Starting phenix.real_space_refine on Tue Feb 11 09:54:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sax_24958/02_2025/7sax_24958.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sax_24958/02_2025/7sax_24958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sax_24958/02_2025/7sax_24958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sax_24958/02_2025/7sax_24958.map" model { file = "/net/cci-nas-00/data/ceres_data/7sax_24958/02_2025/7sax_24958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sax_24958/02_2025/7sax_24958.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 3431 2.51 5 N 882 2.21 5 O 964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5305 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1627 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 6, 'TRANS': 206} Chain: "B" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1614 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 6, 'TRANS': 204} Chain: "C" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 473 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "D" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 430 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "E" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'TRANS': 49} Chain: "F" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'TRANS': 49} Chain: "G" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'TRANS': 49} Time building chain proxies: 3.68, per 1000 atoms: 0.69 Number of scatterers: 5305 At special positions: 0 Unit cell: (66.56, 58.24, 129.792, 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 28 16.00 O 964 8.00 N 882 7.00 C 3431 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 753.8 milliseconds 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1232 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 78.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 7 through 25 removed outlier: 3.823A pdb=" N ALA A 25 " --> pdb=" O LEU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 69 removed outlier: 5.074A pdb=" N LEU A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU A 68 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 104 Proline residue: A 75 - end of helix removed outlier: 3.592A pdb=" N VAL A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 88 " --> pdb=" O GLN A 84 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 132 through 153 removed outlier: 3.690A pdb=" N GLU A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 181 Processing helix chain 'A' and resid 185 through 215 removed outlier: 4.253A pdb=" N MET A 215 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 28 removed outlier: 5.295A pdb=" N LEU B 18 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 63 Processing helix chain 'B' and resid 69 through 104 Proline residue: B 75 - end of helix removed outlier: 3.716A pdb=" N LEU B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 128 Processing helix chain 'B' and resid 132 through 153 removed outlier: 3.519A pdb=" N LEU B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 180 Processing helix chain 'B' and resid 185 through 214 Processing helix chain 'C' and resid 10 through 31 removed outlier: 4.013A pdb=" N LEU C 14 " --> pdb=" O GLY C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 58 removed outlier: 3.869A pdb=" N ILE C 40 " --> pdb=" O GLY C 36 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLY C 41 " --> pdb=" O GLU C 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 31 removed outlier: 3.804A pdb=" N LEU D 14 " --> pdb=" O GLY D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 55 removed outlier: 4.277A pdb=" N MET D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY D 55 " --> pdb=" O PHE D 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 31 removed outlier: 3.750A pdb=" N LEU E 14 " --> pdb=" O GLY E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 54 removed outlier: 3.899A pdb=" N GLY E 41 " --> pdb=" O GLU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 57 No H-bonds generated for 'chain 'E' and resid 55 through 57' Processing helix chain 'F' and resid 10 through 31 removed outlier: 4.125A pdb=" N LEU F 14 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE F 15 " --> pdb=" O ILE F 11 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 55 Processing helix chain 'G' and resid 10 through 31 removed outlier: 4.011A pdb=" N LEU G 14 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 55 removed outlier: 4.193A pdb=" N MET G 39 " --> pdb=" O GLY G 35 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY G 41 " --> pdb=" O GLU G 37 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1215 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1709 1.34 - 1.46: 681 1.46 - 1.57: 2938 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 5384 Sorted by residual: bond pdb=" CG1 ILE D 15 " pdb=" CD1 ILE D 15 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.74e+00 bond pdb=" CB MET A 12 " pdb=" CG MET A 12 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.60e+00 bond pdb=" CB MET E 54 " pdb=" CG MET E 54 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.33e+00 bond pdb=" CG1 ILE B 15 " pdb=" CD1 ILE B 15 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.28e+00 bond pdb=" CG1 ILE D 23 " pdb=" CD1 ILE D 23 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.26e+00 ... (remaining 5379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 7162 2.35 - 4.71: 81 4.71 - 7.06: 10 7.06 - 9.41: 1 9.41 - 11.76: 1 Bond angle restraints: 7255 Sorted by residual: angle pdb=" CB MET D 54 " pdb=" CG MET D 54 " pdb=" SD MET D 54 " ideal model delta sigma weight residual 112.70 100.94 11.76 3.00e+00 1.11e-01 1.54e+01 angle pdb=" C ILE E 53 " pdb=" N MET E 54 " pdb=" CA MET E 54 " ideal model delta sigma weight residual 122.31 115.73 6.58 2.00e+00 2.50e-01 1.08e+01 angle pdb=" CB MET E 54 " pdb=" CG MET E 54 " pdb=" SD MET E 54 " ideal model delta sigma weight residual 112.70 103.40 9.30 3.00e+00 1.11e-01 9.62e+00 angle pdb=" C ARG A 11 " pdb=" N MET A 12 " pdb=" CA MET A 12 " ideal model delta sigma weight residual 122.06 116.31 5.75 1.86e+00 2.89e-01 9.55e+00 angle pdb=" CA ARG A 9 " pdb=" CB ARG A 9 " pdb=" CG ARG A 9 " ideal model delta sigma weight residual 114.10 118.91 -4.81 2.00e+00 2.50e-01 5.79e+00 ... (remaining 7250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 2882 17.57 - 35.14: 267 35.14 - 52.71: 38 52.71 - 70.28: 8 70.28 - 87.85: 2 Dihedral angle restraints: 3197 sinusoidal: 1279 harmonic: 1918 Sorted by residual: dihedral pdb=" CA MET E 54 " pdb=" C MET E 54 " pdb=" N GLY E 55 " pdb=" CA GLY E 55 " ideal model delta harmonic sigma weight residual 180.00 157.94 22.06 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA VAL A 115 " pdb=" C VAL A 115 " pdb=" N LYS A 116 " pdb=" CA LYS A 116 " ideal model delta harmonic sigma weight residual 180.00 161.41 18.59 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA MET A 12 " pdb=" C MET A 12 " pdb=" N ILE A 13 " pdb=" CA ILE A 13 " ideal model delta harmonic sigma weight residual 180.00 161.76 18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 3194 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 589 0.043 - 0.086: 234 0.086 - 0.130: 24 0.130 - 0.173: 5 0.173 - 0.216: 2 Chirality restraints: 854 Sorted by residual: chirality pdb=" CB VAL F 22 " pdb=" CA VAL F 22 " pdb=" CG1 VAL F 22 " pdb=" CG2 VAL F 22 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE B 156 " pdb=" CA ILE B 156 " pdb=" CG1 ILE B 156 " pdb=" CG2 ILE B 156 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CA MET E 54 " pdb=" N MET E 54 " pdb=" C MET E 54 " pdb=" CB MET E 54 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.43e-01 ... (remaining 851 not shown) Planarity restraints: 908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 52 " 0.011 2.00e-02 2.50e+03 1.13e-02 2.24e+00 pdb=" CG PHE C 52 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE C 52 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE C 52 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE C 52 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE C 52 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 52 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 12 " 0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" C MET A 12 " -0.021 2.00e-02 2.50e+03 pdb=" O MET A 12 " 0.008 2.00e-02 2.50e+03 pdb=" N ILE A 13 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 9 " 0.005 2.00e-02 2.50e+03 1.04e-02 1.09e+00 pdb=" C ARG A 9 " -0.018 2.00e-02 2.50e+03 pdb=" O ARG A 9 " 0.007 2.00e-02 2.50e+03 pdb=" N GLN A 10 " 0.006 2.00e-02 2.50e+03 ... (remaining 905 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 234 2.72 - 3.26: 5640 3.26 - 3.81: 8814 3.81 - 4.35: 10573 4.35 - 4.90: 18257 Nonbonded interactions: 43518 Sorted by model distance: nonbonded pdb=" NH1 ARG B 9 " pdb=" OE2 GLU C 47 " model vdw 2.174 3.120 nonbonded pdb=" O ALA B 60 " pdb=" OG1 THR B 64 " model vdw 2.232 3.040 nonbonded pdb=" NE2 GLN A 51 " pdb=" OD1 ASP A 55 " model vdw 2.240 3.120 nonbonded pdb=" OG1 THR A 112 " pdb=" OD1 ASP A 114 " model vdw 2.262 3.040 nonbonded pdb=" OE1 GLU A 131 " pdb=" NH1 ARG A 133 " model vdw 2.283 3.120 ... (remaining 43513 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 215) selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 9 through 60) selection = (chain 'D' and resid 9 through 60) } ncs_group { reference = (chain 'E' and resid 9 through 57) selection = (chain 'F' and resid 9 through 57) selection = (chain 'G' and resid 9 through 57) } 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.020 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 5384 Z= 0.469 Angle : 0.660 11.764 7255 Z= 0.344 Chirality : 0.044 0.216 854 Planarity : 0.003 0.018 908 Dihedral : 13.544 87.846 1965 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.22 (0.33), residues: 675 helix: 1.69 (0.23), residues: 507 sheet: None (None), residues: 0 loop : -2.01 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 38 HIS 0.002 0.001 HIS D 32 PHE 0.026 0.002 PHE C 52 TYR 0.017 0.003 TYR A 117 ARG 0.014 0.001 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.625 Fit side-chains REVERT: A 6 GLU cc_start: 0.7621 (pt0) cc_final: 0.7325 (pt0) REVERT: A 10 GLN cc_start: 0.7704 (mt0) cc_final: 0.7308 (mt0) REVERT: A 88 GLN cc_start: 0.7893 (tp40) cc_final: 0.7247 (tm-30) REVERT: A 96 GLU cc_start: 0.7158 (pt0) cc_final: 0.6717 (mt-10) REVERT: B 34 ASP cc_start: 0.7712 (m-30) cc_final: 0.7494 (m-30) REVERT: B 62 ARG cc_start: 0.7276 (ttm-80) cc_final: 0.7042 (mmt-90) REVERT: B 147 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6974 (mt-10) REVERT: B 194 GLU cc_start: 0.7372 (tp30) cc_final: 0.6803 (tp30) REVERT: B 205 SER cc_start: 0.8607 (p) cc_final: 0.8398 (p) REVERT: C 37 GLU cc_start: 0.7341 (mp0) cc_final: 0.7128 (mp0) REVERT: C 54 MET cc_start: 0.7212 (mmm) cc_final: 0.6882 (mmm) REVERT: D 6 LYS cc_start: 0.5783 (ptpp) cc_final: 0.5258 (ptmt) REVERT: F 34 LYS cc_start: 0.8063 (ttpt) cc_final: 0.7592 (tppt) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 1.1847 time to fit residues: 180.4052 Evaluate side-chains 122 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 0.0470 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.139323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.110927 restraints weight = 6119.426| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.69 r_work: 0.3107 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5384 Z= 0.153 Angle : 0.470 6.342 7255 Z= 0.250 Chirality : 0.037 0.151 854 Planarity : 0.003 0.017 908 Dihedral : 4.007 16.181 705 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.59 % Allowed : 12.93 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.29 (0.33), residues: 675 helix: 2.45 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -1.72 (0.49), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 38 HIS 0.012 0.001 HIS A 210 PHE 0.018 0.001 PHE A 61 TYR 0.010 0.002 TYR A 117 ARG 0.003 0.000 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.645 Fit side-chains REVERT: A 6 GLU cc_start: 0.7701 (pt0) cc_final: 0.7448 (pt0) REVERT: A 88 GLN cc_start: 0.8308 (tp40) cc_final: 0.7745 (tm-30) REVERT: A 96 GLU cc_start: 0.7831 (pt0) cc_final: 0.7362 (mt-10) REVERT: A 139 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7392 (pt0) REVERT: A 163 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7273 (mm-30) REVERT: B 62 ARG cc_start: 0.7354 (ttm-80) cc_final: 0.6938 (mmt-90) REVERT: B 147 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7088 (mt-10) REVERT: B 194 GLU cc_start: 0.8082 (tp30) cc_final: 0.7616 (tp30) REVERT: B 209 LYS cc_start: 0.8279 (tttp) cc_final: 0.8011 (ttpm) REVERT: C 54 MET cc_start: 0.7804 (mmm) cc_final: 0.7480 (mmm) REVERT: D 6 LYS cc_start: 0.5600 (ptpp) cc_final: 0.4941 (ptmt) REVERT: F 34 LYS cc_start: 0.8053 (ttpt) cc_final: 0.7628 (tppt) outliers start: 20 outliers final: 6 residues processed: 131 average time/residue: 1.1412 time to fit residues: 156.1296 Evaluate side-chains 126 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain F residue 27 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 47 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.0670 chunk 62 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.140140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.111971 restraints weight = 6233.940| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.71 r_work: 0.3113 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5384 Z= 0.132 Angle : 0.444 7.225 7255 Z= 0.237 Chirality : 0.036 0.158 854 Planarity : 0.002 0.017 908 Dihedral : 3.757 13.895 705 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.59 % Allowed : 15.62 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.63 (0.33), residues: 675 helix: 2.77 (0.22), residues: 512 sheet: None (None), residues: 0 loop : -1.85 (0.47), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 38 HIS 0.008 0.001 HIS A 210 PHE 0.027 0.001 PHE C 52 TYR 0.010 0.002 TYR B 17 ARG 0.002 0.000 ARG B 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.600 Fit side-chains REVERT: A 6 GLU cc_start: 0.7660 (pt0) cc_final: 0.7327 (pt0) REVERT: A 10 GLN cc_start: 0.7695 (mt0) cc_final: 0.7436 (mt0) REVERT: A 88 GLN cc_start: 0.8189 (tp40) cc_final: 0.7649 (tm-30) REVERT: A 163 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7336 (mm-30) REVERT: B 63 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6562 (pm20) REVERT: B 99 THR cc_start: 0.8368 (t) cc_final: 0.8071 (p) REVERT: B 147 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7186 (mt-10) REVERT: B 194 GLU cc_start: 0.8094 (tp30) cc_final: 0.7594 (tp30) REVERT: B 209 LYS cc_start: 0.8375 (tttp) cc_final: 0.8074 (ttpm) REVERT: C 54 MET cc_start: 0.7658 (mmm) cc_final: 0.7340 (mmm) REVERT: D 6 LYS cc_start: 0.5553 (ptpp) cc_final: 0.4885 (ptmt) REVERT: E 47 GLU cc_start: 0.7667 (tp30) cc_final: 0.7249 (tp30) outliers start: 20 outliers final: 5 residues processed: 133 average time/residue: 1.1898 time to fit residues: 164.8404 Evaluate side-chains 126 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain F residue 27 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN B 27 ASN B 177 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.137180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.108949 restraints weight = 6408.090| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.72 r_work: 0.3079 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5384 Z= 0.184 Angle : 0.465 6.623 7255 Z= 0.248 Chirality : 0.037 0.141 854 Planarity : 0.002 0.021 908 Dihedral : 3.799 15.022 705 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 5.21 % Allowed : 15.62 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.63 (0.33), residues: 675 helix: 2.76 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.86 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 38 HIS 0.011 0.002 HIS A 210 PHE 0.026 0.001 PHE C 52 TYR 0.012 0.002 TYR B 17 ARG 0.006 0.001 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.594 Fit side-chains REVERT: A 10 GLN cc_start: 0.7834 (mt0) cc_final: 0.7621 (mt0) REVERT: A 88 GLN cc_start: 0.8237 (tp40) cc_final: 0.7685 (tm-30) REVERT: A 156 ILE cc_start: 0.7175 (tp) cc_final: 0.6798 (tt) REVERT: B 63 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6536 (pm20) REVERT: B 99 THR cc_start: 0.8418 (t) cc_final: 0.8083 (p) REVERT: B 147 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7438 (mt-10) REVERT: B 194 GLU cc_start: 0.8135 (tp30) cc_final: 0.7633 (tp30) REVERT: B 209 LYS cc_start: 0.8423 (tttp) cc_final: 0.8087 (ttpm) REVERT: C 56 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.6618 (t80) REVERT: C 57 MET cc_start: 0.6945 (mmp) cc_final: 0.6710 (ttm) REVERT: D 6 LYS cc_start: 0.5559 (ptpp) cc_final: 0.4824 (ptmt) REVERT: E 47 GLU cc_start: 0.7729 (tp30) cc_final: 0.7237 (tp30) outliers start: 29 outliers final: 10 residues processed: 132 average time/residue: 1.1393 time to fit residues: 156.9872 Evaluate side-chains 133 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain F residue 27 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 9 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.139060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.111741 restraints weight = 6228.918| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.66 r_work: 0.3106 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 5384 Z= 0.146 Angle : 0.457 7.029 7255 Z= 0.242 Chirality : 0.036 0.121 854 Planarity : 0.002 0.022 908 Dihedral : 3.675 14.408 705 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.95 % Allowed : 18.13 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.81 (0.33), residues: 675 helix: 2.89 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.81 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 38 HIS 0.008 0.001 HIS A 210 PHE 0.010 0.001 PHE A 61 TYR 0.010 0.002 TYR B 17 ARG 0.006 0.001 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.551 Fit side-chains REVERT: A 6 GLU cc_start: 0.7581 (pt0) cc_final: 0.7317 (pt0) REVERT: A 10 GLN cc_start: 0.7805 (mt0) cc_final: 0.7544 (mt0) REVERT: A 88 GLN cc_start: 0.8204 (tp40) cc_final: 0.7588 (tm-30) REVERT: A 156 ILE cc_start: 0.7163 (tp) cc_final: 0.6827 (tt) REVERT: B 74 GLN cc_start: 0.7662 (tp40) cc_final: 0.7434 (mm110) REVERT: B 99 THR cc_start: 0.8359 (t) cc_final: 0.8067 (p) REVERT: B 147 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7452 (mt-10) REVERT: B 194 GLU cc_start: 0.8114 (tp30) cc_final: 0.7654 (tp30) REVERT: B 209 LYS cc_start: 0.8445 (tttp) cc_final: 0.8167 (ttpt) REVERT: D 6 LYS cc_start: 0.5514 (ptpp) cc_final: 0.4897 (ptmt) REVERT: D 39 MET cc_start: 0.8602 (mtm) cc_final: 0.8336 (mtp) REVERT: E 47 GLU cc_start: 0.7705 (tp30) cc_final: 0.7217 (tp30) outliers start: 22 outliers final: 6 residues processed: 132 average time/residue: 1.1833 time to fit residues: 163.5175 Evaluate side-chains 127 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain F residue 27 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 27 optimal weight: 0.0470 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 overall best weight: 0.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.138974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.111006 restraints weight = 6227.470| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.71 r_work: 0.3086 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5384 Z= 0.145 Angle : 0.460 6.556 7255 Z= 0.243 Chirality : 0.036 0.126 854 Planarity : 0.002 0.024 908 Dihedral : 3.644 14.647 705 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.13 % Allowed : 19.39 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.87 (0.33), residues: 675 helix: 2.94 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.79 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 38 HIS 0.007 0.001 HIS A 210 PHE 0.028 0.001 PHE C 52 TYR 0.013 0.002 TYR B 17 ARG 0.006 0.001 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.535 Fit side-chains REVERT: A 6 GLU cc_start: 0.7600 (pt0) cc_final: 0.7303 (pt0) REVERT: A 88 GLN cc_start: 0.8170 (tp40) cc_final: 0.7548 (tm-30) REVERT: A 156 ILE cc_start: 0.7168 (tp) cc_final: 0.6819 (tt) REVERT: B 11 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7622 (mtm-85) REVERT: B 63 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6385 (pm20) REVERT: B 99 THR cc_start: 0.8340 (t) cc_final: 0.8048 (p) REVERT: B 147 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7452 (mt-10) REVERT: B 194 GLU cc_start: 0.8132 (tp30) cc_final: 0.7673 (tp30) REVERT: B 209 LYS cc_start: 0.8456 (tttp) cc_final: 0.8175 (ttpt) REVERT: C 56 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.6658 (t80) REVERT: D 6 LYS cc_start: 0.5267 (ptpp) cc_final: 0.4645 (ptmt) REVERT: E 47 GLU cc_start: 0.7718 (tp30) cc_final: 0.7237 (tp30) outliers start: 23 outliers final: 7 residues processed: 133 average time/residue: 1.1131 time to fit residues: 154.8000 Evaluate side-chains 132 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain F residue 27 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 18 optimal weight: 0.0060 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 0.0670 chunk 40 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 10 optimal weight: 0.2980 overall best weight: 0.3134 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.140490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.112810 restraints weight = 6238.479| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.69 r_work: 0.3144 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5384 Z= 0.120 Angle : 0.450 7.081 7255 Z= 0.239 Chirality : 0.036 0.129 854 Planarity : 0.002 0.030 908 Dihedral : 3.504 13.977 705 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.05 % Allowed : 21.01 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.04 (0.33), residues: 675 helix: 3.02 (0.22), residues: 517 sheet: None (None), residues: 0 loop : -1.69 (0.48), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 38 HIS 0.008 0.001 HIS A 210 PHE 0.010 0.001 PHE A 61 TYR 0.011 0.002 TYR B 17 ARG 0.006 0.001 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.618 Fit side-chains REVERT: A 6 GLU cc_start: 0.7455 (pt0) cc_final: 0.7232 (pt0) REVERT: A 88 GLN cc_start: 0.8111 (tp40) cc_final: 0.7438 (tm-30) REVERT: A 96 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7341 (pp20) REVERT: A 156 ILE cc_start: 0.7133 (tp) cc_final: 0.6862 (tt) REVERT: A 163 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: B 11 ARG cc_start: 0.8009 (mtt-85) cc_final: 0.7622 (mtm-85) REVERT: B 48 GLN cc_start: 0.8598 (mt0) cc_final: 0.8391 (mt0) REVERT: B 63 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6314 (pm20) REVERT: B 99 THR cc_start: 0.8322 (t) cc_final: 0.8043 (p) REVERT: B 147 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7440 (mt-10) REVERT: B 154 ASN cc_start: 0.7251 (m-40) cc_final: 0.6791 (m-40) REVERT: B 194 GLU cc_start: 0.8073 (tp30) cc_final: 0.7582 (tp30) REVERT: B 209 LYS cc_start: 0.8421 (tttp) cc_final: 0.8140 (ttpt) REVERT: C 34 LYS cc_start: 0.8248 (tptp) cc_final: 0.8000 (tptt) REVERT: C 54 MET cc_start: 0.7699 (mmm) cc_final: 0.7132 (mmm) REVERT: C 56 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.6602 (t80) REVERT: D 6 LYS cc_start: 0.5229 (ptpp) cc_final: 0.4603 (ptmt) REVERT: D 39 MET cc_start: 0.8539 (mtm) cc_final: 0.8237 (mtp) REVERT: E 47 GLU cc_start: 0.7638 (tp30) cc_final: 0.7157 (tp30) outliers start: 17 outliers final: 7 residues processed: 139 average time/residue: 1.1394 time to fit residues: 165.1334 Evaluate side-chains 136 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain F residue 27 MET Chi-restraints excluded: chain G residue 37 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.140633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.113341 restraints weight = 6281.321| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.62 r_work: 0.3142 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5384 Z= 0.146 Angle : 0.467 7.061 7255 Z= 0.248 Chirality : 0.036 0.133 854 Planarity : 0.002 0.016 908 Dihedral : 3.556 15.171 705 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.23 % Allowed : 21.18 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.02 (0.33), residues: 675 helix: 3.01 (0.22), residues: 517 sheet: None (None), residues: 0 loop : -1.70 (0.48), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 38 HIS 0.009 0.001 HIS A 210 PHE 0.028 0.001 PHE C 52 TYR 0.013 0.002 TYR B 17 ARG 0.003 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.597 Fit side-chains REVERT: A 6 GLU cc_start: 0.7546 (pt0) cc_final: 0.7300 (pt0) REVERT: A 88 GLN cc_start: 0.8031 (tp40) cc_final: 0.7337 (tm-30) REVERT: A 96 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7245 (pp20) REVERT: A 156 ILE cc_start: 0.7103 (tp) cc_final: 0.6838 (tt) REVERT: B 48 GLN cc_start: 0.8512 (mt0) cc_final: 0.8303 (mt0) REVERT: B 63 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6264 (pm20) REVERT: B 99 THR cc_start: 0.8310 (t) cc_final: 0.8006 (p) REVERT: B 147 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7399 (mt-10) REVERT: B 154 ASN cc_start: 0.7292 (m-40) cc_final: 0.6827 (m-40) REVERT: B 194 GLU cc_start: 0.8034 (tp30) cc_final: 0.7566 (tp30) REVERT: B 209 LYS cc_start: 0.8415 (tttp) cc_final: 0.8127 (ttpp) REVERT: C 34 LYS cc_start: 0.8258 (tptp) cc_final: 0.8007 (tptt) REVERT: C 54 MET cc_start: 0.7557 (mmm) cc_final: 0.7064 (mmm) REVERT: C 56 PHE cc_start: 0.7751 (OUTLIER) cc_final: 0.6637 (t80) REVERT: D 6 LYS cc_start: 0.5212 (ptpp) cc_final: 0.4608 (ptmt) REVERT: E 47 GLU cc_start: 0.7652 (tp30) cc_final: 0.7139 (tp30) outliers start: 18 outliers final: 8 residues processed: 133 average time/residue: 1.1188 time to fit residues: 155.6129 Evaluate side-chains 133 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain F residue 27 MET Chi-restraints excluded: chain G residue 37 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 43 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 47 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN B 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.139514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.111858 restraints weight = 6270.095| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.66 r_work: 0.3096 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5384 Z= 0.144 Angle : 0.468 7.344 7255 Z= 0.249 Chirality : 0.036 0.136 854 Planarity : 0.002 0.025 908 Dihedral : 3.562 15.348 705 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.33 % Allowed : 21.90 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.02 (0.33), residues: 675 helix: 3.00 (0.22), residues: 517 sheet: None (None), residues: 0 loop : -1.70 (0.48), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 38 HIS 0.008 0.001 HIS A 210 PHE 0.007 0.001 PHE A 61 TYR 0.014 0.002 TYR B 17 ARG 0.006 0.001 ARG B 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.651 Fit side-chains REVERT: A 6 GLU cc_start: 0.7493 (pt0) cc_final: 0.7228 (pt0) REVERT: A 88 GLN cc_start: 0.8081 (tp40) cc_final: 0.7398 (tm-30) REVERT: A 96 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7346 (pp20) REVERT: A 156 ILE cc_start: 0.7126 (tp) cc_final: 0.6850 (tt) REVERT: B 63 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.6433 (pm20) REVERT: B 99 THR cc_start: 0.8358 (t) cc_final: 0.8074 (p) REVERT: B 147 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7428 (mt-10) REVERT: B 154 ASN cc_start: 0.7281 (m-40) cc_final: 0.6876 (t0) REVERT: B 194 GLU cc_start: 0.8099 (tp30) cc_final: 0.7644 (tp30) REVERT: B 209 LYS cc_start: 0.8415 (tttp) cc_final: 0.8114 (ttpp) REVERT: C 54 MET cc_start: 0.7641 (mmm) cc_final: 0.7175 (mmm) REVERT: C 56 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.6684 (t80) REVERT: D 6 LYS cc_start: 0.5228 (ptpp) cc_final: 0.4624 (ptmt) REVERT: E 47 GLU cc_start: 0.7696 (tp30) cc_final: 0.7215 (tp30) outliers start: 13 outliers final: 8 residues processed: 132 average time/residue: 1.1374 time to fit residues: 156.8333 Evaluate side-chains 133 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain F residue 27 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 59 optimal weight: 0.4980 chunk 5 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 30 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 60 optimal weight: 0.0000 chunk 0 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.140557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.112031 restraints weight = 6257.330| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.73 r_work: 0.3136 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5384 Z= 0.132 Angle : 0.469 7.574 7255 Z= 0.248 Chirality : 0.036 0.136 854 Planarity : 0.002 0.026 908 Dihedral : 3.546 15.809 705 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.15 % Allowed : 22.26 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.05 (0.33), residues: 675 helix: 3.05 (0.22), residues: 514 sheet: None (None), residues: 0 loop : -1.69 (0.47), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP G 38 HIS 0.010 0.001 HIS A 210 PHE 0.029 0.001 PHE C 52 TYR 0.013 0.002 TYR B 17 ARG 0.006 0.001 ARG B 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.538 Fit side-chains REVERT: A 6 GLU cc_start: 0.7423 (pt0) cc_final: 0.7185 (pt0) REVERT: A 30 ASP cc_start: 0.8301 (m-30) cc_final: 0.7998 (t0) REVERT: A 88 GLN cc_start: 0.8122 (tp40) cc_final: 0.7435 (tm-30) REVERT: A 96 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7315 (pp20) REVERT: A 156 ILE cc_start: 0.7151 (tp) cc_final: 0.6870 (tt) REVERT: B 48 GLN cc_start: 0.8600 (mt0) cc_final: 0.8387 (mt0) REVERT: B 63 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6464 (pm20) REVERT: B 99 THR cc_start: 0.8349 (t) cc_final: 0.8064 (p) REVERT: B 147 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7412 (mt-10) REVERT: B 154 ASN cc_start: 0.7250 (m-40) cc_final: 0.6870 (t0) REVERT: B 194 GLU cc_start: 0.8105 (tp30) cc_final: 0.7651 (tp30) REVERT: B 209 LYS cc_start: 0.8435 (tttp) cc_final: 0.8153 (ttpp) REVERT: C 54 MET cc_start: 0.7660 (mmm) cc_final: 0.7134 (mmm) REVERT: C 56 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.6680 (t80) REVERT: D 6 LYS cc_start: 0.5298 (ptpp) cc_final: 0.4667 (ptmt) REVERT: E 47 GLU cc_start: 0.7631 (tp30) cc_final: 0.7173 (tp30) outliers start: 12 outliers final: 6 residues processed: 130 average time/residue: 1.1476 time to fit residues: 155.6783 Evaluate side-chains 130 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain F residue 27 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 0.0020 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN B 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.141194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.113785 restraints weight = 6325.811| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.63 r_work: 0.3146 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5384 Z= 0.148 Angle : 0.478 7.617 7255 Z= 0.253 Chirality : 0.036 0.138 854 Planarity : 0.002 0.032 908 Dihedral : 3.553 16.961 705 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.15 % Allowed : 23.34 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.06 (0.33), residues: 675 helix: 3.02 (0.22), residues: 517 sheet: None (None), residues: 0 loop : -1.65 (0.48), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 38 HIS 0.010 0.001 HIS A 210 PHE 0.006 0.001 PHE G 51 TYR 0.014 0.002 TYR B 17 ARG 0.008 0.001 ARG B 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4198.39 seconds wall clock time: 74 minutes 43.26 seconds (4483.26 seconds total)