Starting phenix.real_space_refine on Tue Dec 31 04:19:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cl1_16709/12_2024/8cl1_16709.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cl1_16709/12_2024/8cl1_16709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cl1_16709/12_2024/8cl1_16709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cl1_16709/12_2024/8cl1_16709.map" model { file = "/net/cci-nas-00/data/ceres_data/8cl1_16709/12_2024/8cl1_16709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cl1_16709/12_2024/8cl1_16709.cif" } resolution = 3.35 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= 0.002 sd= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5472 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 6660 2.51 5 N 1818 2.21 5 O 1944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10494 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1646 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 103 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, E, G, I, K, D, F, H, J, L Time building chain proxies: 4.65, per 1000 atoms: 0.44 Number of scatterers: 10494 At special positions: 0 Unit cell: (116.25, 108.81, 70.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 1944 8.00 N 1818 7.00 C 6660 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.2 seconds 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2544 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 6 sheets defined 69.2% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 119 Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 175 removed outlier: 3.723A pdb=" N ALA A 174 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.505A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.651A pdb=" N GLY A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'C' and resid 16 through 31 Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 160 through 175 removed outlier: 3.723A pdb=" N ALA C 174 " --> pdb=" O LYS C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 193 removed outlier: 4.505A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.651A pdb=" N GLY C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 219 Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 58 Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 100 through 105 Processing helix chain 'E' and resid 110 through 119 Processing helix chain 'E' and resid 125 through 146 Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 160 through 175 removed outlier: 3.723A pdb=" N ALA E 174 " --> pdb=" O LYS E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 193 removed outlier: 4.505A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.650A pdb=" N GLY E 206 " --> pdb=" O LEU E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 219 Processing helix chain 'G' and resid 16 through 31 Processing helix chain 'G' and resid 35 through 44 Processing helix chain 'G' and resid 48 through 58 Processing helix chain 'G' and resid 62 through 84 Processing helix chain 'G' and resid 100 through 105 Processing helix chain 'G' and resid 110 through 119 Processing helix chain 'G' and resid 125 through 146 Processing helix chain 'G' and resid 149 through 153 Processing helix chain 'G' and resid 160 through 175 removed outlier: 3.723A pdb=" N ALA G 174 " --> pdb=" O LYS G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 193 removed outlier: 4.505A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 removed outlier: 3.651A pdb=" N GLY G 206 " --> pdb=" O LEU G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 219 Processing helix chain 'I' and resid 16 through 31 Processing helix chain 'I' and resid 35 through 44 Processing helix chain 'I' and resid 48 through 58 Processing helix chain 'I' and resid 62 through 84 Processing helix chain 'I' and resid 100 through 105 Processing helix chain 'I' and resid 110 through 119 Processing helix chain 'I' and resid 125 through 146 Processing helix chain 'I' and resid 149 through 153 Processing helix chain 'I' and resid 160 through 175 removed outlier: 3.723A pdb=" N ALA I 174 " --> pdb=" O LYS I 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 193 removed outlier: 4.505A pdb=" N LEU I 190 " --> pdb=" O THR I 186 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL I 191 " --> pdb=" O GLU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 206 removed outlier: 3.651A pdb=" N GLY I 206 " --> pdb=" O LEU I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 219 Processing helix chain 'K' and resid 16 through 31 Processing helix chain 'K' and resid 35 through 44 Processing helix chain 'K' and resid 48 through 58 Processing helix chain 'K' and resid 62 through 84 Processing helix chain 'K' and resid 100 through 105 Processing helix chain 'K' and resid 110 through 119 Processing helix chain 'K' and resid 125 through 146 Processing helix chain 'K' and resid 149 through 153 Processing helix chain 'K' and resid 160 through 175 removed outlier: 3.723A pdb=" N ALA K 174 " --> pdb=" O LYS K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 193 removed outlier: 4.505A pdb=" N LEU K 190 " --> pdb=" O THR K 186 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL K 191 " --> pdb=" O GLU K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 206 removed outlier: 3.650A pdb=" N GLY K 206 " --> pdb=" O LEU K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 219 Processing sheet with id=1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=2, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=3, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=4, first strand: chain 'G' and resid 2 through 4 Processing sheet with id=5, first strand: chain 'I' and resid 2 through 4 Processing sheet with id=6, first strand: chain 'K' and resid 2 through 4 648 hydrogen bonds defined for protein. 1908 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: 2.83 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1776 1.29 - 1.42: 2508 1.42 - 1.55: 6312 1.55 - 1.68: 18 1.68 - 1.81: 132 Bond restraints: 10746 Sorted by residual: bond pdb=" CA ALA I 177 " pdb=" C ALA I 177 " ideal model delta sigma weight residual 1.525 1.428 0.097 1.28e-02 6.10e+03 5.74e+01 bond pdb=" CA ALA C 177 " pdb=" C ALA C 177 " ideal model delta sigma weight residual 1.525 1.428 0.097 1.28e-02 6.10e+03 5.74e+01 bond pdb=" CA ALA G 177 " pdb=" C ALA G 177 " ideal model delta sigma weight residual 1.525 1.428 0.097 1.28e-02 6.10e+03 5.72e+01 bond pdb=" CA ALA A 177 " pdb=" C ALA A 177 " ideal model delta sigma weight residual 1.525 1.428 0.097 1.28e-02 6.10e+03 5.72e+01 bond pdb=" CA ALA E 177 " pdb=" C ALA E 177 " ideal model delta sigma weight residual 1.525 1.428 0.097 1.28e-02 6.10e+03 5.68e+01 ... (remaining 10741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 13266 1.39 - 2.78: 1026 2.78 - 4.17: 276 4.17 - 5.56: 36 5.56 - 6.95: 18 Bond angle restraints: 14622 Sorted by residual: angle pdb=" N ALA C 177 " pdb=" CA ALA C 177 " pdb=" C ALA C 177 " ideal model delta sigma weight residual 110.35 117.30 -6.95 1.36e+00 5.41e-01 2.61e+01 angle pdb=" N ALA I 177 " pdb=" CA ALA I 177 " pdb=" C ALA I 177 " ideal model delta sigma weight residual 110.35 117.30 -6.95 1.36e+00 5.41e-01 2.61e+01 angle pdb=" N ALA K 177 " pdb=" CA ALA K 177 " pdb=" C ALA K 177 " ideal model delta sigma weight residual 110.35 117.29 -6.94 1.36e+00 5.41e-01 2.60e+01 angle pdb=" N ALA E 177 " pdb=" CA ALA E 177 " pdb=" C ALA E 177 " ideal model delta sigma weight residual 110.35 117.29 -6.94 1.36e+00 5.41e-01 2.60e+01 angle pdb=" N ALA G 177 " pdb=" CA ALA G 177 " pdb=" C ALA G 177 " ideal model delta sigma weight residual 110.35 117.25 -6.90 1.36e+00 5.41e-01 2.57e+01 ... (remaining 14617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 6012 15.12 - 30.23: 396 30.23 - 45.35: 96 45.35 - 60.46: 30 60.46 - 75.58: 12 Dihedral angle restraints: 6546 sinusoidal: 2634 harmonic: 3912 Sorted by residual: dihedral pdb=" CA PHE C 32 " pdb=" C PHE C 32 " pdb=" N SER C 33 " pdb=" CA SER C 33 " ideal model delta harmonic sigma weight residual 180.00 149.91 30.09 0 5.00e+00 4.00e-02 3.62e+01 dihedral pdb=" CA PHE I 32 " pdb=" C PHE I 32 " pdb=" N SER I 33 " pdb=" CA SER I 33 " ideal model delta harmonic sigma weight residual 180.00 149.91 30.09 0 5.00e+00 4.00e-02 3.62e+01 dihedral pdb=" CA PHE K 32 " pdb=" C PHE K 32 " pdb=" N SER K 33 " pdb=" CA SER K 33 " ideal model delta harmonic sigma weight residual 180.00 149.92 30.08 0 5.00e+00 4.00e-02 3.62e+01 ... (remaining 6543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1452 0.084 - 0.167: 162 0.167 - 0.250: 18 0.250 - 0.334: 0 0.334 - 0.417: 6 Chirality restraints: 1638 Sorted by residual: chirality pdb=" CA ALA C 177 " pdb=" N ALA C 177 " pdb=" C ALA C 177 " pdb=" CB ALA C 177 " both_signs ideal model delta sigma weight residual False 2.48 2.07 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CA ALA I 177 " pdb=" N ALA I 177 " pdb=" C ALA I 177 " pdb=" CB ALA I 177 " both_signs ideal model delta sigma weight residual False 2.48 2.07 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CA ALA K 177 " pdb=" N ALA K 177 " pdb=" C ALA K 177 " pdb=" CB ALA K 177 " both_signs ideal model delta sigma weight residual False 2.48 2.07 0.41 2.00e-01 2.50e+01 4.30e+00 ... (remaining 1635 not shown) Planarity restraints: 1902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU I 175 " 0.015 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C GLU I 175 " -0.050 2.00e-02 2.50e+03 pdb=" O GLU I 175 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN I 176 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 175 " 0.015 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C GLU A 175 " -0.050 2.00e-02 2.50e+03 pdb=" O GLU A 175 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN A 176 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 175 " -0.015 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C GLU G 175 " 0.050 2.00e-02 2.50e+03 pdb=" O GLU G 175 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN G 176 " -0.017 2.00e-02 2.50e+03 ... (remaining 1899 not shown) Histogram of nonbonded interaction distances: 0.65 - 1.50: 12 1.50 - 2.35: 78 2.35 - 3.20: 10164 3.20 - 4.05: 27452 4.05 - 4.90: 49618 Warning: very small nonbonded interaction distances. Nonbonded interactions: 87324 Sorted by model distance: nonbonded pdb=" NE2 GLN H 319 " pdb=" OE1 GLN I 179 " model vdw 0.646 3.120 nonbonded pdb=" NE2 GLN B 319 " pdb=" OE1 GLN C 179 " model vdw 0.646 3.120 nonbonded pdb=" NE2 GLN J 319 " pdb=" OE1 GLN K 179 " model vdw 0.646 3.120 nonbonded pdb=" NE2 GLN D 319 " pdb=" OE1 GLN E 179 " model vdw 0.646 3.120 nonbonded pdb=" OE1 GLN A 179 " pdb=" NE2 GLN L 319 " model vdw 0.647 3.120 ... (remaining 87319 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 23.370 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 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 : 0.008 0.097 10746 Z= 0.517 Angle : 0.929 6.951 14622 Z= 0.576 Chirality : 0.059 0.417 1638 Planarity : 0.008 0.055 1902 Dihedral : 12.178 75.578 4002 Min Nonbonded Distance : 0.646 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.90 % Allowed : 0.00 % Favored : 99.10 % Rotamer: Outliers : 0.54 % Allowed : 0.00 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -1.05 (0.20), residues: 1326 helix: -0.93 (0.14), residues: 870 sheet: -3.06 (0.31), residues: 54 loop : 0.80 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP E 23 HIS 0.008 0.002 HIS C 84 PHE 0.014 0.003 PHE B 321 TYR 0.026 0.006 TYR C 145 ARG 0.015 0.002 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 226 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.7951 (tpt) cc_final: 0.7734 (tpp) REVERT: A 75 GLU cc_start: 0.7905 (pt0) cc_final: 0.7666 (pt0) REVERT: C 39 MET cc_start: 0.7700 (tpt) cc_final: 0.7151 (tpp) REVERT: G 39 MET cc_start: 0.7952 (tpt) cc_final: 0.7732 (tpp) REVERT: G 75 GLU cc_start: 0.7907 (pt0) cc_final: 0.7669 (pt0) REVERT: I 39 MET cc_start: 0.7691 (tpt) cc_final: 0.7151 (tpp) outliers start: 6 outliers final: 2 residues processed: 226 average time/residue: 0.2801 time to fit residues: 84.0977 Evaluate side-chains 142 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain G residue 176 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 119 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN C 74 ASN E 74 ASN G 74 ASN I 74 ASN K 74 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10746 Z= 0.241 Angle : 0.633 7.194 14622 Z= 0.333 Chirality : 0.043 0.151 1638 Planarity : 0.006 0.043 1902 Dihedral : 5.323 50.265 1434 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.90 % Allowed : 0.45 % Favored : 98.64 % Rotamer: Outliers : 0.90 % Allowed : 3.58 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.16 (0.22), residues: 1326 helix: 1.02 (0.17), residues: 876 sheet: -1.84 (0.35), residues: 54 loop : 0.92 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 117 HIS 0.002 0.001 HIS E 62 PHE 0.006 0.001 PHE D 321 TYR 0.010 0.002 TYR I 145 ARG 0.005 0.001 ARG I 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 GLN cc_start: 0.6544 (OUTLIER) cc_final: 0.6271 (pt0) REVERT: C 39 MET cc_start: 0.7453 (tpt) cc_final: 0.6686 (tpp) REVERT: E 66 MET cc_start: 0.8002 (mmt) cc_final: 0.7436 (mmt) REVERT: G 176 GLN cc_start: 0.6540 (OUTLIER) cc_final: 0.6269 (pt0) REVERT: I 39 MET cc_start: 0.7458 (tpt) cc_final: 0.6687 (tpp) REVERT: K 66 MET cc_start: 0.8002 (mmt) cc_final: 0.7436 (mmt) outliers start: 10 outliers final: 0 residues processed: 184 average time/residue: 0.2696 time to fit residues: 66.9970 Evaluate side-chains 168 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 166 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain G residue 176 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 129 optimal weight: 0.0980 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN E 179 GLN G 179 GLN ** H 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 179 GLN K 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10746 Z= 0.281 Angle : 0.603 6.866 14622 Z= 0.312 Chirality : 0.042 0.158 1638 Planarity : 0.006 0.043 1902 Dihedral : 5.008 47.648 1434 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.36 % Favored : 98.19 % Rotamer: Outliers : 1.43 % Allowed : 5.73 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.48 (0.23), residues: 1326 helix: 1.21 (0.17), residues: 870 sheet: -1.38 (0.39), residues: 54 loop : 1.13 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 117 HIS 0.003 0.001 HIS K 12 PHE 0.006 0.001 PHE G 32 TYR 0.008 0.001 TYR I 169 ARG 0.003 0.001 ARG I 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8583 (mttt) cc_final: 0.7985 (mttm) REVERT: C 25 LYS cc_start: 0.8505 (mttt) cc_final: 0.8062 (mttm) REVERT: C 39 MET cc_start: 0.7444 (tpt) cc_final: 0.6880 (tpp) REVERT: G 25 LYS cc_start: 0.8590 (mttt) cc_final: 0.7988 (mttm) REVERT: I 25 LYS cc_start: 0.8503 (mttt) cc_final: 0.8059 (mttm) REVERT: I 39 MET cc_start: 0.7445 (tpt) cc_final: 0.6881 (tpp) outliers start: 16 outliers final: 12 residues processed: 179 average time/residue: 0.2540 time to fit residues: 62.4190 Evaluate side-chains 173 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain I residue 176 GLN Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 0.0770 chunk 80 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 overall best weight: 0.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10746 Z= 0.238 Angle : 0.567 6.927 14622 Z= 0.292 Chirality : 0.041 0.152 1638 Planarity : 0.005 0.046 1902 Dihedral : 4.841 48.519 1434 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.66 % Favored : 97.89 % Rotamer: Outliers : 1.43 % Allowed : 7.35 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.69 (0.23), residues: 1326 helix: 1.35 (0.17), residues: 870 sheet: -0.79 (0.46), residues: 54 loop : 1.20 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 117 HIS 0.003 0.001 HIS A 12 PHE 0.006 0.001 PHE E 32 TYR 0.008 0.001 TYR C 169 ARG 0.003 0.000 ARG I 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8441 (mttt) cc_final: 0.8101 (mttm) REVERT: A 39 MET cc_start: 0.7421 (tpp) cc_final: 0.6765 (tpp) REVERT: C 117 TRP cc_start: 0.6249 (m-10) cc_final: 0.6006 (m-10) REVERT: G 25 LYS cc_start: 0.8441 (mttt) cc_final: 0.8099 (mttm) REVERT: G 39 MET cc_start: 0.7418 (tpp) cc_final: 0.6763 (tpp) REVERT: I 117 TRP cc_start: 0.6247 (m-10) cc_final: 0.5999 (m-10) outliers start: 16 outliers final: 9 residues processed: 172 average time/residue: 0.2534 time to fit residues: 59.7561 Evaluate side-chains 165 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain I residue 176 GLN Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.8980 chunk 1 optimal weight: 0.4980 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10746 Z= 0.247 Angle : 0.568 6.920 14622 Z= 0.293 Chirality : 0.041 0.153 1638 Planarity : 0.005 0.048 1902 Dihedral : 4.781 48.558 1434 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.66 % Favored : 97.89 % Rotamer: Outliers : 1.79 % Allowed : 7.53 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.78 (0.23), residues: 1326 helix: 1.41 (0.18), residues: 870 sheet: -0.76 (0.54), residues: 54 loop : 1.26 (0.34), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 117 HIS 0.003 0.001 HIS E 12 PHE 0.007 0.001 PHE K 32 TYR 0.008 0.001 TYR C 169 ARG 0.003 0.000 ARG I 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.7405 (tpp) cc_final: 0.6791 (tpp) REVERT: A 82 ARG cc_start: 0.6778 (ttm170) cc_final: 0.6493 (ttm170) REVERT: C 117 TRP cc_start: 0.6230 (m-10) cc_final: 0.5934 (m-10) REVERT: C 144 MET cc_start: 0.8018 (tpp) cc_final: 0.7803 (tpp) REVERT: G 39 MET cc_start: 0.7405 (tpp) cc_final: 0.6788 (tpp) REVERT: G 82 ARG cc_start: 0.6779 (ttm170) cc_final: 0.6495 (ttm170) REVERT: I 117 TRP cc_start: 0.6229 (m-10) cc_final: 0.5927 (m-10) REVERT: I 144 MET cc_start: 0.8020 (tpp) cc_final: 0.7803 (tpp) outliers start: 20 outliers final: 14 residues processed: 172 average time/residue: 0.2517 time to fit residues: 59.0979 Evaluate side-chains 186 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain I residue 176 GLN Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 2.9990 chunk 25 optimal weight: 0.0670 chunk 74 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 127 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 123 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10746 Z= 0.213 Angle : 0.557 7.034 14622 Z= 0.288 Chirality : 0.040 0.145 1638 Planarity : 0.005 0.048 1902 Dihedral : 4.727 50.163 1434 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.36 % Favored : 98.19 % Rotamer: Outliers : 1.61 % Allowed : 8.42 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.87 (0.23), residues: 1326 helix: 1.50 (0.18), residues: 870 sheet: -0.66 (0.57), residues: 54 loop : 1.25 (0.34), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 117 HIS 0.002 0.001 HIS K 12 PHE 0.007 0.001 PHE E 32 TYR 0.008 0.001 TYR I 169 ARG 0.003 0.000 ARG I 154 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.7383 (tpp) cc_final: 0.6812 (tpp) REVERT: A 82 ARG cc_start: 0.6885 (ttm170) cc_final: 0.6617 (ttm170) REVERT: A 113 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6432 (tt0) REVERT: C 117 TRP cc_start: 0.6162 (m-10) cc_final: 0.5774 (m-10) REVERT: G 39 MET cc_start: 0.7382 (tpp) cc_final: 0.6811 (tpp) REVERT: G 82 ARG cc_start: 0.6884 (ttm170) cc_final: 0.6616 (ttm170) REVERT: G 113 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6434 (tt0) REVERT: I 117 TRP cc_start: 0.6162 (m-10) cc_final: 0.5782 (m-10) outliers start: 18 outliers final: 14 residues processed: 179 average time/residue: 0.2581 time to fit residues: 63.7012 Evaluate side-chains 165 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10746 Z= 0.256 Angle : 0.563 6.956 14622 Z= 0.293 Chirality : 0.041 0.152 1638 Planarity : 0.005 0.051 1902 Dihedral : 4.727 50.550 1434 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.66 % Favored : 97.89 % Rotamer: Outliers : 2.33 % Allowed : 8.06 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.93 (0.24), residues: 1326 helix: 1.49 (0.18), residues: 864 sheet: -0.55 (0.60), residues: 54 loop : 1.39 (0.34), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 23 HIS 0.003 0.001 HIS K 12 PHE 0.007 0.001 PHE K 32 TYR 0.007 0.001 TYR C 169 ARG 0.003 0.000 ARG I 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.7408 (tpp) cc_final: 0.6874 (tpp) REVERT: A 82 ARG cc_start: 0.6864 (ttm170) cc_final: 0.6609 (ttm170) REVERT: C 117 TRP cc_start: 0.6140 (m-10) cc_final: 0.5851 (m-10) REVERT: G 39 MET cc_start: 0.7415 (tpp) cc_final: 0.6878 (tpp) REVERT: G 82 ARG cc_start: 0.6864 (ttm170) cc_final: 0.6608 (ttm170) REVERT: G 185 MET cc_start: 0.8070 (mtm) cc_final: 0.7863 (mtt) REVERT: I 117 TRP cc_start: 0.6143 (m-10) cc_final: 0.5859 (m-10) REVERT: K 185 MET cc_start: 0.8130 (mtm) cc_final: 0.7928 (mtt) outliers start: 26 outliers final: 22 residues processed: 160 average time/residue: 0.2630 time to fit residues: 57.0721 Evaluate side-chains 182 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain I residue 176 GLN Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 11 optimal weight: 0.2980 chunk 100 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 121 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10746 Z= 0.204 Angle : 0.537 7.045 14622 Z= 0.279 Chirality : 0.040 0.142 1638 Planarity : 0.005 0.051 1902 Dihedral : 4.632 52.119 1434 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.51 % Favored : 98.04 % Rotamer: Outliers : 1.97 % Allowed : 8.51 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.99 (0.23), residues: 1326 helix: 1.55 (0.17), residues: 864 sheet: -0.27 (0.61), residues: 54 loop : 1.35 (0.34), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 23 HIS 0.002 0.000 HIS E 12 PHE 0.007 0.001 PHE K 32 TYR 0.008 0.001 TYR K 169 ARG 0.003 0.000 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.7391 (tpp) cc_final: 0.6843 (tpp) REVERT: A 82 ARG cc_start: 0.6877 (ttm170) cc_final: 0.6603 (ttm170) REVERT: A 113 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6536 (tt0) REVERT: G 39 MET cc_start: 0.7387 (tpp) cc_final: 0.6832 (tpp) REVERT: G 82 ARG cc_start: 0.6865 (ttm170) cc_final: 0.6604 (ttm170) REVERT: G 113 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6533 (tt0) REVERT: G 185 MET cc_start: 0.8021 (mtm) cc_final: 0.7804 (mtt) outliers start: 22 outliers final: 15 residues processed: 164 average time/residue: 0.2631 time to fit residues: 58.7241 Evaluate side-chains 169 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 125 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10746 Z= 0.255 Angle : 0.562 6.901 14622 Z= 0.292 Chirality : 0.041 0.151 1638 Planarity : 0.005 0.053 1902 Dihedral : 4.636 52.570 1434 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.45 % Allowed : 2.04 % Favored : 97.51 % Rotamer: Outliers : 1.88 % Allowed : 8.87 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.91 (0.23), residues: 1326 helix: 1.49 (0.18), residues: 864 sheet: -0.31 (0.62), residues: 54 loop : 1.30 (0.34), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 23 HIS 0.003 0.001 HIS K 12 PHE 0.008 0.001 PHE E 32 TYR 0.007 0.001 TYR E 169 ARG 0.005 0.000 ARG E 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.7420 (tpp) cc_final: 0.6887 (tpp) REVERT: A 82 ARG cc_start: 0.6857 (ttm170) cc_final: 0.6632 (ttm170) REVERT: A 113 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6521 (tt0) REVERT: A 185 MET cc_start: 0.8075 (mtm) cc_final: 0.7851 (mtt) REVERT: E 39 MET cc_start: 0.7158 (tpp) cc_final: 0.6870 (mmt) REVERT: E 185 MET cc_start: 0.8105 (mtm) cc_final: 0.7873 (mtt) REVERT: G 82 ARG cc_start: 0.6862 (ttm170) cc_final: 0.6640 (ttm170) REVERT: G 113 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6516 (tt0) REVERT: K 39 MET cc_start: 0.7175 (tpp) cc_final: 0.6882 (mmt) outliers start: 21 outliers final: 19 residues processed: 171 average time/residue: 0.2563 time to fit residues: 59.6861 Evaluate side-chains 167 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 200 THR Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.2980 chunk 87 optimal weight: 0.2980 chunk 131 optimal weight: 0.3980 chunk 121 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 176 GLN I 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10746 Z= 0.193 Angle : 0.534 7.000 14622 Z= 0.278 Chirality : 0.040 0.138 1638 Planarity : 0.005 0.052 1902 Dihedral : 4.537 54.928 1434 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.43 % Favored : 98.11 % Rotamer: Outliers : 1.88 % Allowed : 9.05 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.98 (0.23), residues: 1326 helix: 1.56 (0.17), residues: 864 sheet: -0.12 (0.62), residues: 54 loop : 1.27 (0.34), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 23 HIS 0.002 0.000 HIS E 12 PHE 0.009 0.001 PHE K 32 TYR 0.008 0.001 TYR E 169 ARG 0.004 0.000 ARG K 154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.7377 (tpp) cc_final: 0.6828 (tpp) REVERT: A 82 ARG cc_start: 0.6843 (ttm170) cc_final: 0.6632 (ttm170) REVERT: A 185 MET cc_start: 0.8030 (mtm) cc_final: 0.7818 (mtt) REVERT: E 39 MET cc_start: 0.7144 (tpp) cc_final: 0.6820 (mmt) REVERT: E 185 MET cc_start: 0.8066 (mtm) cc_final: 0.7843 (mtt) REVERT: G 82 ARG cc_start: 0.6853 (ttm170) cc_final: 0.6623 (ttm170) REVERT: K 39 MET cc_start: 0.7151 (tpp) cc_final: 0.6822 (mmt) REVERT: K 185 MET cc_start: 0.8116 (mtm) cc_final: 0.7889 (mtt) outliers start: 21 outliers final: 19 residues processed: 159 average time/residue: 0.2697 time to fit residues: 58.3625 Evaluate side-chains 163 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 200 THR Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 104 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 75 optimal weight: 0.0770 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.188382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.153965 restraints weight = 10782.510| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.85 r_work: 0.3430 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10746 Z= 0.200 Angle : 0.540 6.898 14622 Z= 0.281 Chirality : 0.040 0.138 1638 Planarity : 0.005 0.052 1902 Dihedral : 4.507 57.730 1434 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.96 % Favored : 97.59 % Rotamer: Outliers : 1.88 % Allowed : 9.05 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.96 (0.23), residues: 1326 helix: 1.57 (0.17), residues: 864 sheet: -0.07 (0.62), residues: 54 loop : 1.18 (0.34), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 23 HIS 0.002 0.000 HIS E 12 PHE 0.009 0.001 PHE K 32 TYR 0.008 0.001 TYR E 169 ARG 0.004 0.000 ARG K 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2278.38 seconds wall clock time: 42 minutes 43.24 seconds (2563.24 seconds total)