Starting phenix.real_space_refine on Thu Feb 13 07:27:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cp9_30421/02_2025/7cp9_30421.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cp9_30421/02_2025/7cp9_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_30421/02_2025/7cp9_30421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cp9_30421/02_2025/7cp9_30421.map" model { file = "/net/cci-nas-00/data/ceres_data/7cp9_30421/02_2025/7cp9_30421.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cp9_30421/02_2025/7cp9_30421.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3} 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, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3} 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: 5.88, per 1000 atoms: 0.69 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: 2.69 Conformation dependent library (CDL) restraints added in 922.7 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: 0.90 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: 2.60 Time building geometry restraints manager: 2.93 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 - 17.61: 4649 17.61 - 35.21: 437 35.21 - 52.82: 182 52.82 - 70.42: 50 70.42 - 88.03: 21 Dihedral angle restraints: 5339 sinusoidal: 2434 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 5336 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 118 or resid 201 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: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.220 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 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 8687 Z= 0.487 Angle : 1.241 14.685 11640 Z= 0.522 Chirality : 0.042 0.189 1241 Planarity : 0.004 0.056 1431 Dihedral : 17.402 88.028 3469 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP D 57 HIS 0.003 0.001 HIS J 271 PHE 0.017 0.002 PHE A 43 TYR 0.009 0.001 TYR J 275 ARG 0.003 0.000 ARG B 39 *********************** 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 : 0.875 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: 0.6808 (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: 1.1756 time to fit residues: 376.4322 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 : 1.006 ------------------------------------------------------------------------------- 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 81 optimal weight: 0.0070 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 24 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 75 GLN 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 J 223 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.181486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.156485 restraints weight = 11727.116| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 1.87 r_work: 0.3864 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8687 Z= 0.204 Angle : 0.700 8.007 11640 Z= 0.348 Chirality : 0.043 0.200 1241 Planarity : 0.005 0.043 1431 Dihedral : 17.065 96.869 1656 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 6.93 % Allowed : 21.62 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.26), residues: 997 helix: 0.44 (0.27), residues: 378 sheet: -0.99 (0.25), residues: 396 loop : -2.44 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 188 HIS 0.005 0.001 HIS I 220 PHE 0.023 0.001 PHE G 67 TYR 0.017 0.001 TYR I 275 ARG 0.005 0.001 ARG D 60 *********************** 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 260 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 202 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7731 (mmm160) cc_final: 0.7445 (mmp80) REVERT: B 19 LYS cc_start: 0.6681 (mmmm) cc_final: 0.6263 (mmtp) REVERT: B 29 ARG cc_start: 0.7894 (tmt170) cc_final: 0.7579 (tmt170) REVERT: B 47 LYS cc_start: 0.8111 (tttp) cc_final: 0.6155 (ttpt) REVERT: C 38 ARG cc_start: 0.5350 (OUTLIER) cc_final: 0.4841 (tpp-160) REVERT: D 57 TRP cc_start: 0.4078 (OUTLIER) cc_final: 0.2935 (t-100) REVERT: F 34 LEU cc_start: 0.9079 (mt) cc_final: 0.8753 (mt) REVERT: G 76 LYS cc_start: 0.8076 (mptm) cc_final: 0.7500 (mmtt) REVERT: G 77 MET cc_start: 0.8236 (ptt) cc_final: 0.7929 (ptp) REVERT: G 78 TYR cc_start: 0.8814 (t80) cc_final: 0.8539 (t80) REVERT: H 51 LEU cc_start: 0.2164 (OUTLIER) cc_final: 0.1554 (mp) REVERT: H 53 GLU cc_start: 0.2327 (OUTLIER) cc_final: 0.2113 (tp30) REVERT: H 77 MET cc_start: 0.6924 (ptt) cc_final: 0.5741 (tmt) REVERT: H 78 TYR cc_start: 0.8860 (t80) cc_final: 0.8591 (t80) REVERT: H 81 SER cc_start: 0.8953 (t) cc_final: 0.8722 (m) REVERT: H 109 GLU cc_start: 0.7486 (tt0) cc_final: 0.7248 (tt0) REVERT: J 84 GLU cc_start: 0.8118 (pm20) cc_final: 0.7573 (pp20) REVERT: J 176 MET cc_start: 0.7633 (mpt) cc_final: 0.7365 (mpt) outliers start: 58 outliers final: 28 residues processed: 240 average time/residue: 1.1216 time to fit residues: 287.0407 Evaluate side-chains 225 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 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 G residue 53 GLU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 53 GLU 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 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 111 ASN 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 83 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 GLN G 75 GLN I 140 GLN I 220 HIS ** I 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 ASN J 163 GLN J 181 GLN J 189 GLN J 223 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.173745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.149982 restraints weight = 12018.856| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 1.87 r_work: 0.3776 rms_B_bonded: 2.69 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: 0.7594 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8687 Z= 0.218 Angle : 0.664 8.417 11640 Z= 0.335 Chirality : 0.042 0.187 1241 Planarity : 0.004 0.044 1431 Dihedral : 16.487 88.816 1642 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 7.89 % Allowed : 23.30 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.27), residues: 997 helix: 0.88 (0.27), residues: 378 sheet: -0.75 (0.25), residues: 396 loop : -2.11 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 188 HIS 0.004 0.001 HIS J 271 PHE 0.022 0.001 PHE B 31 TYR 0.019 0.002 TYR B 34 ARG 0.005 0.000 ARG D 60 *********************** 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: 66 poor density : 204 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7669 (mmm160) cc_final: 0.7438 (mmp80) REVERT: B 19 LYS cc_start: 0.6787 (mmmm) cc_final: 0.6355 (mmtp) REVERT: B 47 LYS cc_start: 0.8097 (tttp) cc_final: 0.6112 (ttpt) REVERT: C 38 ARG cc_start: 0.5322 (OUTLIER) cc_final: 0.4771 (tpp-160) REVERT: C 49 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7646 (mp) REVERT: D 49 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7546 (tt) REVERT: D 57 TRP cc_start: 0.4178 (OUTLIER) cc_final: 0.2889 (t-100) REVERT: F 34 LEU cc_start: 0.9135 (mt) cc_final: 0.8782 (mt) REVERT: G 76 LYS cc_start: 0.8023 (mptm) cc_final: 0.7454 (mmtt) REVERT: G 77 MET cc_start: 0.8188 (ptt) cc_final: 0.7885 (ptp) REVERT: G 78 TYR cc_start: 0.8869 (t80) cc_final: 0.8588 (t80) REVERT: G 106 LEU cc_start: 0.9026 (tp) cc_final: 0.8684 (tt) REVERT: H 78 TYR cc_start: 0.8902 (t80) cc_final: 0.8680 (t80) REVERT: H 81 SER cc_start: 0.8942 (t) cc_final: 0.8717 (m) REVERT: H 109 GLU cc_start: 0.7559 (tt0) cc_final: 0.7320 (tt0) REVERT: H 117 ARG cc_start: 0.3799 (OUTLIER) cc_final: 0.1397 (mmm-85) REVERT: I 315 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8700 (mtmm) REVERT: J 114 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7978 (mt0) REVERT: J 176 MET cc_start: 0.7663 (mpt) cc_final: 0.7385 (mpt) REVERT: J 180 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8828 (t) REVERT: J 280 ASP cc_start: 0.8646 (m-30) cc_final: 0.8433 (m-30) REVERT: J 294 MET cc_start: 0.8363 (mpm) cc_final: 0.8145 (mmp) REVERT: J 337 LEU cc_start: 0.8873 (tp) cc_final: 0.8625 (mt) outliers start: 66 outliers final: 38 residues processed: 245 average time/residue: 1.0937 time to fit residues: 286.0304 Evaluate side-chains 246 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 200 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 117 ARG Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 123 THR 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 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 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 212 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 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 77 optimal weight: 0.0070 chunk 26 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 GLN I 220 HIS I 295 GLN J 111 ASN J 163 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 = 0.4140 r_free = 0.4140 target = 0.174299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.150508 restraints weight = 11989.295| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 1.87 r_work: 0.3782 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8687 Z= 0.203 Angle : 0.665 11.168 11640 Z= 0.332 Chirality : 0.042 0.182 1241 Planarity : 0.004 0.044 1431 Dihedral : 16.185 87.751 1642 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 8.24 % Allowed : 23.78 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.27), residues: 997 helix: 1.02 (0.27), residues: 376 sheet: -0.50 (0.26), residues: 396 loop : -2.00 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 57 HIS 0.004 0.001 HIS J 271 PHE 0.026 0.001 PHE G 67 TYR 0.018 0.001 TYR J 275 ARG 0.006 0.000 ARG E 38 *********************** 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 271 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 202 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 LYS cc_start: 0.8085 (tttp) cc_final: 0.6068 (ttpt) REVERT: C 38 ARG cc_start: 0.5401 (OUTLIER) cc_final: 0.4879 (tpp-160) REVERT: C 43 ARG cc_start: 0.7859 (tmt-80) cc_final: 0.7119 (ptm160) REVERT: C 49 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7707 (mp) REVERT: D 49 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7528 (tt) REVERT: D 57 TRP cc_start: 0.4175 (OUTLIER) cc_final: 0.2844 (t-100) REVERT: F 34 LEU cc_start: 0.9142 (mt) cc_final: 0.8792 (mt) REVERT: G 76 LYS cc_start: 0.8043 (mptm) cc_final: 0.7468 (mmtt) REVERT: G 77 MET cc_start: 0.8161 (ptt) cc_final: 0.7838 (ptp) REVERT: G 78 TYR cc_start: 0.8891 (t80) cc_final: 0.8604 (t80) REVERT: H 54 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7577 (pp-130) REVERT: H 79 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7106 (tmt170) REVERT: H 81 SER cc_start: 0.8917 (t) cc_final: 0.8666 (m) REVERT: H 109 GLU cc_start: 0.7523 (tt0) cc_final: 0.7299 (tt0) REVERT: H 117 ARG cc_start: 0.3951 (OUTLIER) cc_final: 0.1635 (mmm-85) REVERT: J 84 GLU cc_start: 0.7911 (pp20) cc_final: 0.6927 (pp20) REVERT: J 114 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7980 (mt0) REVERT: J 176 MET cc_start: 0.7670 (mpt) cc_final: 0.7422 (mpt) REVERT: J 180 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8804 (t) REVERT: J 240 ARG cc_start: 0.7094 (mpp80) cc_final: 0.6836 (mtp180) REVERT: J 280 ASP cc_start: 0.8661 (m-30) cc_final: 0.8456 (m-30) REVERT: J 294 MET cc_start: 0.8339 (mpm) cc_final: 0.8070 (mmp) REVERT: J 337 LEU cc_start: 0.8850 (tp) cc_final: 0.8634 (mt) outliers start: 69 outliers final: 36 residues processed: 243 average time/residue: 1.0690 time to fit residues: 277.9282 Evaluate side-chains 243 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 198 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 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 53 LEU 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 54 MET 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 154 MET 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 328 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU 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 14 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 44 optimal weight: 0.0870 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 220 HIS J 189 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.175160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.151311 restraints weight = 11855.829| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.84 r_work: 0.3793 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8687 Z= 0.184 Angle : 0.673 9.943 11640 Z= 0.329 Chirality : 0.042 0.227 1241 Planarity : 0.004 0.045 1431 Dihedral : 15.805 86.122 1641 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 6.69 % Allowed : 26.64 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.27), residues: 997 helix: 1.19 (0.27), residues: 376 sheet: -0.27 (0.26), residues: 396 loop : -1.82 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 57 HIS 0.007 0.001 HIS J 112 PHE 0.021 0.001 PHE B 31 TYR 0.019 0.001 TYR J 275 ARG 0.005 0.000 ARG E 38 *********************** 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 262 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 206 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.6812 (OUTLIER) cc_final: 0.6150 (t70) REVERT: B 47 LYS cc_start: 0.8079 (tttp) cc_final: 0.6015 (ttpt) REVERT: C 38 ARG cc_start: 0.5367 (OUTLIER) cc_final: 0.4742 (tpp-160) REVERT: C 43 ARG cc_start: 0.7900 (tmt-80) cc_final: 0.7617 (ptm-80) REVERT: C 49 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7704 (mp) REVERT: D 57 TRP cc_start: 0.4033 (OUTLIER) cc_final: 0.2387 (t-100) REVERT: F 34 LEU cc_start: 0.9130 (mt) cc_final: 0.8793 (mt) REVERT: G 76 LYS cc_start: 0.8006 (mptm) cc_final: 0.7412 (mmtt) REVERT: G 77 MET cc_start: 0.8189 (ptt) cc_final: 0.7860 (ptp) REVERT: G 78 TYR cc_start: 0.8860 (t80) cc_final: 0.8608 (t80) REVERT: H 77 MET cc_start: 0.6942 (ptt) cc_final: 0.5942 (ttp) REVERT: H 79 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7095 (tmt170) REVERT: H 81 SER cc_start: 0.8911 (t) cc_final: 0.8640 (m) REVERT: H 109 GLU cc_start: 0.7563 (tt0) cc_final: 0.7339 (tt0) REVERT: H 117 ARG cc_start: 0.3958 (OUTLIER) cc_final: 0.1642 (mmm-85) REVERT: J 84 GLU cc_start: 0.7823 (pp20) cc_final: 0.6848 (pp20) REVERT: J 114 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.8015 (mt0) REVERT: J 176 MET cc_start: 0.7667 (mpt) cc_final: 0.7421 (mpt) REVERT: J 180 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8794 (t) outliers start: 56 outliers final: 27 residues processed: 238 average time/residue: 1.1113 time to fit residues: 282.0232 Evaluate side-chains 230 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 14 GLU 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 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 69 LEU 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 155 ASP 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 256 LEU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 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 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 360 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 2 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 10 GLN I 220 HIS I 295 GLN J 163 GLN J 189 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.174064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.151100 restraints weight = 11847.188| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.01 r_work: 0.3767 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8687 Z= 0.233 Angle : 0.681 9.280 11640 Z= 0.340 Chirality : 0.043 0.183 1241 Planarity : 0.004 0.047 1431 Dihedral : 15.638 88.804 1634 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 6.21 % Allowed : 28.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.28), residues: 997 helix: 1.23 (0.27), residues: 376 sheet: -0.15 (0.26), residues: 396 loop : -1.79 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 57 HIS 0.005 0.001 HIS J 271 PHE 0.023 0.001 PHE B 31 TYR 0.019 0.001 TYR J 275 ARG 0.007 0.001 ARG D 60 *********************** 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 248 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 196 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.6644 (OUTLIER) cc_final: 0.6354 (t0) REVERT: B 47 LYS cc_start: 0.8125 (tttp) cc_final: 0.6005 (ttpt) REVERT: C 38 ARG cc_start: 0.5396 (OUTLIER) cc_final: 0.5031 (tpp80) REVERT: C 43 ARG cc_start: 0.7940 (tmt-80) cc_final: 0.7665 (ptm-80) REVERT: D 57 TRP cc_start: 0.4175 (OUTLIER) cc_final: 0.2333 (t-100) REVERT: F 34 LEU cc_start: 0.9151 (mt) cc_final: 0.8786 (mt) REVERT: G 76 LYS cc_start: 0.7986 (mptm) cc_final: 0.7390 (mmtt) REVERT: G 77 MET cc_start: 0.8240 (ptt) cc_final: 0.7901 (ptp) REVERT: G 78 TYR cc_start: 0.8898 (t80) cc_final: 0.8644 (t80) REVERT: G 87 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8534 (mp) REVERT: H 54 MET cc_start: 0.6962 (ppp) cc_final: 0.6595 (pp-130) REVERT: H 77 MET cc_start: 0.7002 (ptt) cc_final: 0.5977 (ttp) REVERT: H 79 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7146 (tmt170) REVERT: H 81 SER cc_start: 0.8917 (t) cc_final: 0.8627 (m) REVERT: H 109 GLU cc_start: 0.7609 (tt0) cc_final: 0.7377 (tt0) REVERT: H 117 ARG cc_start: 0.4167 (OUTLIER) cc_final: 0.1795 (mmm-85) REVERT: I 267 GLN cc_start: 0.7378 (tp40) cc_final: 0.6875 (tm-30) REVERT: J 114 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8062 (mt0) REVERT: J 180 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8783 (t) REVERT: J 240 ARG cc_start: 0.7219 (mpp80) cc_final: 0.6859 (mtm180) outliers start: 52 outliers final: 31 residues processed: 227 average time/residue: 1.1072 time to fit residues: 268.8507 Evaluate side-chains 232 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 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 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 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 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 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 328 LEU 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 360 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 63 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 0.2980 chunk 11 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 220 HIS J 181 GLN J 189 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.175107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.151327 restraints weight = 11951.623| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.83 r_work: 0.3793 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8687 Z= 0.188 Angle : 0.669 9.083 11640 Z= 0.330 Chirality : 0.042 0.192 1241 Planarity : 0.004 0.047 1431 Dihedral : 15.292 89.276 1634 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 5.85 % Allowed : 28.91 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.28), residues: 997 helix: 1.40 (0.27), residues: 376 sheet: 0.02 (0.26), residues: 394 loop : -1.58 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 57 HIS 0.004 0.001 HIS J 271 PHE 0.022 0.001 PHE B 31 TYR 0.019 0.001 TYR J 275 ARG 0.006 0.000 ARG D 60 *********************** 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 251 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 LYS cc_start: 0.8080 (tttp) cc_final: 0.5962 (ttpt) REVERT: C 38 ARG cc_start: 0.5193 (OUTLIER) cc_final: 0.4513 (tpp80) REVERT: C 41 PHE cc_start: 0.7103 (t80) cc_final: 0.6833 (t80) REVERT: C 43 ARG cc_start: 0.7947 (tmt-80) cc_final: 0.7432 (ptm-80) REVERT: C 49 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7685 (mp) REVERT: D 57 TRP cc_start: 0.4341 (OUTLIER) cc_final: 0.3797 (m100) REVERT: F 34 LEU cc_start: 0.9117 (mt) cc_final: 0.8785 (mt) REVERT: G 76 LYS cc_start: 0.7997 (mptm) cc_final: 0.7380 (mmtt) REVERT: G 77 MET cc_start: 0.8271 (ptt) cc_final: 0.7927 (ptp) REVERT: G 78 TYR cc_start: 0.8883 (t80) cc_final: 0.8649 (t80) REVERT: G 87 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8492 (mp) REVERT: G 102 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7776 (mm-30) REVERT: G 107 GLN cc_start: 0.8318 (tp40) cc_final: 0.7868 (tm-30) REVERT: H 54 MET cc_start: 0.6886 (ppp) cc_final: 0.6454 (pp-130) REVERT: H 77 MET cc_start: 0.6927 (ptt) cc_final: 0.6107 (tpp) REVERT: H 79 ARG cc_start: 0.8058 (tpt170) cc_final: 0.7181 (tmt170) REVERT: H 81 SER cc_start: 0.8883 (t) cc_final: 0.8582 (m) REVERT: H 109 GLU cc_start: 0.7614 (tt0) cc_final: 0.7395 (tt0) REVERT: H 117 ARG cc_start: 0.4068 (OUTLIER) cc_final: 0.1782 (mmm-85) REVERT: I 267 GLN cc_start: 0.7310 (tp40) cc_final: 0.6744 (tm-30) REVERT: I 315 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8690 (mtmm) REVERT: J 84 GLU cc_start: 0.7707 (pp20) cc_final: 0.6721 (pp20) REVERT: J 114 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.8038 (mt0) REVERT: J 180 THR cc_start: 0.9018 (OUTLIER) cc_final: 0.8767 (t) outliers start: 49 outliers final: 24 residues processed: 229 average time/residue: 1.0944 time to fit residues: 267.2952 Evaluate side-chains 222 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU 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 117 ARG Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 176 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 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 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 181 GLN 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 360 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 13 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 70 optimal weight: 0.4980 chunk 46 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 110 GLN I 220 HIS J 189 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.174614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.150616 restraints weight = 11979.754| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 1.85 r_work: 0.3781 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8687 Z= 0.220 Angle : 0.687 10.276 11640 Z= 0.341 Chirality : 0.042 0.181 1241 Planarity : 0.004 0.048 1431 Dihedral : 15.120 89.610 1630 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 5.02 % Allowed : 30.47 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.28), residues: 997 helix: 1.43 (0.27), residues: 376 sheet: 0.05 (0.27), residues: 396 loop : -1.60 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 57 HIS 0.004 0.001 HIS J 271 PHE 0.027 0.001 PHE B 31 TYR 0.022 0.001 TYR B 34 ARG 0.006 0.000 ARG D 60 *********************** 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 233 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 191 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 47 LYS cc_start: 0.8096 (tttp) cc_final: 0.5961 (ttpt) REVERT: C 43 ARG cc_start: 0.7930 (tmt-80) cc_final: 0.7713 (ptm-80) REVERT: C 49 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7682 (mp) REVERT: D 57 TRP cc_start: 0.4285 (OUTLIER) cc_final: 0.3351 (m100) REVERT: F 34 LEU cc_start: 0.9142 (mt) cc_final: 0.8789 (mt) REVERT: G 76 LYS cc_start: 0.8000 (mptm) cc_final: 0.7377 (mmtt) REVERT: G 77 MET cc_start: 0.8295 (ptt) cc_final: 0.7927 (ptp) REVERT: G 78 TYR cc_start: 0.8886 (t80) cc_final: 0.8641 (t80) REVERT: G 87 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8510 (mp) REVERT: G 102 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7823 (mm-30) REVERT: G 107 GLN cc_start: 0.8283 (tp40) cc_final: 0.7848 (tm-30) REVERT: H 54 MET cc_start: 0.6750 (ppp) cc_final: 0.6346 (pp-130) REVERT: H 79 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7034 (tmt170) REVERT: H 81 SER cc_start: 0.8902 (t) cc_final: 0.8595 (m) REVERT: H 117 ARG cc_start: 0.4080 (OUTLIER) cc_final: 0.1765 (mmm-85) REVERT: I 315 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8674 (mtmm) REVERT: J 84 GLU cc_start: 0.7731 (pp20) cc_final: 0.6758 (pp20) REVERT: J 114 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.8041 (mt0) outliers start: 42 outliers final: 27 residues processed: 214 average time/residue: 1.1969 time to fit residues: 272.6552 Evaluate side-chains 224 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 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 154 MET Chi-restraints excluded: chain I residue 155 ASP 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 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 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 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 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 60 optimal weight: 1.9990 chunk 6 optimal weight: 0.0170 chunk 15 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 110 GLN I 220 HIS J 189 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.174867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.150878 restraints weight = 11987.807| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 1.83 r_work: 0.3787 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8687 Z= 0.208 Angle : 0.696 11.084 11640 Z= 0.341 Chirality : 0.042 0.180 1241 Planarity : 0.004 0.047 1431 Dihedral : 14.914 87.812 1626 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.14 % Allowed : 30.70 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.28), residues: 997 helix: 1.48 (0.27), residues: 376 sheet: 0.10 (0.27), residues: 396 loop : -1.53 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 57 HIS 0.004 0.001 HIS J 271 PHE 0.025 0.001 PHE B 31 TYR 0.022 0.001 TYR J 275 ARG 0.007 0.000 ARG D 60 *********************** 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 238 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 195 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 LYS cc_start: 0.8097 (tttp) cc_final: 0.5962 (ttpt) REVERT: C 43 ARG cc_start: 0.8016 (tmt-80) cc_final: 0.7808 (ptm-80) REVERT: C 49 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7726 (mp) REVERT: F 34 LEU cc_start: 0.9138 (mt) cc_final: 0.8794 (mt) REVERT: G 76 LYS cc_start: 0.8008 (mptm) cc_final: 0.7372 (mmtt) REVERT: G 77 MET cc_start: 0.8279 (ptt) cc_final: 0.7936 (ptp) REVERT: G 78 TYR cc_start: 0.8885 (t80) cc_final: 0.8649 (t80) REVERT: G 87 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8510 (mp) REVERT: G 102 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7799 (mm-30) REVERT: G 107 GLN cc_start: 0.8292 (tp40) cc_final: 0.7881 (tm-30) REVERT: H 54 MET cc_start: 0.6678 (ppp) cc_final: 0.6271 (pp-130) REVERT: H 77 MET cc_start: 0.6935 (ptt) cc_final: 0.6133 (tpp) REVERT: H 79 ARG cc_start: 0.8037 (tpt170) cc_final: 0.7158 (tmt170) REVERT: H 81 SER cc_start: 0.8886 (t) cc_final: 0.8579 (m) REVERT: H 117 ARG cc_start: 0.4102 (OUTLIER) cc_final: 0.1824 (mmm-85) REVERT: I 267 GLN cc_start: 0.7227 (tp40) cc_final: 0.6750 (tm-30) REVERT: I 315 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8676 (mtmm) REVERT: J 84 GLU cc_start: 0.7783 (pp20) cc_final: 0.6750 (pp20) REVERT: J 114 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7965 (mt0) REVERT: J 180 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8768 (t) REVERT: J 348 ARG cc_start: 0.8268 (tpt90) cc_final: 0.7769 (tpp80) outliers start: 43 outliers final: 28 residues processed: 219 average time/residue: 1.1054 time to fit residues: 258.4157 Evaluate side-chains 224 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 93 MET 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 235 LEU 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 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 72 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 53 optimal weight: 0.0870 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 110 GLN I 220 HIS J 189 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.175291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.151495 restraints weight = 11869.025| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 1.82 r_work: 0.3796 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8687 Z= 0.196 Angle : 0.711 11.586 11640 Z= 0.346 Chirality : 0.042 0.179 1241 Planarity : 0.004 0.045 1431 Dihedral : 14.762 87.481 1624 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.30 % Allowed : 31.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.28), residues: 997 helix: 1.57 (0.27), residues: 376 sheet: 0.20 (0.26), residues: 406 loop : -1.64 (0.43), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 57 HIS 0.004 0.001 HIS J 271 PHE 0.025 0.001 PHE B 31 TYR 0.022 0.001 TYR J 275 ARG 0.007 0.000 ARG D 60 ********************** 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 233 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 197 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 LYS cc_start: 0.8061 (tttp) cc_final: 0.5940 (ttpt) REVERT: C 38 ARG cc_start: 0.5389 (OUTLIER) cc_final: 0.4837 (tpp80) REVERT: C 49 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7742 (mp) REVERT: F 34 LEU cc_start: 0.9125 (mt) cc_final: 0.8800 (mt) REVERT: G 76 LYS cc_start: 0.7995 (mptm) cc_final: 0.7362 (mmtt) REVERT: G 77 MET cc_start: 0.8258 (ptt) cc_final: 0.7913 (ptp) REVERT: G 78 TYR cc_start: 0.8863 (t80) cc_final: 0.8625 (t80) REVERT: G 87 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8508 (mp) REVERT: G 107 GLN cc_start: 0.8318 (tp40) cc_final: 0.8056 (tm-30) REVERT: H 54 MET cc_start: 0.6642 (ppp) cc_final: 0.6238 (pp-130) REVERT: H 77 MET cc_start: 0.6918 (ptt) cc_final: 0.6107 (tpp) REVERT: H 79 ARG cc_start: 0.8027 (tpt170) cc_final: 0.7161 (tmt170) REVERT: H 81 SER cc_start: 0.8867 (t) cc_final: 0.8552 (m) REVERT: H 117 ARG cc_start: 0.4118 (OUTLIER) cc_final: 0.1823 (mmm-85) REVERT: I 267 GLN cc_start: 0.7201 (tp40) cc_final: 0.6721 (tm-30) REVERT: I 315 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8660 (mtmm) REVERT: J 84 GLU cc_start: 0.7778 (pp20) cc_final: 0.6798 (pp20) REVERT: J 180 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8716 (t) REVERT: J 280 ASP cc_start: 0.8565 (m-30) cc_final: 0.8351 (m-30) REVERT: J 348 ARG cc_start: 0.8240 (tpt90) cc_final: 0.7808 (tpp80) outliers start: 36 outliers final: 26 residues processed: 218 average time/residue: 1.1346 time to fit residues: 263.7095 Evaluate side-chains 222 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 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 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 93 MET Chi-restraints excluded: chain H residue 117 ARG 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 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 J residue 111 ASN Chi-restraints excluded: chain J residue 113 PHE Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 235 LEU 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 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 45 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 110 GLN I 220 HIS J 189 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.174487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.150494 restraints weight = 12142.163| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 1.86 r_work: 0.3780 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8687 Z= 0.226 Angle : 0.716 11.202 11640 Z= 0.351 Chirality : 0.043 0.181 1241 Planarity : 0.004 0.046 1431 Dihedral : 14.759 87.070 1624 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.54 % Allowed : 31.42 % Favored : 64.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.28), residues: 997 helix: 1.51 (0.27), residues: 376 sheet: 0.21 (0.26), residues: 406 loop : -1.63 (0.43), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 57 HIS 0.005 0.001 HIS J 271 PHE 0.028 0.001 PHE B 31 TYR 0.022 0.001 TYR J 275 ARG 0.007 0.000 ARG D 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8345.52 seconds wall clock time: 147 minutes 23.36 seconds (8843.36 seconds total)