Starting phenix.real_space_refine on Wed Aug 5 00:28:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zfz_74167/08_2026/9zfz_74167.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zfz_74167/08_2026/9zfz_74167.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/9zfz_74167/08_2026/9zfz_74167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zfz_74167/08_2026/9zfz_74167.map" model { file = "/net/cci-nas-00/data/ceres_data/9zfz_74167/08_2026/9zfz_74167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zfz_74167/08_2026/9zfz_74167.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= -0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 4780 2.51 5 N 1294 2.21 5 O 1466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s 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: 7576 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 928 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "B" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 880 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "C" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 928 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "D" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 880 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "E" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 928 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "F" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 880 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 928 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "L" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 880 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "W" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 344 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 12, 'TRANS': 36} Time building chain proxies: 1.72, per 1000 atoms: 0.23 Number of scatterers: 7576 At special positions: 0 Unit cell: (89.75, 104.828, 105.546, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1466 8.00 N 1294 7.00 C 4780 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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: 0.46 Conformation dependent library (CDL) restraints added in 399.6 milliseconds 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1778 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 21 sheets defined 3.4% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'E' and resid 52A through 54 Processing helix chain 'E' and resid 61 through 64 removed outlier: 3.724A pdb=" N LYS E 64 " --> pdb=" O ALA E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.868A pdb=" N THR E 87 " --> pdb=" O THR E 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.559A pdb=" N LYS H 64 " --> pdb=" O ALA H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'W' and resid 33 through 37 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.963A pdb=" N SER A 35 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA A 40 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 12 removed outlier: 4.111A pdb=" N VAL A 102 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.846A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 19 through 23 Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 6 removed outlier: 6.803A pdb=" N SER C 17 " --> pdb=" O ASN C 82A" (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN C 82A" --> pdb=" O SER C 17 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ARG C 19 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLN C 81 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N SER C 21 " --> pdb=" O TYR C 79 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TYR C 79 " --> pdb=" O SER C 21 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR C 23 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ILE C 77 " --> pdb=" O THR C 23 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 12 removed outlier: 5.837A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AA9, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.591A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.630A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'E' and resid 57 through 59 removed outlier: 4.994A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA E 33 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER E 35 " --> pdb=" O THR E 93 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG E 94 " --> pdb=" O VAL E 102 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 57 through 59 removed outlier: 4.994A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA E 33 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER E 35 " --> pdb=" O THR E 93 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 11 through 13 removed outlier: 4.045A pdb=" N LEU F 11 " --> pdb=" O LYS F 103 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 11 through 13 removed outlier: 4.045A pdb=" N LEU F 11 " --> pdb=" O LYS F 103 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 19 through 23 Processing sheet with id=AB8, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AB9, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.435A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER H 35 " --> pdb=" O THR H 93 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP H 101 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.435A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER H 35 " --> pdb=" O THR H 93 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.692A pdb=" N GLY L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 19 through 23 267 hydrogen bonds defined for protein. 633 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.12 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2467 1.34 - 1.46: 1869 1.46 - 1.58: 3363 1.58 - 1.70: 0 1.70 - 1.82: 56 Bond restraints: 7755 Sorted by residual: bond pdb=" N ASP B 1 " pdb=" CA ASP B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N ASN W 1 " pdb=" CA ASN W 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.84e+00 bond pdb=" N ASP F 1 " pdb=" CA ASP F 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.75e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.74e+00 bond pdb=" N ASP D 1 " pdb=" CA ASP D 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.71e+00 ... (remaining 7750 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 10113 1.41 - 2.83: 319 2.83 - 4.24: 72 4.24 - 5.66: 21 5.66 - 7.07: 3 Bond angle restraints: 10528 Sorted by residual: angle pdb=" CB MET L 4 " pdb=" CG MET L 4 " pdb=" SD MET L 4 " ideal model delta sigma weight residual 112.70 119.77 -7.07 3.00e+00 1.11e-01 5.55e+00 angle pdb=" CA TYR H 79 " pdb=" CB TYR H 79 " pdb=" CG TYR H 79 " ideal model delta sigma weight residual 113.90 117.76 -3.86 1.80e+00 3.09e-01 4.59e+00 angle pdb=" N GLU D 50 " pdb=" CA GLU D 50 " pdb=" C GLU D 50 " ideal model delta sigma weight residual 109.32 105.47 3.85 1.84e+00 2.95e-01 4.38e+00 angle pdb=" CA TYR F 49 " pdb=" CB TYR F 49 " pdb=" CG TYR F 49 " ideal model delta sigma weight residual 113.90 117.61 -3.71 1.80e+00 3.09e-01 4.26e+00 angle pdb=" C PRO W 14 " pdb=" N ASN W 15 " pdb=" CA ASN W 15 " ideal model delta sigma weight residual 122.46 125.16 -2.70 1.41e+00 5.03e-01 3.68e+00 ... (remaining 10523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.02: 4094 14.02 - 28.04: 365 28.04 - 42.06: 119 42.06 - 56.08: 20 56.08 - 70.10: 10 Dihedral angle restraints: 4608 sinusoidal: 1814 harmonic: 2794 Sorted by residual: dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sinusoidal sigma weight residual 93.00 160.88 -67.88 1 1.00e+01 1.00e-02 5.98e+01 dihedral pdb=" CA ARG C 96 " pdb=" C ARG C 96 " pdb=" N THR C 97 " pdb=" CA THR C 97 " ideal model delta harmonic sigma weight residual 180.00 162.37 17.63 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA VAL D 13 " pdb=" C VAL D 13 " pdb=" N THR D 14 " pdb=" CA THR D 14 " ideal model delta harmonic sigma weight residual 180.00 162.48 17.52 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 4605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 562 0.030 - 0.060: 383 0.060 - 0.090: 102 0.090 - 0.120: 74 0.120 - 0.150: 20 Chirality restraints: 1141 Sorted by residual: chirality pdb=" CA ILE D 75 " pdb=" N ILE D 75 " pdb=" C ILE D 75 " pdb=" CB ILE D 75 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CG LEU L 33 " pdb=" CB LEU L 33 " pdb=" CD1 LEU L 33 " pdb=" CD2 LEU L 33 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA ILE L 75 " pdb=" N ILE L 75 " pdb=" C ILE L 75 " pdb=" CB ILE L 75 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.52e-01 ... (remaining 1138 not shown) Planarity restraints: 1369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN W 1 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO W 2 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO W 2 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO W 2 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 7 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO F 8 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO F 8 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 8 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 79 " 0.008 2.00e-02 2.50e+03 1.00e-02 2.02e+00 pdb=" CG TYR H 79 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR H 79 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR H 79 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR H 79 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR H 79 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR H 79 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 79 " 0.001 2.00e-02 2.50e+03 ... (remaining 1366 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 466 2.72 - 3.27: 7174 3.27 - 3.81: 11749 3.81 - 4.36: 15273 4.36 - 4.90: 26686 Nonbonded interactions: 61348 Sorted by model distance: nonbonded pdb=" O THR C 97 " pdb=" ND2 ASN W 23 " model vdw 2.179 3.120 nonbonded pdb=" NH1 ARG F 61 " pdb=" O ARG F 77 " model vdw 2.198 3.120 nonbonded pdb=" N GLU H 6 " pdb=" OE1 GLU H 6 " model vdw 2.215 3.120 nonbonded pdb=" NH2 ARG E 52 " pdb=" O ASN W 3 " model vdw 2.228 3.120 nonbonded pdb=" NH2 ARG E 96 " pdb=" OD2 ASP E 100B" model vdw 2.232 3.120 ... (remaining 61343 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 8.160 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 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 0.039 7763 Z= 0.200 Angle : 0.655 7.070 10544 Z= 0.331 Chirality : 0.047 0.150 1141 Planarity : 0.005 0.049 1369 Dihedral : 12.228 70.097 2806 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.27), residues: 963 helix: None (None), residues: 0 sheet: -1.04 (0.25), residues: 388 loop : -0.94 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 54 TYR 0.024 0.002 TYR H 79 PHE 0.016 0.002 PHE E 50 TRP 0.016 0.002 TRP A 103 HIS 0.003 0.001 HIS D 27D Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 ( 7755) covalent geometry : angle 0.65362 / 0.33 (10528) SS BOND : bond 0.00448 / 0.22 ( 8) SS BOND : angle 1.09963 / 0.71 ( 16) hydrogen bonds : bond 0.12198 / 8.35 ( 230) hydrogen bonds : angle 7.62541 / 5.18 ( 633) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.292 Fit side-chains REVERT: A 100 ARG cc_start: 0.7221 (mtt-85) cc_final: 0.6355 (mtt-85) REVERT: B 4 MET cc_start: 0.7066 (mmm) cc_final: 0.6509 (mmm) REVERT: B 87 TYR cc_start: 0.8049 (m-80) cc_final: 0.7412 (m-80) REVERT: C 75 LYS cc_start: 0.8206 (mtmm) cc_final: 0.7847 (ptpt) REVERT: D 28 ASP cc_start: 0.8680 (p0) cc_final: 0.8431 (p0) REVERT: H 59 TYR cc_start: 0.8646 (m-80) cc_final: 0.8274 (m-80) REVERT: H 66 ARG cc_start: 0.7761 (mtm110) cc_final: 0.7470 (mtm110) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.0949 time to fit residues: 15.5077 Evaluate side-chains 107 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82AASN L 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.199067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.141044 restraints weight = 8817.011| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 3.13 r_work: 0.3415 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7763 Z= 0.148 Angle : 0.579 8.975 10544 Z= 0.296 Chirality : 0.046 0.205 1141 Planarity : 0.004 0.038 1369 Dihedral : 4.397 16.568 1068 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.61 % Allowed : 5.94 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.27), residues: 963 helix: None (None), residues: 0 sheet: -0.78 (0.26), residues: 383 loop : -0.76 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 61 TYR 0.012 0.001 TYR L 49 PHE 0.014 0.002 PHE F 98 TRP 0.012 0.001 TRP A 103 HIS 0.002 0.001 HIS B 27D Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 7755) covalent geometry : angle 0.57857 / 0.30 (10528) SS BOND : bond 0.00338 / 0.14 ( 8) SS BOND : angle 0.81267 / 0.45 ( 16) hydrogen bonds : bond 0.02967 / 2.10 ( 230) hydrogen bonds : angle 5.73368 / 3.93 ( 633) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 0.301 Fit side-chains REVERT: A 100 ARG cc_start: 0.6930 (mtt-85) cc_final: 0.6073 (mtt-85) REVERT: B 4 MET cc_start: 0.7092 (mmm) cc_final: 0.6705 (mmm) REVERT: B 87 TYR cc_start: 0.7866 (m-80) cc_final: 0.7283 (m-80) REVERT: D 10 SER cc_start: 0.8975 (t) cc_final: 0.8771 (p) REVERT: F 86 TYR cc_start: 0.8093 (m-80) cc_final: 0.7829 (m-80) REVERT: H 59 TYR cc_start: 0.8516 (m-80) cc_final: 0.8207 (m-80) outliers start: 5 outliers final: 5 residues processed: 105 average time/residue: 0.0883 time to fit residues: 12.8339 Evaluate side-chains 104 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 27 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 60 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 12 optimal weight: 0.0030 chunk 92 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 53 ASN W 23 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.193915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.139724 restraints weight = 8596.941| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.64 r_work: 0.3445 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7763 Z= 0.189 Angle : 0.579 8.949 10544 Z= 0.296 Chirality : 0.046 0.231 1141 Planarity : 0.004 0.034 1369 Dihedral : 4.446 16.908 1068 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.21 % Allowed : 8.48 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.27), residues: 963 helix: None (None), residues: 0 sheet: -0.64 (0.26), residues: 383 loop : -0.75 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 19 TYR 0.013 0.002 TYR F 49 PHE 0.014 0.002 PHE E 50 TRP 0.016 0.002 TRP A 103 HIS 0.003 0.001 HIS D 27D Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 ( 7755) covalent geometry : angle 0.57838 / 0.30 (10528) SS BOND : bond 0.00333 / 0.14 ( 8) SS BOND : angle 0.78404 / 0.48 ( 16) hydrogen bonds : bond 0.02893 / 2.05 ( 230) hydrogen bonds : angle 5.49265 / 3.76 ( 633) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.6985 (mtt-85) cc_final: 0.6160 (mtt-85) REVERT: B 4 MET cc_start: 0.7261 (mmm) cc_final: 0.6805 (mmm) REVERT: B 87 TYR cc_start: 0.7965 (m-80) cc_final: 0.7396 (m-80) REVERT: H 66 ARG cc_start: 0.7849 (mtm110) cc_final: 0.7565 (mtm110) REVERT: H 79 TYR cc_start: 0.8082 (m-10) cc_final: 0.7880 (m-10) outliers start: 10 outliers final: 9 residues processed: 112 average time/residue: 0.0986 time to fit residues: 14.9917 Evaluate side-chains 112 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 31 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 53 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 75 optimal weight: 0.0770 chunk 73 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 = 0.4252 r_free = 0.4252 target = 0.200081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.147724 restraints weight = 8830.847| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.54 r_work: 0.3430 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7763 Z= 0.148 Angle : 0.545 7.515 10544 Z= 0.278 Chirality : 0.044 0.169 1141 Planarity : 0.004 0.034 1369 Dihedral : 4.326 17.099 1068 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.33 % Allowed : 9.94 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.01 (0.28), residues: 963 helix: -4.57 (0.79), residues: 6 sheet: -0.52 (0.26), residues: 383 loop : -0.67 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 96 TYR 0.013 0.001 TYR L 49 PHE 0.013 0.001 PHE C 50 TRP 0.016 0.001 TRP A 103 HIS 0.002 0.001 HIS B 27D Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 7755) covalent geometry : angle 0.54471 / 0.28 (10528) SS BOND : bond 0.00319 / 0.14 ( 8) SS BOND : angle 0.62818 / 0.37 ( 16) hydrogen bonds : bond 0.02639 / 1.88 ( 230) hydrogen bonds : angle 5.23187 / 3.58 ( 633) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.297 Fit side-chains REVERT: A 100 ARG cc_start: 0.6960 (mtt-85) cc_final: 0.6092 (mmt180) REVERT: B 4 MET cc_start: 0.7070 (mmm) cc_final: 0.6694 (mmm) REVERT: B 87 TYR cc_start: 0.7846 (m-80) cc_final: 0.7318 (m-80) outliers start: 11 outliers final: 11 residues processed: 105 average time/residue: 0.0957 time to fit residues: 13.6462 Evaluate side-chains 110 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 31 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 74 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 53 ASN L 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.198668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.143481 restraints weight = 8800.864| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.86 r_work: 0.3389 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7763 Z= 0.175 Angle : 0.558 7.625 10544 Z= 0.284 Chirality : 0.045 0.165 1141 Planarity : 0.004 0.034 1369 Dihedral : 4.350 17.084 1068 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.94 % Allowed : 11.76 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.28), residues: 963 helix: None (None), residues: 0 sheet: -0.49 (0.26), residues: 383 loop : -0.68 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 61 TYR 0.013 0.001 TYR L 49 PHE 0.015 0.002 PHE C 50 TRP 0.018 0.002 TRP A 103 HIS 0.002 0.001 HIS B 27D Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 ( 7755) covalent geometry : angle 0.55787 / 0.28 (10528) SS BOND : bond 0.00317 / 0.14 ( 8) SS BOND : angle 0.63698 / 0.39 ( 16) hydrogen bonds : bond 0.02694 / 1.92 ( 230) hydrogen bonds : angle 5.19638 / 3.56 ( 633) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.6992 (mtt-85) cc_final: 0.6008 (mtt-85) REVERT: B 4 MET cc_start: 0.7110 (mmm) cc_final: 0.6685 (mmm) REVERT: B 87 TYR cc_start: 0.7865 (m-80) cc_final: 0.7392 (m-80) REVERT: C 19 ARG cc_start: 0.8365 (ttm-80) cc_final: 0.7874 (ttm-80) REVERT: C 81 GLN cc_start: 0.8299 (tp40) cc_final: 0.8035 (tp40) REVERT: E 58 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7156 (mt-10) outliers start: 16 outliers final: 11 residues processed: 118 average time/residue: 0.0915 time to fit residues: 14.6210 Evaluate side-chains 120 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 31 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 91 optimal weight: 0.0470 chunk 2 optimal weight: 20.0000 chunk 84 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 6 GLN F 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.200481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.148290 restraints weight = 8761.656| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.65 r_work: 0.3413 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7763 Z= 0.136 Angle : 0.537 7.372 10544 Z= 0.274 Chirality : 0.044 0.163 1141 Planarity : 0.004 0.029 1369 Dihedral : 4.240 16.775 1068 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.70 % Allowed : 13.45 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.28), residues: 963 helix: None (None), residues: 0 sheet: -0.38 (0.27), residues: 383 loop : -0.66 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 19 TYR 0.014 0.001 TYR H 79 PHE 0.012 0.001 PHE C 50 TRP 0.018 0.001 TRP A 103 HIS 0.001 0.000 HIS B 27D Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 7755) covalent geometry : angle 0.53673 / 0.27 (10528) SS BOND : bond 0.00283 / 0.13 ( 8) SS BOND : angle 0.56916 / 0.34 ( 16) hydrogen bonds : bond 0.02555 / 1.81 ( 230) hydrogen bonds : angle 5.00075 / 3.42 ( 633) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.279 Fit side-chains REVERT: A 100 ARG cc_start: 0.6965 (mtt-85) cc_final: 0.5987 (mtt-85) REVERT: B 4 MET cc_start: 0.7064 (mmm) cc_final: 0.6681 (mmm) REVERT: B 87 TYR cc_start: 0.7831 (m-80) cc_final: 0.7361 (m-80) REVERT: C 19 ARG cc_start: 0.8289 (ttm-80) cc_final: 0.7869 (ttm-80) REVERT: C 81 GLN cc_start: 0.8278 (tp40) cc_final: 0.8048 (tp40) REVERT: E 58 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7101 (mt-10) REVERT: H 79 TYR cc_start: 0.7902 (m-10) cc_final: 0.7507 (m-80) outliers start: 14 outliers final: 10 residues processed: 113 average time/residue: 0.0972 time to fit residues: 14.8506 Evaluate side-chains 112 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 31 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 57 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 6 GLN F 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.198602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.144549 restraints weight = 8800.512| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.85 r_work: 0.3409 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7763 Z= 0.169 Angle : 0.558 6.893 10544 Z= 0.284 Chirality : 0.044 0.145 1141 Planarity : 0.004 0.031 1369 Dihedral : 4.312 17.007 1068 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.30 % Allowed : 13.09 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.28), residues: 963 helix: None (None), residues: 0 sheet: -0.39 (0.27), residues: 383 loop : -0.67 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 19 TYR 0.013 0.001 TYR L 49 PHE 0.014 0.002 PHE C 50 TRP 0.019 0.002 TRP A 103 HIS 0.002 0.001 HIS B 27D Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 7755) covalent geometry : angle 0.55814 / 0.28 (10528) SS BOND : bond 0.00308 / 0.14 ( 8) SS BOND : angle 0.64799 / 0.41 ( 16) hydrogen bonds : bond 0.02637 / 1.86 ( 230) hydrogen bonds : angle 5.04952 / 3.47 ( 633) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.213 Fit side-chains REVERT: A 100 ARG cc_start: 0.6963 (mtt-85) cc_final: 0.5847 (mtt-85) REVERT: B 4 MET cc_start: 0.7048 (mmm) cc_final: 0.6627 (mmm) REVERT: B 87 TYR cc_start: 0.7824 (m-80) cc_final: 0.7353 (m-80) REVERT: C 19 ARG cc_start: 0.8322 (ttm-80) cc_final: 0.7923 (ttm-80) REVERT: C 81 GLN cc_start: 0.8303 (tp40) cc_final: 0.8062 (tp40) REVERT: E 58 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7146 (mt-10) outliers start: 19 outliers final: 12 residues processed: 120 average time/residue: 0.0806 time to fit residues: 13.1429 Evaluate side-chains 120 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 31 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 6 GLN F 45 GLN F 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.198921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.145271 restraints weight = 8806.317| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.90 r_work: 0.3388 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7763 Z= 0.158 Angle : 0.559 8.542 10544 Z= 0.283 Chirality : 0.044 0.131 1141 Planarity : 0.004 0.031 1369 Dihedral : 4.290 20.599 1068 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.06 % Allowed : 14.55 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.28), residues: 963 helix: None (None), residues: 0 sheet: -0.37 (0.27), residues: 383 loop : -0.70 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 19 TYR 0.014 0.001 TYR L 49 PHE 0.013 0.001 PHE C 50 TRP 0.020 0.002 TRP A 103 HIS 0.002 0.000 HIS B 27D Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 7755) covalent geometry : angle 0.55932 / 0.28 (10528) SS BOND : bond 0.00297 / 0.13 ( 8) SS BOND : angle 0.57066 / 0.36 ( 16) hydrogen bonds : bond 0.02649 / 1.87 ( 230) hydrogen bonds : angle 5.00620 / 3.43 ( 633) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7015 (mtt-85) cc_final: 0.5854 (mtt-85) REVERT: B 4 MET cc_start: 0.7083 (mmm) cc_final: 0.6681 (mmm) REVERT: B 87 TYR cc_start: 0.7842 (m-80) cc_final: 0.7361 (m-80) REVERT: B 89 MET cc_start: 0.7739 (ptt) cc_final: 0.6947 (ptm) REVERT: C 19 ARG cc_start: 0.8345 (ttm-80) cc_final: 0.8103 (ttm170) REVERT: E 58 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7171 (mt-10) REVERT: H 79 TYR cc_start: 0.7985 (m-10) cc_final: 0.7340 (m-80) outliers start: 17 outliers final: 13 residues processed: 113 average time/residue: 0.0761 time to fit residues: 11.7234 Evaluate side-chains 117 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 31 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 62 optimal weight: 0.0570 chunk 36 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 43 optimal weight: 0.0770 chunk 65 optimal weight: 7.9990 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.200662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.147676 restraints weight = 8762.381| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.68 r_work: 0.3439 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7763 Z= 0.131 Angle : 0.542 7.854 10544 Z= 0.274 Chirality : 0.044 0.148 1141 Planarity : 0.004 0.029 1369 Dihedral : 4.195 19.808 1068 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.94 % Allowed : 15.03 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.28), residues: 963 helix: None (None), residues: 0 sheet: -0.31 (0.27), residues: 383 loop : -0.68 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 19 TYR 0.013 0.001 TYR L 49 PHE 0.011 0.001 PHE F 98 TRP 0.020 0.001 TRP A 103 HIS 0.001 0.000 HIS B 27D Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 7755) covalent geometry : angle 0.54165 / 0.27 (10528) SS BOND : bond 0.00265 / 0.12 ( 8) SS BOND : angle 0.49794 / 0.30 ( 16) hydrogen bonds : bond 0.02528 / 1.79 ( 230) hydrogen bonds : angle 4.86151 / 3.33 ( 633) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.6989 (mtt-85) cc_final: 0.5848 (mtt-85) REVERT: B 4 MET cc_start: 0.7039 (mmm) cc_final: 0.6632 (mmm) REVERT: B 87 TYR cc_start: 0.7779 (m-80) cc_final: 0.7353 (m-80) REVERT: C 19 ARG cc_start: 0.8301 (ttm-80) cc_final: 0.7834 (ttm170) REVERT: C 81 GLN cc_start: 0.8293 (tp40) cc_final: 0.8070 (tp40) REVERT: E 58 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7130 (mt-10) outliers start: 16 outliers final: 12 residues processed: 115 average time/residue: 0.0776 time to fit residues: 12.0811 Evaluate side-chains 118 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 31 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 81 optimal weight: 0.0040 chunk 71 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 62 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 53 ASN W 13 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.196328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.138164 restraints weight = 8686.121| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.54 r_work: 0.3456 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7763 Z= 0.126 Angle : 0.548 7.615 10544 Z= 0.277 Chirality : 0.043 0.129 1141 Planarity : 0.004 0.029 1369 Dihedral : 4.168 19.387 1068 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.82 % Allowed : 15.76 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.28), residues: 963 helix: None (None), residues: 0 sheet: -0.27 (0.27), residues: 381 loop : -0.68 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 19 TYR 0.013 0.001 TYR L 49 PHE 0.011 0.001 PHE F 98 TRP 0.020 0.001 TRP A 103 HIS 0.001 0.000 HIS B 27D Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 7755) covalent geometry : angle 0.54777 / 0.28 (10528) SS BOND : bond 0.00278 / 0.13 ( 8) SS BOND : angle 0.50784 / 0.31 ( 16) hydrogen bonds : bond 0.02529 / 1.79 ( 230) hydrogen bonds : angle 4.79991 / 3.28 ( 633) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.6928 (mtt-85) cc_final: 0.5800 (mtt-85) REVERT: B 4 MET cc_start: 0.6997 (mmm) cc_final: 0.6651 (mmm) REVERT: B 87 TYR cc_start: 0.7795 (m-80) cc_final: 0.7377 (m-80) REVERT: C 19 ARG cc_start: 0.8247 (ttm-80) cc_final: 0.7807 (ttm170) REVERT: E 58 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7130 (mt-10) outliers start: 15 outliers final: 12 residues processed: 111 average time/residue: 0.0822 time to fit residues: 12.4868 Evaluate side-chains 115 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 31 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 0.0470 chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 0.0980 chunk 13 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.197387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.154161 restraints weight = 8700.818| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 3.87 r_work: 0.3348 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7763 Z= 0.125 Angle : 0.547 8.618 10544 Z= 0.276 Chirality : 0.043 0.129 1141 Planarity : 0.004 0.029 1369 Dihedral : 4.122 18.979 1068 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.82 % Allowed : 15.76 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.27), residues: 963 helix: None (None), residues: 0 sheet: -0.21 (0.27), residues: 381 loop : -0.69 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 19 TYR 0.012 0.001 TYR F 49 PHE 0.011 0.001 PHE F 98 TRP 0.020 0.001 TRP A 103 HIS 0.001 0.000 HIS B 27D Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 ( 7755) covalent geometry : angle 0.54689 / 0.28 (10528) SS BOND : bond 0.00272 / 0.13 ( 8) SS BOND : angle 0.50822 / 0.31 ( 16) hydrogen bonds : bond 0.02498 / 1.77 ( 230) hydrogen bonds : angle 4.75026 / 3.25 ( 633) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1959.56 seconds wall clock time: 34 minutes 18.38 seconds (2058.38 seconds total)