: 0.7571 (tp) REVERT: L 18 MET cc_start: 0.5797 (ppp) cc_final: 0.5533 (ppp) REVERT: L 236 MET cc_start: 0.8804 (mmp) cc_final: 0.8464 (mmp) outliers start: 15 outliers final: 12 residues processed: 132 average time/residue: 0.1362 time to fit residues: 26.2286 Evaluate side-chains 129 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 31 LYS 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 292 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 120 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 71 optimal weight: 0.2980 chunk 23 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.095735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.057085 restraints weight = 98546.140| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.49 r_work: 0.2805 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15514 Z= 0.143 Angle : 0.567 9.677 22189 Z= 0.334 Chirality : 0.040 0.235 2508 Planarity : 0.003 0.040 1800 Dihedral : 29.777 173.205 4405 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.31 % Allowed : 12.19 % Favored : 86.51 % 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: 2.47 (0.27), residues: 1067 helix: 2.37 (0.20), residues: 731 sheet: 0.61 (0.68), residues: 36 loop : -0.04 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 71 TYR 0.030 0.002 TYR H 40 PHE 0.006 0.001 PHE E 67 TRP 0.001 0.000 TRP L 325 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 (15514) covalent geometry : angle 0.56739 / 0.33 (22189) hydrogen bonds : bond 0.03854 / 2.69 ( 899) hydrogen bonds : angle 3.14219 / 2.30 ( 2296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5392.59 seconds wall clock time: 92 minutes 43.28 seconds (5563.28 seconds total)