Starting phenix.real_space_refine on Thu Jul 2 12:58:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cp9_30421/07_2026/7cp9_30421.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cp9_30421/07_2026/7cp9_30421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cp9_30421/07_2026/7cp9_30421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cp9_30421/07_2026/7cp9_30421.map" model { file = "/net/cci-nas-00/data/ceres_data/7cp9_30421/07_2026/7cp9_30421.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cp9_30421/07_2026/7cp9_30421.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7cp9_30421/07_2026/7cp9_30421.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cp9_30421/07_2026/7cp9_30421.cif" } resolution = 3.0 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= 0.051 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 11 5.49 5 S 36 5.16 5 C 5572 2.51 5 N 1390 2.21 5 O 1521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 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: 8530 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 320 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "B" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 312 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 2, 'TRANS': 34} Chain: "C" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 400 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "D" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 400 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "E" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 417 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "F" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 417 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "G" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 646 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "H" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 646 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "I" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2189 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 272} Chain: "J" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2189 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 272} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PC1': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.74, per 1000 atoms: 0.20 Number of scatterers: 8530 At special positions: 0 Unit cell: (122.694, 140.946, 100.386, 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 36 16.00 P 11 15.00 O 1521 8.00 N 1390 7.00 C 5572 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 331.0 milliseconds 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1870 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 39.5% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 12 through 41 Processing helix chain 'A' and resid 41 through 46 removed outlier: 4.419A pdb=" N LEU A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 40 removed outlier: 4.086A pdb=" N MET B 20 " --> pdb=" O MET B 16 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG B 21 " --> pdb=" O LYS B 17 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B 22 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 removed outlier: 3.912A pdb=" N LEU B 45 " --> pdb=" O THR B 41 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 41 through 46' Processing helix chain 'C' and resid 19 through 33 removed outlier: 3.630A pdb=" N ASP C 26 " --> pdb=" O ASP C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 60 Processing helix chain 'D' and resid 19 through 33 removed outlier: 3.631A pdb=" N ASP D 26 " --> pdb=" O ASP D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 60 Processing helix chain 'E' and resid 5 through 38 removed outlier: 5.665A pdb=" N ILE E 28 " --> pdb=" O ARG E 24 " (cutoff:3.500A) Proline residue: E 29 - end of helix removed outlier: 4.156A pdb=" N ARG E 38 " --> pdb=" O LEU E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 53 Processing helix chain 'F' and resid 5 through 38 removed outlier: 5.664A pdb=" N ILE F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) Proline residue: F 29 - end of helix removed outlier: 4.156A pdb=" N ARG F 38 " --> pdb=" O LEU F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 53 Processing helix chain 'G' and resid 30 through 39 Processing helix chain 'G' and resid 45 through 55 Processing helix chain 'G' and resid 58 through 96 removed outlier: 4.092A pdb=" N ALA G 62 " --> pdb=" O ARG G 58 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA G 63 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA G 65 " --> pdb=" O SER G 61 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR G 78 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER G 81 " --> pdb=" O MET G 77 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA G 83 " --> pdb=" O ARG G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 117 Processing helix chain 'H' and resid 30 through 39 Processing helix chain 'H' and resid 45 through 55 Processing helix chain 'H' and resid 58 through 96 removed outlier: 4.091A pdb=" N ALA H 62 " --> pdb=" O ARG H 58 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA H 63 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA H 65 " --> pdb=" O SER H 61 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU H 69 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER H 81 " --> pdb=" O MET H 77 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA H 83 " --> pdb=" O ARG H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 117 Processing helix chain 'I' and resid 84 through 92 removed outlier: 3.603A pdb=" N ARG I 88 " --> pdb=" O GLU I 84 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N CYS I 90 " --> pdb=" O CYS I 86 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU I 92 " --> pdb=" O ARG I 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 92 removed outlier: 3.602A pdb=" N ARG J 88 " --> pdb=" O GLU J 84 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N CYS J 90 " --> pdb=" O CYS J 86 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU J 92 " --> pdb=" O ARG J 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 100 through 107 removed outlier: 6.203A pdb=" N GLN I 181 " --> pdb=" O PHE I 185 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N PHE I 185 " --> pdb=" O GLN I 181 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU I 282 " --> pdb=" O ALA I 278 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE I 323 " --> pdb=" O ASP I 319 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU I 337 " --> pdb=" O LEU I 332 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLY I 100 " --> pdb=" O PHE I 356 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU I 358 " --> pdb=" O GLY I 100 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LYS I 102 " --> pdb=" O LEU I 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 100 through 107 removed outlier: 6.203A pdb=" N GLN J 181 " --> pdb=" O PHE J 185 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N PHE J 185 " --> pdb=" O GLN J 181 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU J 282 " --> pdb=" O ALA J 278 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE J 323 " --> pdb=" O ASP J 319 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU J 337 " --> pdb=" O LEU J 332 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLY J 100 " --> pdb=" O PHE J 356 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU J 358 " --> pdb=" O GLY J 100 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LYS J 102 " --> pdb=" O LEU J 358 " (cutoff:3.500A) 568 hydrogen bonds defined for protein. 1620 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: 1.19 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1316 1.30 - 1.43: 2165 1.43 - 1.56: 5121 1.56 - 1.68: 23 1.68 - 1.81: 62 Bond restraints: 8687 Sorted by residual: bond pdb=" C31 PC1 E 102 " pdb=" O31 PC1 E 102 " ideal model delta sigma weight residual 1.330 1.402 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C21 PC1 E 102 " pdb=" O21 PC1 E 102 " ideal model delta sigma weight residual 1.331 1.403 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C21 PC1 C 101 " pdb=" O21 PC1 C 101 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C31 PC1 F 102 " pdb=" O31 PC1 F 102 " ideal model delta sigma weight residual 1.330 1.398 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C31 PC1 G 202 " pdb=" O31 PC1 G 202 " ideal model delta sigma weight residual 1.330 1.398 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 8682 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 11070 2.94 - 5.87: 510 5.87 - 8.81: 31 8.81 - 11.75: 18 11.75 - 14.69: 11 Bond angle restraints: 11640 Sorted by residual: angle pdb=" O12 PC1 C 101 " pdb=" P PC1 C 101 " pdb=" O14 PC1 C 101 " ideal model delta sigma weight residual 123.67 108.98 14.69 3.00e+00 1.11e-01 2.40e+01 angle pdb=" O12 PC1 E 102 " pdb=" P PC1 E 102 " pdb=" O14 PC1 E 102 " ideal model delta sigma weight residual 123.67 108.99 14.68 3.00e+00 1.11e-01 2.39e+01 angle pdb=" O12 PC1 G 201 " pdb=" P PC1 G 201 " pdb=" O14 PC1 G 201 " ideal model delta sigma weight residual 123.67 109.09 14.58 3.00e+00 1.11e-01 2.36e+01 angle pdb=" O12 PC1 G 202 " pdb=" P PC1 G 202 " pdb=" O14 PC1 G 202 " ideal model delta sigma weight residual 123.67 109.22 14.45 3.00e+00 1.11e-01 2.32e+01 angle pdb=" O12 PC1 F 101 " pdb=" P PC1 F 101 " pdb=" O14 PC1 F 101 " ideal model delta sigma weight residual 123.67 109.23 14.44 3.00e+00 1.11e-01 2.32e+01 ... (remaining 11635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 4566 16.71 - 33.42: 424 33.42 - 50.13: 168 50.13 - 66.84: 62 66.84 - 83.55: 20 Dihedral angle restraints: 5240 sinusoidal: 2335 harmonic: 2905 Sorted by residual: dihedral pdb=" CA LYS A 47 " pdb=" C LYS A 47 " pdb=" N LEU A 48 " pdb=" CA LEU A 48 " ideal model delta harmonic sigma weight residual 180.00 158.81 21.19 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA LEU A 45 " pdb=" C LEU A 45 " pdb=" N LYS A 46 " pdb=" CA LYS A 46 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ASP E 41 " pdb=" C ASP E 41 " pdb=" N PRO E 42 " pdb=" CA PRO E 42 " ideal model delta harmonic sigma weight residual -180.00 -160.53 -19.47 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 849 0.038 - 0.075: 289 0.075 - 0.113: 87 0.113 - 0.151: 15 0.151 - 0.189: 1 Chirality restraints: 1241 Sorted by residual: chirality pdb=" CA THR A 41 " pdb=" N THR A 41 " pdb=" C THR A 41 " pdb=" CB THR A 41 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" CA ASP I 198 " pdb=" N ASP I 198 " pdb=" C ASP I 198 " pdb=" CB ASP I 198 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA ASP J 198 " pdb=" N ASP J 198 " pdb=" C ASP J 198 " pdb=" CB ASP J 198 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 1238 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 41 " 0.037 5.00e-02 4.00e+02 5.59e-02 4.99e+00 pdb=" N PRO B 42 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 42 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 42 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 332 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO J 333 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO J 333 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO J 333 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU I 332 " -0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO I 333 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO I 333 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO I 333 " -0.027 5.00e-02 4.00e+02 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 595 2.73 - 3.27: 7923 3.27 - 3.81: 12858 3.81 - 4.36: 14991 4.36 - 4.90: 27520 Nonbonded interactions: 63887 Sorted by model distance: nonbonded pdb=" OH TYR J 221 " pdb=" OE1 GLN J 223 " model vdw 2.183 3.040 nonbonded pdb=" OH TYR I 221 " pdb=" OE1 GLN I 223 " model vdw 2.183 3.040 nonbonded pdb=" OG SER I 122 " pdb=" O ILE I 124 " model vdw 2.263 3.040 nonbonded pdb=" OG SER J 122 " pdb=" O ILE J 124 " model vdw 2.263 3.040 nonbonded pdb=" OD1 ASN C 15 " pdb=" OG1 THR C 17 " model vdw 2.266 3.040 ... (remaining 63882 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 11 through 47) selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 15 through 63) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 29 through 202) selection = chain 'H' } ncs_group { reference = chain 'I' selection = (chain 'J' and resid 76 through 361) } 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: 3.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.050 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:5.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 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 : 0.007 0.072 8688 Z= 0.371 Angle : 1.241 14.685 11640 Z= 0.522 Chirality : 0.042 0.189 1241 Planarity : 0.004 0.056 1431 Dihedral : 16.750 83.555 3370 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 7.05 % Allowed : 10.04 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -2.50 (0.25), residues: 997 helix: -0.82 (0.25), residues: 368 sheet: -1.22 (0.25), residues: 380 loop : -3.24 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 39 TYR 0.009 0.001 TYR J 275 PHE 0.017 0.002 PHE A 43 TRP 0.010 0.001 TRP D 57 HIS 0.003 0.001 HIS J 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00746 / 0.37 ( 8687) covalent geometry : angle 1.24078 / 0.52 (11640) hydrogen bonds : bond 0.09341 / 6.27 ( 568) hydrogen bonds : angle 4.86580 / 3.34 ( 1620) Misc. bond : bond 0.00057 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 258 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ARG cc_start: 0.5327 (OUTLIER) cc_final: 0.4913 (tpp-160) REVERT: C 57 TRP cc_start: 0.5840 (OUTLIER) cc_final: 0.5115 (m100) REVERT: D 57 TRP cc_start: 0.3468 (OUTLIER) cc_final: 0.2925 (t-100) REVERT: F 34 LEU cc_start: 0.9042 (mt) cc_final: 0.8704 (mt) REVERT: G 76 LYS cc_start: 0.7863 (mptm) cc_final: 0.7212 (mmpt) REVERT: G 78 TYR cc_start: 0.8715 (t80) cc_final: 0.8387 (t80) REVERT: H 78 TYR cc_start: 0.8841 (t80) cc_final: 0.8619 (t80) REVERT: H 81 SER cc_start: 0.8942 (t) cc_final: 0.8729 (m) REVERT: H 109 GLU cc_start: 0.7017 (tt0) cc_final: 0.6807 (tt0) REVERT: I 265 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8251 (mm) REVERT: I 297 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8667 (m) REVERT: J 306 ASP cc_start: 0.7594 (p0) cc_final: 0.7253 (p0) outliers start: 59 outliers final: 21 residues processed: 301 average time/residue: 0.4644 time to fit residues: 148.8396 Evaluate side-chains 229 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 289 GLU Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 297 THR Chi-restraints excluded: chain J residue 338 THR 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: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 110 GLN I 163 GLN I 220 HIS I 295 GLN J 111 ASN J 163 GLN J 166 HIS J 181 GLN J 189 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.179652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.154681 restraints weight = 11798.858| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 1.89 r_work: 0.3843 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3723 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8688 Z= 0.194 Angle : 0.721 8.132 11640 Z= 0.363 Chirality : 0.044 0.197 1241 Planarity : 0.005 0.042 1431 Dihedral : 15.830 95.559 1557 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 7.41 % Allowed : 21.39 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.41 (0.26), residues: 997 helix: 0.31 (0.27), residues: 378 sheet: -1.05 (0.25), residues: 396 loop : -2.50 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 60 TYR 0.017 0.002 TYR I 275 PHE 0.023 0.002 PHE G 67 TRP 0.012 0.001 TRP I 188 HIS 0.005 0.001 HIS J 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 ( 8687) covalent geometry : angle 0.72147 / 0.36 (11640) hydrogen bonds : bond 0.04364 / 2.91 ( 568) hydrogen bonds : angle 4.39067 / 3.05 ( 1620) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 207 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 LYS cc_start: 0.6740 (mmmm) cc_final: 0.6339 (mmtp) REVERT: B 47 LYS cc_start: 0.8152 (tttp) cc_final: 0.6188 (ttpt) REVERT: C 38 ARG cc_start: 0.5256 (OUTLIER) cc_final: 0.4713 (tpp-160) REVERT: D 57 TRP cc_start: 0.4047 (OUTLIER) cc_final: 0.2941 (t-100) REVERT: F 34 LEU cc_start: 0.9081 (mt) cc_final: 0.8755 (mt) REVERT: G 76 LYS cc_start: 0.8072 (mptm) cc_final: 0.7581 (mmpt) REVERT: G 77 MET cc_start: 0.8269 (ptt) cc_final: 0.7963 (ptp) REVERT: G 78 TYR cc_start: 0.8832 (t80) cc_final: 0.8581 (t80) REVERT: H 78 TYR cc_start: 0.8884 (t80) cc_final: 0.8672 (t80) REVERT: H 81 SER cc_start: 0.8977 (t) cc_final: 0.8775 (m) REVERT: H 109 GLU cc_start: 0.7521 (tt0) cc_final: 0.7297 (tt0) REVERT: H 117 ARG cc_start: 0.4127 (tmm160) cc_final: 0.1874 (mmm-85) REVERT: I 240 ARG cc_start: 0.7401 (mpp80) cc_final: 0.7166 (mpp80) REVERT: I 315 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8713 (mtmm) REVERT: J 84 GLU cc_start: 0.8139 (pm20) cc_final: 0.7877 (pp20) REVERT: J 114 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7950 (mt0) REVERT: J 176 MET cc_start: 0.7642 (mpt) cc_final: 0.7375 (mpt) outliers start: 62 outliers final: 33 residues processed: 247 average time/residue: 0.4923 time to fit residues: 129.5335 Evaluate side-chains 236 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 111 ASN Chi-restraints excluded: chain J residue 114 GLN Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 338 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 48 ASN G 75 GLN I 140 GLN I 220 HIS J 111 ASN J 163 GLN J 181 GLN J 189 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.173673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.150068 restraints weight = 11882.058| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 1.86 r_work: 0.3777 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8688 Z= 0.151 Angle : 0.658 8.103 11640 Z= 0.333 Chirality : 0.042 0.186 1241 Planarity : 0.004 0.046 1431 Dihedral : 15.117 88.486 1545 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 8.24 % Allowed : 22.46 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.80 (0.27), residues: 997 helix: 0.86 (0.27), residues: 378 sheet: -0.80 (0.25), residues: 396 loop : -2.11 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 38 TYR 0.019 0.002 TYR B 34 PHE 0.023 0.001 PHE B 31 TRP 0.009 0.001 TRP I 188 HIS 0.004 0.001 HIS J 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 8687) covalent geometry : angle 0.65817 / 0.33 (11640) hydrogen bonds : bond 0.03980 / 2.67 ( 568) hydrogen bonds : angle 4.29734 / 3.00 ( 1620) Misc. bond : bond 0.00004 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 201 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7740 (mmm160) cc_final: 0.7359 (mmm160) REVERT: B 19 LYS cc_start: 0.6716 (mmmm) cc_final: 0.6294 (mmtp) REVERT: B 47 LYS cc_start: 0.8082 (tttp) cc_final: 0.6070 (ttpt) REVERT: C 38 ARG cc_start: 0.5384 (OUTLIER) cc_final: 0.4805 (tpp-160) REVERT: C 49 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7675 (mp) REVERT: D 49 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7575 (tt) REVERT: D 57 TRP cc_start: 0.4251 (OUTLIER) cc_final: 0.2834 (t-100) REVERT: F 34 LEU cc_start: 0.9145 (mt) cc_final: 0.8805 (mt) REVERT: G 76 LYS cc_start: 0.8030 (mptm) cc_final: 0.7457 (mmtt) REVERT: G 77 MET cc_start: 0.8190 (ptt) cc_final: 0.7886 (ptp) REVERT: G 78 TYR cc_start: 0.8878 (t80) cc_final: 0.8622 (t80) REVERT: G 106 LEU cc_start: 0.9007 (tp) cc_final: 0.8649 (tt) REVERT: H 51 LEU cc_start: 0.2040 (OUTLIER) cc_final: 0.1442 (mp) REVERT: H 78 TYR cc_start: 0.8913 (t80) cc_final: 0.8703 (t80) REVERT: H 79 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7192 (mpt180) REVERT: H 81 SER cc_start: 0.8927 (t) cc_final: 0.8687 (m) REVERT: H 109 GLU cc_start: 0.7538 (tt0) cc_final: 0.7295 (tt0) REVERT: H 117 ARG cc_start: 0.3833 (OUTLIER) cc_final: 0.1448 (mmm-85) REVERT: I 315 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8698 (mtmm) REVERT: J 176 MET cc_start: 0.7650 (mpt) cc_final: 0.7380 (mpt) REVERT: J 180 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8822 (t) REVERT: J 280 ASP cc_start: 0.8645 (m-30) cc_final: 0.8442 (m-30) REVERT: J 294 MET cc_start: 0.8365 (mpm) cc_final: 0.8130 (mmp) REVERT: J 337 LEU cc_start: 0.8847 (tp) cc_final: 0.8596 (mt) outliers start: 69 outliers final: 38 residues processed: 244 average time/residue: 0.4606 time to fit residues: 120.3683 Evaluate side-chains 246 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 111 ASN Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 47 optimal weight: 0.7980 chunk 64 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 10 GLN ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 HIS I 295 GLN ** I 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 ASN J 181 GLN J 189 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.172563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.148746 restraints weight = 12103.607| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.88 r_work: 0.3760 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8688 Z= 0.194 Angle : 0.691 8.864 11640 Z= 0.348 Chirality : 0.043 0.187 1241 Planarity : 0.005 0.054 1431 Dihedral : 14.983 84.242 1545 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 8.96 % Allowed : 23.89 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.53 (0.27), residues: 997 helix: 1.02 (0.28), residues: 376 sheet: -0.59 (0.26), residues: 394 loop : -1.98 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 60 TYR 0.019 0.002 TYR B 34 PHE 0.028 0.002 PHE G 67 TRP 0.011 0.001 TRP D 57 HIS 0.005 0.001 HIS J 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 ( 8687) covalent geometry : angle 0.69110 / 0.35 (11640) hydrogen bonds : bond 0.04212 / 2.81 ( 568) hydrogen bonds : angle 4.36111 / 3.05 ( 1620) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 205 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 LYS cc_start: 0.8064 (tttp) cc_final: 0.6017 (ttpt) REVERT: C 38 ARG cc_start: 0.5378 (OUTLIER) cc_final: 0.4689 (tpp80) REVERT: C 43 ARG cc_start: 0.7880 (ttt-90) cc_final: 0.7532 (ptm-80) REVERT: D 57 TRP cc_start: 0.4362 (OUTLIER) cc_final: 0.2856 (t-100) REVERT: F 34 LEU cc_start: 0.9167 (mt) cc_final: 0.8809 (mt) REVERT: G 76 LYS cc_start: 0.8073 (mptm) cc_final: 0.7494 (mmtt) REVERT: G 77 MET cc_start: 0.8175 (ptt) cc_final: 0.7843 (ptp) REVERT: G 78 TYR cc_start: 0.8922 (t80) cc_final: 0.8674 (t80) REVERT: H 51 LEU cc_start: 0.2050 (OUTLIER) cc_final: 0.1406 (mp) REVERT: H 79 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7093 (tmt170) REVERT: H 81 SER cc_start: 0.8957 (t) cc_final: 0.8698 (m) REVERT: H 109 GLU cc_start: 0.7561 (tt0) cc_final: 0.7341 (tt0) REVERT: H 117 ARG cc_start: 0.3883 (OUTLIER) cc_final: 0.1616 (mmm-85) REVERT: I 112 HIS cc_start: 0.8451 (OUTLIER) cc_final: 0.8117 (m170) REVERT: I 315 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8704 (mtmm) REVERT: J 84 GLU cc_start: 0.7950 (pp20) cc_final: 0.7077 (pp20) REVERT: J 114 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7971 (mt0) REVERT: J 176 MET cc_start: 0.7669 (mpt) cc_final: 0.7434 (mpt) REVERT: J 180 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8836 (t) REVERT: J 337 LEU cc_start: 0.8856 (tp) cc_final: 0.8635 (mt) outliers start: 75 outliers final: 40 residues processed: 249 average time/residue: 0.4839 time to fit residues: 128.7564 Evaluate side-chains 254 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 205 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 67 PHE Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 112 HIS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 111 ASN Chi-restraints excluded: chain J residue 114 GLN Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 140 GLN ** I 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 HIS J 181 GLN J 189 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.168251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.144468 restraints weight = 12039.381| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.84 r_work: 0.3706 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 8688 Z= 0.352 Angle : 0.833 10.360 11640 Z= 0.425 Chirality : 0.048 0.216 1241 Planarity : 0.006 0.050 1431 Dihedral : 15.386 80.016 1540 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 10.27 % Allowed : 24.25 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.88 (0.27), residues: 997 helix: 0.54 (0.27), residues: 378 sheet: -0.66 (0.25), residues: 402 loop : -2.06 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 33 TYR 0.021 0.002 TYR J 275 PHE 0.030 0.002 PHE D 34 TRP 0.016 0.002 TRP D 57 HIS 0.009 0.002 HIS J 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00743 / 0.35 ( 8687) covalent geometry : angle 0.83331 / 0.43 (11640) hydrogen bonds : bond 0.05181 / 3.47 ( 568) hydrogen bonds : angle 4.75623 / 3.33 ( 1620) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 207 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 LYS cc_start: 0.7023 (mmmm) cc_final: 0.6604 (mptm) REVERT: C 38 ARG cc_start: 0.5350 (OUTLIER) cc_final: 0.5085 (ttt180) REVERT: C 43 ARG cc_start: 0.8007 (ttt-90) cc_final: 0.7549 (ptm-80) REVERT: C 49 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7685 (mp) REVERT: D 57 TRP cc_start: 0.4377 (OUTLIER) cc_final: 0.2669 (t-100) REVERT: F 34 LEU cc_start: 0.9191 (mt) cc_final: 0.8838 (mt) REVERT: G 76 LYS cc_start: 0.7987 (mptm) cc_final: 0.7430 (mmtt) REVERT: G 77 MET cc_start: 0.8182 (ptt) cc_final: 0.7848 (ptp) REVERT: G 78 TYR cc_start: 0.8985 (t80) cc_final: 0.8780 (t80) REVERT: G 87 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8642 (mp) REVERT: H 51 LEU cc_start: 0.2081 (OUTLIER) cc_final: 0.1384 (mp) REVERT: H 67 PHE cc_start: 0.5301 (OUTLIER) cc_final: 0.5079 (m-80) REVERT: H 79 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7176 (tmt170) REVERT: H 81 SER cc_start: 0.9052 (t) cc_final: 0.8810 (m) REVERT: H 117 ARG cc_start: 0.3993 (OUTLIER) cc_final: 0.1761 (mmm-85) REVERT: I 112 HIS cc_start: 0.8558 (OUTLIER) cc_final: 0.8169 (m170) REVERT: I 315 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8657 (mtmm) REVERT: J 114 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8076 (mt0) REVERT: J 176 MET cc_start: 0.7607 (mpt) cc_final: 0.7394 (mpt) REVERT: J 180 THR cc_start: 0.9228 (OUTLIER) cc_final: 0.8947 (t) outliers start: 86 outliers final: 47 residues processed: 255 average time/residue: 0.4689 time to fit residues: 127.4856 Evaluate side-chains 259 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 200 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 112 HIS Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 111 ASN Chi-restraints excluded: chain J residue 113 PHE Chi-restraints excluded: chain J residue 114 GLN Chi-restraints excluded: chain J residue 126 GLU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 3 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 77 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 10 GLN F 20 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 HIS I 295 GLN J 181 GLN J 189 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.172667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.149954 restraints weight = 11907.992| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.89 r_work: 0.3762 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8688 Z= 0.154 Angle : 0.693 9.357 11640 Z= 0.349 Chirality : 0.043 0.198 1241 Planarity : 0.005 0.042 1431 Dihedral : 14.860 81.735 1539 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 7.17 % Allowed : 27.72 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.41 (0.27), residues: 997 helix: 1.05 (0.28), residues: 376 sheet: -0.42 (0.26), residues: 394 loop : -1.99 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 60 TYR 0.019 0.001 TYR J 275 PHE 0.024 0.001 PHE B 31 TRP 0.012 0.001 TRP C 57 HIS 0.005 0.001 HIS J 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 8687) covalent geometry : angle 0.69332 / 0.35 (11640) hydrogen bonds : bond 0.04063 / 2.71 ( 568) hydrogen bonds : angle 4.41394 / 3.09 ( 1620) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 209 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7633 (tt) REVERT: C 38 ARG cc_start: 0.5285 (OUTLIER) cc_final: 0.4577 (ttm-80) REVERT: C 41 PHE cc_start: 0.7213 (t80) cc_final: 0.6365 (t80) REVERT: C 43 ARG cc_start: 0.7943 (ttt-90) cc_final: 0.7616 (ptm-80) REVERT: C 49 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7683 (mp) REVERT: D 57 TRP cc_start: 0.4413 (OUTLIER) cc_final: 0.3870 (m100) REVERT: F 34 LEU cc_start: 0.9139 (mt) cc_final: 0.8797 (mt) REVERT: G 76 LYS cc_start: 0.7990 (mptm) cc_final: 0.7270 (mmmt) REVERT: G 77 MET cc_start: 0.8182 (ptt) cc_final: 0.7810 (ptp) REVERT: G 78 TYR cc_start: 0.8915 (t80) cc_final: 0.8694 (t80) REVERT: G 87 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8588 (mp) REVERT: H 51 LEU cc_start: 0.2066 (OUTLIER) cc_final: 0.1213 (mt) REVERT: H 79 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7142 (tmt170) REVERT: H 81 SER cc_start: 0.8910 (t) cc_final: 0.8636 (m) REVERT: H 117 ARG cc_start: 0.3968 (OUTLIER) cc_final: 0.1833 (mmm-85) REVERT: I 112 HIS cc_start: 0.8378 (OUTLIER) cc_final: 0.8125 (m170) REVERT: I 315 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8687 (mtmm) REVERT: J 84 GLU cc_start: 0.7819 (pp20) cc_final: 0.6886 (pp20) REVERT: J 114 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8056 (mt0) REVERT: J 180 THR cc_start: 0.9076 (OUTLIER) cc_final: 0.8794 (t) REVERT: J 240 ARG cc_start: 0.7216 (mpp80) cc_final: 0.6998 (mtp180) outliers start: 60 outliers final: 29 residues processed: 244 average time/residue: 0.5011 time to fit residues: 130.4221 Evaluate side-chains 243 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 112 HIS Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 113 PHE Chi-restraints excluded: chain J residue 114 GLN Chi-restraints excluded: chain J residue 126 GLU Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 61 optimal weight: 0.0040 chunk 29 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 44 ASN F 20 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 HIS J 181 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.172672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.148823 restraints weight = 12134.143| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.86 r_work: 0.3757 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8688 Z= 0.171 Angle : 0.707 9.692 11640 Z= 0.354 Chirality : 0.043 0.187 1241 Planarity : 0.005 0.046 1431 Dihedral : 14.580 80.718 1539 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 7.41 % Allowed : 27.96 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.25 (0.27), residues: 997 helix: 1.17 (0.28), residues: 376 sheet: -0.31 (0.26), residues: 394 loop : -1.96 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 60 TYR 0.020 0.002 TYR J 275 PHE 0.027 0.002 PHE B 31 TRP 0.011 0.001 TRP C 57 HIS 0.005 0.001 HIS J 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 ( 8687) covalent geometry : angle 0.70729 / 0.35 (11640) hydrogen bonds : bond 0.04071 / 2.73 ( 568) hydrogen bonds : angle 4.37582 / 3.06 ( 1620) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 206 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ARG cc_start: 0.5205 (OUTLIER) cc_final: 0.4532 (ttm-80) REVERT: C 43 ARG cc_start: 0.7875 (ttt-90) cc_final: 0.7545 (ptm-80) REVERT: C 49 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7653 (mp) REVERT: D 57 TRP cc_start: 0.4410 (OUTLIER) cc_final: 0.3960 (m100) REVERT: F 34 LEU cc_start: 0.9162 (mt) cc_final: 0.8815 (mt) REVERT: G 76 LYS cc_start: 0.7990 (mptm) cc_final: 0.7329 (mmpt) REVERT: G 77 MET cc_start: 0.8208 (ptt) cc_final: 0.7851 (ptp) REVERT: G 78 TYR cc_start: 0.8929 (t80) cc_final: 0.8718 (t80) REVERT: G 87 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8573 (mp) REVERT: G 107 GLN cc_start: 0.7879 (tm-30) cc_final: 0.7540 (mt0) REVERT: G 108 MET cc_start: 0.7828 (ttp) cc_final: 0.7423 (ttp) REVERT: H 79 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7111 (tmt170) REVERT: H 81 SER cc_start: 0.8922 (t) cc_final: 0.8628 (m) REVERT: H 117 ARG cc_start: 0.4029 (OUTLIER) cc_final: 0.1803 (mmm-85) REVERT: I 112 HIS cc_start: 0.8445 (OUTLIER) cc_final: 0.8188 (m170) REVERT: I 315 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8683 (mtmm) REVERT: J 84 GLU cc_start: 0.7775 (pp20) cc_final: 0.6836 (pp20) REVERT: J 114 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.8061 (mt0) REVERT: J 180 THR cc_start: 0.9082 (OUTLIER) cc_final: 0.8807 (t) outliers start: 62 outliers final: 34 residues processed: 242 average time/residue: 0.4923 time to fit residues: 126.8825 Evaluate side-chains 242 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 112 HIS Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 111 ASN Chi-restraints excluded: chain J residue 113 PHE Chi-restraints excluded: chain J residue 114 GLN Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 287 GLU Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 5 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 81 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 HIS J 281 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.173243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.149801 restraints weight = 11926.086| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.85 r_work: 0.3772 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8688 Z= 0.154 Angle : 0.712 9.628 11640 Z= 0.352 Chirality : 0.043 0.182 1241 Planarity : 0.005 0.043 1431 Dihedral : 14.306 81.317 1539 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 5.97 % Allowed : 29.75 % Favored : 64.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.03 (0.28), residues: 997 helix: 1.36 (0.28), residues: 376 sheet: -0.17 (0.26), residues: 394 loop : -1.91 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 60 TYR 0.021 0.002 TYR J 275 PHE 0.027 0.001 PHE B 31 TRP 0.012 0.001 TRP C 57 HIS 0.005 0.001 HIS J 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 8687) covalent geometry : angle 0.71187 / 0.35 (11640) hydrogen bonds : bond 0.03859 / 2.59 ( 568) hydrogen bonds : angle 4.29148 / 3.01 ( 1620) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 202 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ARG cc_start: 0.5240 (OUTLIER) cc_final: 0.4576 (ttm-80) REVERT: C 43 ARG cc_start: 0.7910 (ttt-90) cc_final: 0.7595 (ptm-80) REVERT: C 49 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7657 (mp) REVERT: D 57 TRP cc_start: 0.4754 (OUTLIER) cc_final: 0.4437 (m100) REVERT: F 34 LEU cc_start: 0.9151 (mt) cc_final: 0.8807 (mt) REVERT: G 76 LYS cc_start: 0.8018 (mptm) cc_final: 0.7368 (mmpt) REVERT: G 77 MET cc_start: 0.8179 (ptt) cc_final: 0.7828 (ptp) REVERT: G 87 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8534 (mp) REVERT: H 79 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7104 (tmt170) REVERT: H 81 SER cc_start: 0.8895 (t) cc_final: 0.8592 (m) REVERT: H 117 ARG cc_start: 0.4017 (OUTLIER) cc_final: 0.1764 (mmm-85) REVERT: I 315 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8699 (mtmm) REVERT: J 84 GLU cc_start: 0.7880 (pp20) cc_final: 0.6946 (pp20) REVERT: J 114 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8041 (mt0) REVERT: J 180 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8788 (t) outliers start: 50 outliers final: 29 residues processed: 231 average time/residue: 0.4744 time to fit residues: 116.8314 Evaluate side-chains 232 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 194 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 111 ASN Chi-restraints excluded: chain J residue 113 PHE Chi-restraints excluded: chain J residue 114 GLN Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 287 GLU Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 4 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 HIS I 220 HIS I 295 GLN J 181 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.172000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.149224 restraints weight = 11992.711| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.08 r_work: 0.3744 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8688 Z= 0.208 Angle : 0.750 10.097 11640 Z= 0.375 Chirality : 0.044 0.205 1241 Planarity : 0.005 0.048 1431 Dihedral : 14.378 79.760 1539 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.85 % Allowed : 30.94 % Favored : 63.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.01 (0.28), residues: 997 helix: 1.27 (0.28), residues: 376 sheet: 0.08 (0.27), residues: 378 loop : -2.01 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 60 TYR 0.022 0.002 TYR J 275 PHE 0.029 0.002 PHE B 31 TRP 0.011 0.001 TRP D 57 HIS 0.006 0.001 HIS J 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.21 ( 8687) covalent geometry : angle 0.74956 / 0.37 (11640) hydrogen bonds : bond 0.04211 / 2.82 ( 568) hydrogen bonds : angle 4.41323 / 3.09 ( 1620) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 199 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.6704 (OUTLIER) cc_final: 0.6148 (t0) REVERT: C 43 ARG cc_start: 0.7922 (ttt-90) cc_final: 0.7597 (ptm-80) REVERT: C 49 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7668 (mp) REVERT: D 57 TRP cc_start: 0.4842 (OUTLIER) cc_final: 0.4457 (m100) REVERT: E 38 ARG cc_start: 0.7454 (ppp80) cc_final: 0.7250 (ptm160) REVERT: F 34 LEU cc_start: 0.9177 (mt) cc_final: 0.8828 (mt) REVERT: G 76 LYS cc_start: 0.7961 (mptm) cc_final: 0.7303 (mmpt) REVERT: G 77 MET cc_start: 0.8184 (ptt) cc_final: 0.7847 (ptp) REVERT: G 87 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8556 (mp) REVERT: G 107 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7501 (mt0) REVERT: H 79 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7139 (tmt170) REVERT: H 81 SER cc_start: 0.8931 (t) cc_final: 0.8635 (m) REVERT: H 117 ARG cc_start: 0.4114 (OUTLIER) cc_final: 0.1886 (mmm-85) REVERT: I 315 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8693 (mtmm) REVERT: J 84 GLU cc_start: 0.7996 (pp20) cc_final: 0.7049 (pp20) REVERT: J 114 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8065 (mt0) REVERT: J 180 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8817 (t) outliers start: 49 outliers final: 32 residues processed: 227 average time/residue: 0.4981 time to fit residues: 120.6354 Evaluate side-chains 238 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 111 ASN Chi-restraints excluded: chain J residue 113 PHE Chi-restraints excluded: chain J residue 114 GLN Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 287 GLU Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 12 optimal weight: 0.0870 chunk 19 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 56 optimal weight: 0.2980 chunk 86 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 220 HIS I 295 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.174653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.151134 restraints weight = 11967.044| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 1.85 r_work: 0.3789 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8688 Z= 0.140 Angle : 0.723 11.027 11640 Z= 0.354 Chirality : 0.043 0.198 1241 Planarity : 0.004 0.044 1431 Dihedral : 13.906 81.249 1535 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.66 % Allowed : 31.78 % Favored : 63.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.30 (0.28), residues: 997 helix: 1.52 (0.28), residues: 378 sheet: 0.18 (0.27), residues: 380 loop : -1.83 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 60 TYR 0.022 0.002 TYR J 275 PHE 0.023 0.001 PHE B 31 TRP 0.013 0.001 TRP C 57 HIS 0.003 0.001 HIS J 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 8687) covalent geometry : angle 0.72286 / 0.35 (11640) hydrogen bonds : bond 0.03664 / 2.45 ( 568) hydrogen bonds : angle 4.21701 / 2.96 ( 1620) Misc. bond : bond 0.00022 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 203 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 ARG cc_start: 0.7886 (ttt-90) cc_final: 0.7437 (ptm-80) REVERT: C 49 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7698 (mp) REVERT: F 34 LEU cc_start: 0.9136 (mt) cc_final: 0.8807 (mt) REVERT: G 76 LYS cc_start: 0.7994 (mptm) cc_final: 0.7331 (mmpt) REVERT: G 77 MET cc_start: 0.8161 (ptt) cc_final: 0.7825 (ptp) REVERT: G 87 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8520 (mp) REVERT: G 107 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7428 (tt0) REVERT: H 79 ARG cc_start: 0.8060 (tpt170) cc_final: 0.7224 (tmt170) REVERT: H 81 SER cc_start: 0.8878 (t) cc_final: 0.8571 (m) REVERT: H 117 ARG cc_start: 0.4053 (OUTLIER) cc_final: 0.1748 (mmm-85) REVERT: J 84 GLU cc_start: 0.7892 (pp20) cc_final: 0.7004 (pp20) REVERT: J 114 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7993 (mt0) REVERT: J 180 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8786 (t) REVERT: J 240 ARG cc_start: 0.7110 (mtp85) cc_final: 0.6736 (mtm-85) outliers start: 39 outliers final: 27 residues processed: 226 average time/residue: 0.4915 time to fit residues: 118.8782 Evaluate side-chains 230 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 111 ASN Chi-restraints excluded: chain J residue 113 PHE Chi-restraints excluded: chain J residue 114 GLN Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 287 GLU Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 59 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 GLN J 189 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.173526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.150130 restraints weight = 11897.778| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 1.83 r_work: 0.3782 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8688 Z= 0.159 Angle : 0.718 10.989 11640 Z= 0.355 Chirality : 0.042 0.184 1241 Planarity : 0.004 0.046 1431 Dihedral : 13.659 80.368 1531 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.54 % Allowed : 32.74 % Favored : 62.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.34 (0.28), residues: 997 helix: 1.54 (0.28), residues: 376 sheet: 0.23 (0.27), residues: 380 loop : -1.81 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 38 TYR 0.022 0.002 TYR J 275 PHE 0.025 0.002 PHE H 92 TRP 0.011 0.001 TRP C 57 HIS 0.005 0.001 HIS J 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 8687) covalent geometry : angle 0.71817 / 0.35 (11640) hydrogen bonds : bond 0.03791 / 2.54 ( 568) hydrogen bonds : angle 4.25724 / 2.99 ( 1620) Misc. bond : bond 0.00004 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3899.65 seconds wall clock time: 67 minutes 4.32 seconds (4024.32 seconds total)