Starting phenix.real_space_refine on Fri Jul 3 03:07:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d3r_46545/07_2026/9d3r_46545.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d3r_46545/07_2026/9d3r_46545.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/9d3r_46545/07_2026/9d3r_46545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d3r_46545/07_2026/9d3r_46545.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d3r_46545/07_2026/9d3r_46545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d3r_46545/07_2026/9d3r_46545.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= 0.001 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 14 5.16 5 C 6540 2.51 5 N 2227 2.21 5 O 2787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11858 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 792 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 636 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 749 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "H" Number of atoms: 736 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 734 Chain: "I" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2978 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2967 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "C" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 791 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 777 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 96} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 2.52, per 1000 atoms: 0.21 Number of scatterers: 11858 At special positions: 0 Unit cell: (116.875, 82.28, 118.745, 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 14 16.00 P 290 15.00 O 2787 8.00 N 2227 7.00 C 6540 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: 1.06 Conformation dependent library (CDL) restraints added in 319.7 milliseconds 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1398 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 72.5% alpha, 2.9% beta 140 base pairs and 239 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.183A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.879A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.517A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 56 through 85 removed outlier: 3.884A pdb=" N MET D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.749A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.966A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.705A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.570A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.538A pdb=" N LYS H 43 " --> pdb=" O VAL H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 67 Processing helix chain 'H' and resid 68 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.500A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.782A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU H 113 " --> pdb=" O HIS H 109 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR H 122 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.434A 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 Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.523A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.967A 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 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.601A 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 'D' and resid 53 through 54 removed outlier: 6.807A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.773A 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 Processing sheet with id=AA8, first strand: chain 'F' and resid 96 through 98 removed outlier: 6.370A pdb=" N THR F 96 " --> pdb=" O THR C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54 removed outlier: 7.180A pdb=" N GLY H 53 " --> pdb=" O ILE G 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 88 through 89 394 hydrogen bonds defined for protein. 1172 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 366 hydrogen bonds 732 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 239 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 1 1.12 - 1.29: 1228 1.29 - 1.47: 6187 1.47 - 1.64: 5217 1.64 - 1.82: 27 Bond restraints: 12660 Sorted by residual: bond pdb=" CB PRO G 26 " pdb=" CG PRO G 26 " ideal model delta sigma weight residual 1.492 0.942 0.550 5.00e-02 4.00e+02 1.21e+02 bond pdb=" CG PRO C 48 " pdb=" CD PRO C 48 " ideal model delta sigma weight residual 1.503 1.189 0.314 3.40e-02 8.65e+02 8.52e+01 bond pdb=" CG PRO G 26 " pdb=" CD PRO G 26 " ideal model delta sigma weight residual 1.503 1.211 0.292 3.40e-02 8.65e+02 7.35e+01 bond pdb=" CG PRO A 66 " pdb=" CD PRO A 66 " ideal model delta sigma weight residual 1.503 1.232 0.271 3.40e-02 8.65e+02 6.37e+01 bond pdb=" N PRO C 48 " pdb=" CD PRO C 48 " ideal model delta sigma weight residual 1.473 1.557 -0.084 1.40e-02 5.10e+03 3.64e+01 ... (remaining 12655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.72: 18337 11.72 - 23.43: 5 23.43 - 35.15: 2 35.15 - 46.87: 0 46.87 - 58.58: 1 Bond angle restraints: 18345 Sorted by residual: angle pdb=" CB PRO G 26 " pdb=" CG PRO G 26 " pdb=" CD PRO G 26 " ideal model delta sigma weight residual 106.10 164.68 -58.58 3.20e+00 9.77e-02 3.35e+02 angle pdb=" N PRO G 26 " pdb=" CD PRO G 26 " pdb=" CG PRO G 26 " ideal model delta sigma weight residual 103.20 76.33 26.87 1.50e+00 4.44e-01 3.21e+02 angle pdb=" CA PRO G 26 " pdb=" CB PRO G 26 " pdb=" CG PRO G 26 " ideal model delta sigma weight residual 104.50 74.47 30.03 1.90e+00 2.77e-01 2.50e+02 angle pdb=" CA PRO C 48 " pdb=" N PRO C 48 " pdb=" CD PRO C 48 " ideal model delta sigma weight residual 112.00 94.11 17.89 1.40e+00 5.10e-01 1.63e+02 angle pdb=" CA PRO A 66 " pdb=" N PRO A 66 " pdb=" CD PRO A 66 " ideal model delta sigma weight residual 112.00 96.36 15.64 1.40e+00 5.10e-01 1.25e+02 ... (remaining 18340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.75: 5307 34.75 - 69.50: 1488 69.50 - 104.24: 34 104.24 - 138.99: 0 138.99 - 173.74: 2 Dihedral angle restraints: 6831 sinusoidal: 4659 harmonic: 2172 Sorted by residual: dihedral pdb=" N PRO G 26 " pdb=" CG PRO G 26 " pdb=" CD PRO G 26 " pdb=" CB PRO G 26 " ideal model delta sinusoidal sigma weight residual 30.00 111.03 -81.03 1 1.50e+01 4.44e-03 3.60e+01 dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual -180.00 -159.63 -20.37 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C4' DA J -17 " pdb=" C3' DA J -17 " pdb=" O3' DA J -17 " pdb=" P DG J -16 " ideal model delta sinusoidal sigma weight residual -140.00 33.74 -173.74 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 6828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1869 0.074 - 0.148: 217 0.148 - 0.222: 0 0.222 - 0.296: 1 0.296 - 0.369: 2 Chirality restraints: 2089 Sorted by residual: chirality pdb=" CA PRO C 48 " pdb=" N PRO C 48 " pdb=" C PRO C 48 " pdb=" CB PRO C 48 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA PRO A 66 " pdb=" N PRO A 66 " pdb=" C PRO A 66 " pdb=" CB PRO A 66 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB VAL H 111 " pdb=" CA VAL H 111 " pdb=" CG1 VAL H 111 " pdb=" CG2 VAL H 111 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 2086 not shown) Planarity restraints: 1318 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " 0.086 5.00e-02 4.00e+02 1.17e-01 2.17e+01 pdb=" N PRO A 66 " -0.201 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 47 " 0.071 5.00e-02 4.00e+02 9.44e-02 1.43e+01 pdb=" N PRO C 48 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO C 48 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 48 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 47 " -0.062 5.00e-02 4.00e+02 8.82e-02 1.24e+01 pdb=" N PRO G 48 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO G 48 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO G 48 " -0.050 5.00e-02 4.00e+02 ... (remaining 1315 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1792 2.76 - 3.30: 10668 3.30 - 3.83: 23767 3.83 - 4.37: 27473 4.37 - 4.90: 39166 Nonbonded interactions: 102866 Sorted by model distance: nonbonded pdb=" OG SER D 64 " pdb=" O GLY F 101 " model vdw 2.229 3.040 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH2 ARG E 131 " model vdw 2.249 3.120 nonbonded pdb=" OP1 DA I 58 " pdb=" OG1 THR G 76 " model vdw 2.255 3.040 nonbonded pdb=" O SER H 123 " pdb=" OG SER H 123 " model vdw 2.258 3.040 nonbonded pdb=" O THR A 58 " pdb=" OG1 THR A 58 " model vdw 2.270 3.040 ... (remaining 102861 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 39 through 78 or (resid 79 and (name N or name CA or name \ C or name O or name CB )) or resid 80 through 133)) selection = (chain 'E' and (resid 39 through 80 or (resid 81 and (name N or name CA or name \ C or name O or name CB )) or resid 82 through 93 or (resid 94 through 95 and (na \ me N or name CA or name C or name O or name CB )) or resid 96 through 133)) } ncs_group { reference = chain 'B' selection = (chain 'F' and ((resid 22 through 23 and (name N or name CA or name C or name O \ or name CB )) or resid 24 through 101 or (resid 102 and (name N or name CA or na \ me C or name O )))) } ncs_group { reference = (chain 'C' and (resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB )) or resid 18 through 117)) selection = (chain 'G' and (resid 16 through 19 or (resid 20 through 21 and (name N or name \ CA or name C or name O or name CB )) or resid 22 through 117)) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 123)) selection = (chain 'H' and ((resid 31 and (name N or name CA or name C or name O or name CB \ )) or resid 32 through 107 or resid 109 through 123)) } 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: 0.710 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.620 Find NCS groups from input model: 0.110 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 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 : 0.009 0.550 12660 Z= 0.541 Angle : 1.004 58.583 18345 Z= 0.744 Chirality : 0.045 0.369 2089 Planarity : 0.007 0.117 1318 Dihedral : 29.305 173.740 5433 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.49 % Allowed : 30.84 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.30), residues: 735 helix: 0.97 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -1.92 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.041 0.002 TYR E 54 PHE 0.021 0.002 PHE C 25 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00906 / 0.54 (12660) covalent geometry : angle 1.00438 / 0.74 (18345) hydrogen bonds : bond 0.08191 / 5.27 ( 760) hydrogen bonds : angle 3.94698 / 2.71 ( 1904) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 103 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.7275 (mmt-90) cc_final: 0.6833 (mmt90) REVERT: D 62 MET cc_start: 0.7634 (tpp) cc_final: 0.7412 (mmt) outliers start: 3 outliers final: 0 residues processed: 104 average time/residue: 0.1285 time to fit residues: 17.9498 Evaluate side-chains 98 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 40.0000 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 40.0000 chunk 62 optimal weight: 40.0000 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 30.0000 chunk 45 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4601 r_free = 0.4601 target = 0.202878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.158122 restraints weight = 39891.190| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 2.68 r_work: 0.3861 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3873 r_free = 0.3873 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3873 r_free = 0.3873 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.0601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 12660 Z= 0.146 Angle : 0.637 9.499 18345 Z= 0.378 Chirality : 0.044 0.250 2089 Planarity : 0.005 0.061 1318 Dihedral : 31.471 169.914 3977 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.25 % Allowed : 28.57 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.30), residues: 735 helix: 1.15 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -1.75 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.027 0.002 TYR E 54 PHE 0.014 0.002 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.15 (12660) covalent geometry : angle 0.63670 / 0.38 (18345) hydrogen bonds : bond 0.05027 / 3.33 ( 760) hydrogen bonds : angle 3.35041 / 2.30 ( 1904) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.192 Fit side-chains REVERT: A 129 ARG cc_start: 0.7455 (mmt-90) cc_final: 0.6945 (mmt90) REVERT: B 84 MET cc_start: 0.7798 (mmm) cc_final: 0.7557 (mmm) outliers start: 20 outliers final: 10 residues processed: 131 average time/residue: 0.1094 time to fit residues: 19.9055 Evaluate side-chains 112 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 40 TYR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 67 optimal weight: 50.0000 chunk 71 optimal weight: 30.0000 chunk 70 optimal weight: 30.0000 chunk 5 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 78 optimal weight: 30.0000 chunk 8 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 = 0.4560 r_free = 0.4560 target = 0.198728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.152051 restraints weight = 45183.676| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 3.02 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3982 r_free = 0.3982 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3982 r_free = 0.3982 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12660 Z= 0.208 Angle : 0.690 8.777 18345 Z= 0.397 Chirality : 0.047 0.248 2089 Planarity : 0.005 0.060 1318 Dihedral : 31.758 170.612 3977 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 5.84 % Allowed : 28.57 % Favored : 65.58 % 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: 0.09 (0.29), residues: 735 helix: 0.80 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -1.98 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 86 TYR 0.026 0.002 TYR E 54 PHE 0.013 0.002 PHE E 67 HIS 0.008 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.21 (12660) covalent geometry : angle 0.68958 / 0.40 (18345) hydrogen bonds : bond 0.06009 / 4.03 ( 760) hydrogen bonds : angle 3.58757 / 2.47 ( 1904) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.7035 (mmt-90) cc_final: 0.6706 (mmt90) REVERT: D 40 TYR cc_start: 0.5746 (OUTLIER) cc_final: 0.5065 (m-80) REVERT: E 131 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7914 (ptp-170) REVERT: F 53 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6287 (mp0) REVERT: C 51 MET cc_start: 0.5693 (OUTLIER) cc_final: 0.5243 (ttt) REVERT: G 88 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8339 (mmt180) outliers start: 36 outliers final: 17 residues processed: 138 average time/residue: 0.1067 time to fit residues: 20.1129 Evaluate side-chains 121 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain G residue 88 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 50.0000 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 66 optimal weight: 50.0000 chunk 21 optimal weight: 1.9990 chunk 70 optimal weight: 30.0000 chunk 75 optimal weight: 40.0000 chunk 2 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.199597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.153968 restraints weight = 36394.166| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 2.52 r_work: 0.3828 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12660 Z= 0.172 Angle : 0.642 7.454 18345 Z= 0.374 Chirality : 0.045 0.254 2089 Planarity : 0.005 0.059 1318 Dihedral : 31.797 169.498 3977 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 6.17 % Allowed : 28.57 % Favored : 65.26 % 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: 0.27 (0.30), residues: 735 helix: 0.94 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -1.95 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 86 TYR 0.019 0.002 TYR E 54 PHE 0.015 0.002 PHE B 100 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 (12660) covalent geometry : angle 0.64203 / 0.37 (18345) hydrogen bonds : bond 0.05357 / 3.59 ( 760) hydrogen bonds : angle 3.41749 / 2.36 ( 1904) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 106 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.7408 (pm20) REVERT: A 129 ARG cc_start: 0.7386 (mmt-90) cc_final: 0.6905 (mmt90) REVERT: D 40 TYR cc_start: 0.5768 (OUTLIER) cc_final: 0.5112 (m-80) REVERT: E 84 PHE cc_start: 0.7933 (OUTLIER) cc_final: 0.7402 (t80) REVERT: E 131 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7710 (ptp-170) REVERT: F 53 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.6238 (mp0) REVERT: C 51 MET cc_start: 0.5852 (OUTLIER) cc_final: 0.5459 (ttt) outliers start: 38 outliers final: 24 residues processed: 135 average time/residue: 0.1154 time to fit residues: 20.9583 Evaluate side-chains 127 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 40 TYR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 115 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 5 optimal weight: 0.9980 chunk 56 optimal weight: 40.0000 chunk 32 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 75 optimal weight: 40.0000 chunk 71 optimal weight: 30.0000 chunk 77 optimal weight: 40.0000 chunk 93 optimal weight: 0.9990 chunk 74 optimal weight: 30.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.201326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.156011 restraints weight = 27026.235| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 2.20 r_work: 0.3887 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3894 r_free = 0.3894 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3894 r_free = 0.3894 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12660 Z= 0.145 Angle : 0.608 7.405 18345 Z= 0.359 Chirality : 0.044 0.238 2089 Planarity : 0.004 0.057 1318 Dihedral : 31.744 169.567 3977 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.36 % Allowed : 28.90 % Favored : 65.75 % 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: 0.70 (0.30), residues: 735 helix: 1.24 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.77 (0.39), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 86 TYR 0.012 0.001 TYR G 57 PHE 0.014 0.002 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.15 (12660) covalent geometry : angle 0.60814 / 0.36 (18345) hydrogen bonds : bond 0.04869 / 3.25 ( 760) hydrogen bonds : angle 3.26068 / 2.25 ( 1904) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.7323 (pm20) REVERT: A 129 ARG cc_start: 0.7362 (mmt-90) cc_final: 0.6905 (mmt90) REVERT: E 65 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7453 (mm) REVERT: E 84 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7296 (t80) REVERT: F 53 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.6137 (mp0) REVERT: C 51 MET cc_start: 0.5691 (ttt) cc_final: 0.5353 (ttt) REVERT: C 91 GLU cc_start: 0.6859 (pm20) cc_final: 0.5612 (tp30) REVERT: G 88 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8365 (mmt180) outliers start: 33 outliers final: 20 residues processed: 134 average time/residue: 0.1117 time to fit residues: 20.4707 Evaluate side-chains 123 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 40 TYR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 61 optimal weight: 30.0000 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 56 optimal weight: 40.0000 chunk 68 optimal weight: 50.0000 chunk 41 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 28 optimal weight: 0.5980 chunk 82 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- 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 = 0.4559 r_free = 0.4559 target = 0.198734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.152328 restraints weight = 42450.569| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.91 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3981 r_free = 0.3981 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3981 r_free = 0.3981 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12660 Z= 0.203 Angle : 0.670 7.787 18345 Z= 0.384 Chirality : 0.046 0.228 2089 Planarity : 0.005 0.057 1318 Dihedral : 31.886 169.109 3977 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 6.66 % Allowed : 28.25 % Favored : 65.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.30), residues: 735 helix: 0.91 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -1.86 (0.39), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 17 TYR 0.015 0.002 TYR E 54 PHE 0.013 0.002 PHE A 67 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.20 (12660) covalent geometry : angle 0.66975 / 0.38 (18345) hydrogen bonds : bond 0.05729 / 3.85 ( 760) hydrogen bonds : angle 3.48196 / 2.40 ( 1904) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 108 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7291 (pm20) REVERT: A 129 ARG cc_start: 0.7058 (mmt-90) cc_final: 0.6718 (mmt90) REVERT: D 40 TYR cc_start: 0.5701 (OUTLIER) cc_final: 0.5048 (m-80) REVERT: D 59 MET cc_start: 0.6945 (tpt) cc_final: 0.6549 (tpp) REVERT: E 65 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7275 (mm) REVERT: E 84 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7291 (t80) REVERT: E 131 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7942 (ptp-170) REVERT: F 53 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.6131 (mp0) REVERT: F 93 GLN cc_start: 0.6855 (OUTLIER) cc_final: 0.5930 (mp10) REVERT: C 51 MET cc_start: 0.5460 (OUTLIER) cc_final: 0.4954 (ttt) outliers start: 41 outliers final: 29 residues processed: 139 average time/residue: 0.1065 time to fit residues: 20.0480 Evaluate side-chains 140 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 103 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 54 optimal weight: 40.0000 chunk 68 optimal weight: 50.0000 chunk 83 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 72 optimal weight: 20.0000 chunk 70 optimal weight: 30.0000 chunk 71 optimal weight: 30.0000 chunk 36 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.200440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.155457 restraints weight = 38300.562| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 2.65 r_work: 0.3830 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12660 Z= 0.151 Angle : 0.624 7.040 18345 Z= 0.364 Chirality : 0.044 0.231 2089 Planarity : 0.004 0.057 1318 Dihedral : 31.823 168.517 3977 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 6.49 % Allowed : 29.22 % Favored : 64.29 % 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: 0.56 (0.30), residues: 735 helix: 1.13 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.83 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 17 TYR 0.019 0.002 TYR E 54 PHE 0.014 0.002 PHE B 100 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (12660) covalent geometry : angle 0.62448 / 0.36 (18345) hydrogen bonds : bond 0.05003 / 3.34 ( 760) hydrogen bonds : angle 3.29295 / 2.27 ( 1904) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.7357 (pm20) REVERT: A 129 ARG cc_start: 0.7456 (mmt-90) cc_final: 0.7015 (mmt90) REVERT: D 40 TYR cc_start: 0.5704 (OUTLIER) cc_final: 0.5132 (m-80) REVERT: E 65 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7523 (mm) REVERT: E 84 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7389 (t80) REVERT: E 93 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7212 (tt0) REVERT: E 131 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7715 (ptp-170) REVERT: F 53 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.6238 (mp0) REVERT: C 51 MET cc_start: 0.5760 (OUTLIER) cc_final: 0.5454 (ttt) REVERT: C 91 GLU cc_start: 0.6464 (pm20) cc_final: 0.5227 (tp30) REVERT: C 92 GLU cc_start: 0.7166 (tp30) cc_final: 0.6907 (tp30) outliers start: 40 outliers final: 25 residues processed: 135 average time/residue: 0.1129 time to fit residues: 20.8554 Evaluate side-chains 135 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 3.9990 chunk 65 optimal weight: 50.0000 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 52 optimal weight: 40.0000 chunk 61 optimal weight: 30.0000 chunk 83 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 84 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.202634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.156849 restraints weight = 41581.637| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 2.82 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4043 r_free = 0.4043 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4043 r_free = 0.4043 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (12 function evaluations) r_final: 0.4043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 12660 Z= 0.136 Angle : 0.599 7.363 18345 Z= 0.353 Chirality : 0.043 0.230 2089 Planarity : 0.004 0.057 1318 Dihedral : 31.703 168.817 3977 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.55 % Allowed : 30.84 % Favored : 64.61 % 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: 1.01 (0.30), residues: 735 helix: 1.46 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.69 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 86 TYR 0.018 0.001 TYR E 54 PHE 0.014 0.002 PHE E 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.14 (12660) covalent geometry : angle 0.59939 / 0.35 (18345) hydrogen bonds : bond 0.04558 / 3.04 ( 760) hydrogen bonds : angle 3.14854 / 2.18 ( 1904) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7195 (pm20) REVERT: A 129 ARG cc_start: 0.7035 (mmt-90) cc_final: 0.6811 (mmt90) REVERT: E 65 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7149 (mm) REVERT: E 84 PHE cc_start: 0.7544 (OUTLIER) cc_final: 0.7143 (t80) REVERT: E 131 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7796 (ptp-170) REVERT: F 92 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.7095 (mtp85) REVERT: H 84 ASN cc_start: 0.7309 (OUTLIER) cc_final: 0.7103 (t0) REVERT: C 91 GLU cc_start: 0.6460 (pm20) cc_final: 0.5186 (tp30) outliers start: 28 outliers final: 17 residues processed: 135 average time/residue: 0.1246 time to fit residues: 22.6869 Evaluate side-chains 126 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 78 optimal weight: 30.0000 chunk 12 optimal weight: 7.9990 chunk 57 optimal weight: 40.0000 chunk 76 optimal weight: 30.0000 chunk 56 optimal weight: 40.0000 chunk 46 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 84 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.202751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.158563 restraints weight = 36629.120| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 2.54 r_work: 0.3873 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3890 r_free = 0.3890 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3890 r_free = 0.3890 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.155 12660 Z= 0.182 Angle : 0.838 59.157 18345 Z= 0.507 Chirality : 0.043 0.231 2089 Planarity : 0.005 0.060 1318 Dihedral : 31.703 168.830 3977 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.06 % Allowed : 31.82 % Favored : 64.12 % Cbeta Deviations : 0.14 % 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 (0.30), residues: 735 helix: 1.46 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.67 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 86 TYR 0.026 0.002 TYR D 37 PHE 0.031 0.002 PHE D 70 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (12660) covalent geometry : angle 0.83791 / 0.51 (18345) hydrogen bonds : bond 0.04560 / 3.04 ( 760) hydrogen bonds : angle 3.16462 / 2.20 ( 1904) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7351 (pm20) REVERT: A 129 ARG cc_start: 0.7450 (mmt-90) cc_final: 0.7087 (mmt90) REVERT: E 65 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7348 (mm) REVERT: E 84 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.7329 (t80) REVERT: E 131 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7694 (ptp-170) REVERT: C 91 GLU cc_start: 0.6549 (pm20) cc_final: 0.5209 (tp30) outliers start: 25 outliers final: 17 residues processed: 124 average time/residue: 0.1184 time to fit residues: 19.6653 Evaluate side-chains 120 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 40 TYR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 8 optimal weight: 2.9990 chunk 76 optimal weight: 30.0000 chunk 99 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 40.0000 chunk 7 optimal weight: 2.9990 chunk 71 optimal weight: 30.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 84 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.202632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.157030 restraints weight = 44351.075| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 2.99 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4046 r_free = 0.4046 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4046 r_free = 0.4046 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.4046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.155 12660 Z= 0.182 Angle : 0.838 59.156 18345 Z= 0.507 Chirality : 0.043 0.231 2089 Planarity : 0.005 0.060 1318 Dihedral : 31.703 168.830 3977 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.41 % Allowed : 32.63 % Favored : 63.96 % Cbeta Deviations : 0.14 % 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 (0.30), residues: 735 helix: 1.46 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.67 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 86 TYR 0.026 0.002 TYR D 37 PHE 0.031 0.002 PHE D 70 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (12660) covalent geometry : angle 0.83794 / 0.51 (18345) hydrogen bonds : bond 0.04560 / 3.04 ( 760) hydrogen bonds : angle 3.16462 / 2.20 ( 1904) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.7220 (pm20) REVERT: A 129 ARG cc_start: 0.6571 (mmt-90) cc_final: 0.6347 (mmt90) REVERT: E 65 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7087 (mm) REVERT: E 84 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.7140 (t80) REVERT: E 131 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7902 (ptp-170) REVERT: C 91 GLU cc_start: 0.6411 (pm20) cc_final: 0.5177 (tp30) outliers start: 21 outliers final: 17 residues processed: 117 average time/residue: 0.1168 time to fit residues: 18.6053 Evaluate side-chains 120 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 40 TYR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 0.0770 chunk 59 optimal weight: 30.0000 chunk 54 optimal weight: 40.0000 chunk 23 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 78 optimal weight: 30.0000 chunk 20 optimal weight: 0.7980 chunk 63 optimal weight: 40.0000 chunk 84 optimal weight: 4.9990 overall best weight: 1.3340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 84 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.202764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.157611 restraints weight = 28639.109| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 2.28 r_work: 0.3907 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3909 r_free = 0.3909 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3909 r_free = 0.3909 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.155 12660 Z= 0.182 Angle : 0.838 59.156 18345 Z= 0.507 Chirality : 0.043 0.231 2089 Planarity : 0.005 0.060 1318 Dihedral : 31.703 168.830 3977 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.41 % Allowed : 32.47 % Favored : 64.12 % Cbeta Deviations : 0.14 % 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 (0.30), residues: 735 helix: 1.46 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.67 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 86 TYR 0.026 0.002 TYR D 37 PHE 0.031 0.002 PHE D 70 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (12660) covalent geometry : angle 0.83794 / 0.51 (18345) hydrogen bonds : bond 0.04560 / 3.04 ( 760) hydrogen bonds : angle 3.16462 / 2.20 ( 1904) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2217.46 seconds wall clock time: 38 minutes 39.99 seconds (2319.99 seconds total)