Starting phenix.real_space_refine on Fri Jun 13 06:32:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cl1_16709/06_2025/8cl1_16709.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cl1_16709/06_2025/8cl1_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_16709/06_2025/8cl1_16709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cl1_16709/06_2025/8cl1_16709.map" model { file = "/net/cci-nas-00/data/ceres_data/8cl1_16709/06_2025/8cl1_16709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cl1_16709/06_2025/8cl1_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-5710/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: 4.37, per 1000 atoms: 0.42 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: 2.67 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: 0.94 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: 2.86 Time building geometry restraints manager: 3.16 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: 0.08 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.440 Find NCS groups from input model: 0.210 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.470 ------------------------------------------------------------------------------- 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 : 0.026 1.037 10752 Z= 2.503 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 Details of bonding type rmsd hydrogen bonds : bond 0.10318 ( 648) hydrogen bonds : angle 6.60367 ( 1908) covalent geometry : bond 0.00784 (10746) covalent geometry : angle 0.92891 (14622) Misc. bond : bond 1.03695 ( 6) *********************** 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 : 1.041 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: 0.2583 time to fit residues: 77.6041 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 : 1.035 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.202592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.168946 restraints weight = 10399.178| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 1.82 r_work: 0.3886 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3718 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 10752 Z= 0.156 Angle : 0.633 7.194 14622 Z= 0.333 Chirality : 0.043 0.151 1638 Planarity : 0.006 0.043 1902 Dihedral : 5.323 50.264 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 Details of bonding type rmsd hydrogen bonds : bond 0.04167 ( 648) hydrogen bonds : angle 4.42284 ( 1908) covalent geometry : bond 0.00372 (10746) covalent geometry : angle 0.63318 (14622) Misc. bond : bond 0.00132 ( 6) *********************** 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 : 1.179 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: 0.6905 (OUTLIER) cc_final: 0.6532 (pt0) REVERT: C 39 MET cc_start: 0.7947 (tpt) cc_final: 0.7315 (tpp) REVERT: C 176 GLN cc_start: 0.7245 (pt0) cc_final: 0.6939 (pm20) REVERT: E 66 MET cc_start: 0.8225 (mmt) cc_final: 0.7711 (mmt) REVERT: E 187 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6893 (mp0) REVERT: G 176 GLN cc_start: 0.6902 (OUTLIER) cc_final: 0.6528 (pt0) REVERT: I 39 MET cc_start: 0.7917 (tpt) cc_final: 0.7306 (tpp) REVERT: I 176 GLN cc_start: 0.7330 (pt0) cc_final: 0.7016 (pm20) REVERT: K 66 MET cc_start: 0.8184 (mmt) cc_final: 0.7653 (mmt) REVERT: K 187 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6873 (mp0) outliers start: 10 outliers final: 0 residues processed: 184 average time/residue: 0.2587 time to fit residues: 64.3703 Evaluate side-chains 170 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 166 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain K residue 187 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 0 optimal weight: 8.9990 chunk 117 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 131 optimal weight: 0.3980 chunk 102 optimal weight: 0.0870 chunk 75 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 chunk 105 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN C 179 GLN E 179 GLN G 179 GLN I 179 GLN K 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.191212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.156826 restraints weight = 10769.852| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.80 r_work: 0.3467 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10752 Z= 0.129 Angle : 0.558 6.724 14622 Z= 0.287 Chirality : 0.040 0.142 1638 Planarity : 0.005 0.043 1902 Dihedral : 4.894 49.131 1434 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.51 % Favored : 98.04 % Rotamer: Outliers : 1.43 % Allowed : 5.20 % Favored : 93.37 % 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: 1.60 (0.22), residues: 1326 helix: 1.33 (0.17), residues: 870 sheet: -1.25 (0.37), residues: 54 loop : 1.11 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 117 HIS 0.002 0.000 HIS A 12 PHE 0.006 0.001 PHE E 32 TYR 0.007 0.001 TYR K 169 ARG 0.004 0.000 ARG C 143 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 648) hydrogen bonds : angle 4.12714 ( 1908) covalent geometry : bond 0.00299 (10746) covalent geometry : angle 0.55752 (14622) Misc. bond : bond 0.00022 ( 6) *********************** 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 191 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 1.100 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: 0.8212 (mttt) cc_final: 0.7988 (mttm) REVERT: A 39 MET cc_start: 0.7825 (tpp) cc_final: 0.7306 (tpp) REVERT: A 176 GLN cc_start: 0.6654 (OUTLIER) cc_final: 0.6297 (pt0) REVERT: C 39 MET cc_start: 0.7664 (tpt) cc_final: 0.7216 (tpp) REVERT: G 25 LYS cc_start: 0.8293 (mttt) cc_final: 0.8048 (mttm) REVERT: G 39 MET cc_start: 0.7870 (tpp) cc_final: 0.7350 (tpp) REVERT: G 176 GLN cc_start: 0.6663 (OUTLIER) cc_final: 0.6311 (pt0) REVERT: I 39 MET cc_start: 0.7683 (tpt) cc_final: 0.7227 (tpp) outliers start: 16 outliers final: 4 residues processed: 187 average time/residue: 0.2470 time to fit residues: 63.3377 Evaluate side-chains 161 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 155 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 212 GLU 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 94 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 5 optimal weight: 0.0270 chunk 17 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 104 optimal weight: 0.0970 chunk 50 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.4636 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.189447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.154268 restraints weight = 10732.938| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.84 r_work: 0.3437 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10752 Z= 0.129 Angle : 0.552 6.901 14622 Z= 0.284 Chirality : 0.040 0.140 1638 Planarity : 0.005 0.046 1902 Dihedral : 4.761 47.892 1434 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.06 % Favored : 98.49 % Rotamer: Outliers : 0.90 % Allowed : 7.35 % Favored : 91.76 % 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: 1.84 (0.23), residues: 1326 helix: 1.50 (0.17), residues: 870 sheet: -0.88 (0.47), residues: 54 loop : 1.19 (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 K 32 TYR 0.007 0.001 TYR C 169 ARG 0.003 0.000 ARG K 143 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 648) hydrogen bonds : angle 4.07460 ( 1908) covalent geometry : bond 0.00304 (10746) covalent geometry : angle 0.55238 (14622) Misc. bond : bond 0.00020 ( 6) *********************** 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: 10 poor density : 170 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 176 average time/residue: 0.2507 time to fit residues: 60.1913 Evaluate side-chains 164 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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 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 K residue 212 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 13 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 0.0980 chunk 108 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 9 optimal weight: 0.0010 chunk 55 optimal weight: 0.2980 chunk 83 optimal weight: 0.9980 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.190558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.155524 restraints weight = 10706.922| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.86 r_work: 0.3444 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10752 Z= 0.120 Angle : 0.542 7.045 14622 Z= 0.279 Chirality : 0.039 0.135 1638 Planarity : 0.005 0.047 1902 Dihedral : 4.675 49.252 1434 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.36 % Favored : 98.19 % Rotamer: Outliers : 1.25 % Allowed : 8.24 % Favored : 90.50 % 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 (0.23), residues: 1326 helix: 1.55 (0.17), residues: 870 sheet: -0.60 (0.54), residues: 54 loop : 1.23 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 117 HIS 0.002 0.000 HIS E 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 Details of bonding type rmsd hydrogen bonds : bond 0.03264 ( 648) hydrogen bonds : angle 4.01849 ( 1908) covalent geometry : bond 0.00278 (10746) covalent geometry : angle 0.54166 (14622) Misc. bond : bond 0.00014 ( 6) *********************** 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 174 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ARG cc_start: 0.7493 (ttm170) cc_final: 0.7168 (ttm170) REVERT: C 117 TRP cc_start: 0.7684 (m-10) cc_final: 0.7195 (m-10) REVERT: G 82 ARG cc_start: 0.7487 (ttm170) cc_final: 0.7162 (ttm170) REVERT: I 117 TRP cc_start: 0.7685 (m-10) cc_final: 0.7198 (m-10) outliers start: 14 outliers final: 8 residues processed: 166 average time/residue: 0.2487 time to fit residues: 56.3754 Evaluate side-chains 160 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 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 K residue 212 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 81 optimal weight: 0.1980 chunk 19 optimal weight: 0.5980 chunk 131 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.188375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.153280 restraints weight = 10819.484| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.85 r_work: 0.3420 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10752 Z= 0.143 Angle : 0.556 6.954 14622 Z= 0.286 Chirality : 0.040 0.142 1638 Planarity : 0.005 0.049 1902 Dihedral : 4.670 46.710 1434 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.36 % Favored : 98.19 % Rotamer: Outliers : 1.61 % Allowed : 8.60 % Favored : 89.78 % 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: 1.95 (0.23), residues: 1326 helix: 1.57 (0.17), residues: 870 sheet: -0.59 (0.56), residues: 54 loop : 1.23 (0.34), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 23 HIS 0.003 0.001 HIS I 12 PHE 0.006 0.001 PHE G 32 TYR 0.008 0.001 TYR C 169 ARG 0.004 0.000 ARG I 154 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 648) hydrogen bonds : angle 4.14210 ( 1908) covalent geometry : bond 0.00343 (10746) covalent geometry : angle 0.55600 (14622) Misc. bond : bond 0.00012 ( 6) *********************** 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 169 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ARG cc_start: 0.7553 (ttm170) cc_final: 0.7223 (ttm170) REVERT: C 117 TRP cc_start: 0.7612 (m-10) cc_final: 0.7186 (m-10) REVERT: G 82 ARG cc_start: 0.7533 (ttm170) cc_final: 0.7203 (ttm170) REVERT: I 117 TRP cc_start: 0.7605 (m-10) cc_final: 0.7183 (m-10) outliers start: 18 outliers final: 13 residues processed: 163 average time/residue: 0.3371 time to fit residues: 75.3084 Evaluate side-chains 158 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 1.214 ------------------------------------------------------------------------------- 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 186 THR Chi-restraints excluded: chain A 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 146 SER Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 186 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 28 optimal weight: 0.0470 chunk 60 optimal weight: 0.3980 chunk 0 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 0.1980 chunk 91 optimal weight: 0.0970 chunk 125 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 overall best weight: 0.2676 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.192171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.157562 restraints weight = 10915.018| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.85 r_work: 0.3469 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10752 Z= 0.110 Angle : 0.525 7.121 14622 Z= 0.269 Chirality : 0.038 0.130 1638 Planarity : 0.005 0.050 1902 Dihedral : 4.584 50.643 1434 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.06 % Favored : 98.49 % Rotamer: Outliers : 1.97 % Allowed : 8.06 % 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: 2.05 (0.23), residues: 1326 helix: 1.67 (0.17), residues: 870 sheet: -0.43 (0.57), residues: 54 loop : 1.20 (0.34), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 23 HIS 0.001 0.000 HIS A 12 PHE 0.007 0.001 PHE E 32 TYR 0.007 0.001 TYR A 169 ARG 0.004 0.000 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 648) hydrogen bonds : angle 4.04242 ( 1908) covalent geometry : bond 0.00250 (10746) covalent geometry : angle 0.52504 (14622) Misc. bond : bond 0.00012 ( 6) *********************** 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 164 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ARG cc_start: 0.7580 (ttm170) cc_final: 0.7311 (ttm170) REVERT: C 117 TRP cc_start: 0.7575 (m-10) cc_final: 0.7232 (m-10) REVERT: G 82 ARG cc_start: 0.7559 (ttm170) cc_final: 0.7284 (ttm170) REVERT: I 117 TRP cc_start: 0.7583 (m-10) cc_final: 0.7247 (m-10) outliers start: 22 outliers final: 15 residues processed: 152 average time/residue: 0.2742 time to fit residues: 56.9031 Evaluate side-chains 153 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 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 212 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 7 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 113 optimal weight: 0.4980 chunk 130 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN C 176 GLN G 176 GLN I 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.194390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.163312 restraints weight = 10807.485| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.73 r_work: 0.3401 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10752 Z= 0.201 Angle : 0.607 6.776 14622 Z= 0.315 Chirality : 0.043 0.158 1638 Planarity : 0.005 0.051 1902 Dihedral : 4.729 49.599 1434 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.45 % Allowed : 2.11 % Favored : 97.44 % Rotamer: Outliers : 1.79 % Allowed : 8.60 % 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: 1.81 (0.24), residues: 1326 helix: 1.44 (0.18), residues: 870 sheet: -0.49 (0.58), residues: 54 loop : 1.23 (0.34), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 23 HIS 0.004 0.001 HIS K 12 PHE 0.006 0.001 PHE A 168 TYR 0.008 0.001 TYR C 169 ARG 0.004 0.000 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 648) hydrogen bonds : angle 4.37275 ( 1908) covalent geometry : bond 0.00498 (10746) covalent geometry : angle 0.60685 (14622) Misc. bond : bond 0.00007 ( 6) *********************** 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 172 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ARG cc_start: 0.7491 (ttm170) cc_final: 0.7282 (ttm170) REVERT: C 68 MET cc_start: 0.7679 (mtt) cc_final: 0.7478 (mtt) REVERT: G 82 ARG cc_start: 0.7500 (ttm170) cc_final: 0.7291 (ttm170) REVERT: I 68 MET cc_start: 0.7671 (mtt) cc_final: 0.7470 (mtt) outliers start: 20 outliers final: 18 residues processed: 164 average time/residue: 0.3073 time to fit residues: 68.6928 Evaluate side-chains 172 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 1.232 ------------------------------------------------------------------------------- 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 186 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 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 186 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 200 THR 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 126 optimal weight: 0.1980 chunk 48 optimal weight: 0.4980 chunk 31 optimal weight: 0.0670 chunk 68 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 131 optimal weight: 0.0070 chunk 81 optimal weight: 2.9990 overall best weight: 0.2936 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.199832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.166329 restraints weight = 10935.680| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.87 r_work: 0.3457 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10752 Z= 0.115 Angle : 0.535 7.076 14622 Z= 0.276 Chirality : 0.039 0.133 1638 Planarity : 0.005 0.050 1902 Dihedral : 4.525 49.405 1434 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.21 % Favored : 98.34 % Rotamer: Outliers : 1.43 % Allowed : 9.32 % 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: 2.04 (0.23), residues: 1326 helix: 1.58 (0.17), residues: 864 sheet: -0.18 (0.60), residues: 54 loop : 1.36 (0.34), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 23 HIS 0.001 0.000 HIS K 12 PHE 0.009 0.001 PHE E 32 TYR 0.007 0.001 TYR A 169 ARG 0.003 0.000 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.03252 ( 648) hydrogen bonds : angle 4.15784 ( 1908) covalent geometry : bond 0.00266 (10746) covalent geometry : angle 0.53530 (14622) Misc. bond : bond 0.00015 ( 6) *********************** 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 160 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ARG cc_start: 0.7604 (ttm170) cc_final: 0.7369 (ttm170) REVERT: A 113 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7286 (tt0) REVERT: C 68 MET cc_start: 0.7611 (mtt) cc_final: 0.7411 (mtt) REVERT: E 39 MET cc_start: 0.7251 (tpp) cc_final: 0.6969 (mmt) REVERT: G 82 ARG cc_start: 0.7586 (ttm170) cc_final: 0.7347 (ttm170) REVERT: G 113 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7241 (tt0) REVERT: I 68 MET cc_start: 0.7594 (mtt) cc_final: 0.7386 (mtt) REVERT: K 39 MET cc_start: 0.7286 (tpp) cc_final: 0.6995 (mmt) outliers start: 16 outliers final: 11 residues processed: 154 average time/residue: 0.2623 time to fit residues: 54.7993 Evaluate side-chains 155 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain E residue 200 THR 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 212 GLU 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: 0.5980 chunk 119 optimal weight: 0.9990 chunk 9 optimal weight: 0.0050 chunk 49 optimal weight: 0.9980 chunk 115 optimal weight: 0.2980 chunk 127 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 overall best weight: 0.3794 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.190586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.155914 restraints weight = 10906.838| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.85 r_work: 0.3449 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10752 Z= 0.121 Angle : 0.552 6.959 14622 Z= 0.284 Chirality : 0.040 0.131 1638 Planarity : 0.005 0.053 1902 Dihedral : 4.477 49.570 1434 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.81 % Favored : 97.74 % Rotamer: Outliers : 1.25 % Allowed : 9.68 % 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: 2.07 (0.23), residues: 1326 helix: 1.63 (0.17), residues: 864 sheet: -0.08 (0.61), residues: 54 loop : 1.31 (0.34), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 23 HIS 0.002 0.000 HIS E 12 PHE 0.008 0.001 PHE E 32 TYR 0.007 0.001 TYR G 169 ARG 0.004 0.000 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.03236 ( 648) hydrogen bonds : angle 4.14051 ( 1908) covalent geometry : bond 0.00284 (10746) covalent geometry : angle 0.55228 (14622) Misc. bond : bond 0.00013 ( 6) ********************** 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 154 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ARG cc_start: 0.7595 (ttm170) cc_final: 0.7380 (ttm170) REVERT: A 113 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7290 (tt0) REVERT: E 39 MET cc_start: 0.7287 (tpp) cc_final: 0.7008 (mmt) REVERT: E 185 MET cc_start: 0.8314 (mtm) cc_final: 0.8062 (mtt) REVERT: G 82 ARG cc_start: 0.7588 (ttm170) cc_final: 0.7370 (ttm170) REVERT: G 113 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7235 (tt0) REVERT: K 39 MET cc_start: 0.7307 (tpp) cc_final: 0.7026 (mmt) REVERT: K 185 MET cc_start: 0.8308 (mtm) cc_final: 0.8052 (mtt) outliers start: 14 outliers final: 11 residues processed: 150 average time/residue: 0.2420 time to fit residues: 49.5418 Evaluate side-chains 150 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain E residue 200 THR 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 212 GLU 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 20 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.188246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.153154 restraints weight = 10819.729| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.85 r_work: 0.3415 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10752 Z= 0.149 Angle : 0.572 7.132 14622 Z= 0.297 Chirality : 0.040 0.139 1638 Planarity : 0.005 0.052 1902 Dihedral : 4.556 52.519 1434 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.96 % Favored : 97.59 % Rotamer: Outliers : 1.43 % Allowed : 9.32 % 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: 2.03 (0.24), residues: 1326 helix: 1.58 (0.18), residues: 864 sheet: -0.04 (0.62), residues: 54 loop : 1.31 (0.34), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 23 HIS 0.002 0.001 HIS E 12 PHE 0.007 0.001 PHE E 32 TYR 0.008 0.001 TYR I 169 ARG 0.004 0.000 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 648) hydrogen bonds : angle 4.25834 ( 1908) covalent geometry : bond 0.00364 (10746) covalent geometry : angle 0.57162 (14622) Misc. bond : bond 0.00014 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4806.88 seconds wall clock time: 84 minutes 47.69 seconds (5087.69 seconds total)