Starting phenix.real_space_refine on Tue Jan 14 05:09:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jqt_61741/01_2025/9jqt_61741.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jqt_61741/01_2025/9jqt_61741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jqt_61741/01_2025/9jqt_61741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jqt_61741/01_2025/9jqt_61741.map" model { file = "/net/cci-nas-00/data/ceres_data/9jqt_61741/01_2025/9jqt_61741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jqt_61741/01_2025/9jqt_61741.cif" } resolution = 2.7 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= 0.014 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 23 5.16 5 C 3581 2.51 5 N 963 2.21 5 O 1102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 5669 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1599 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 177} Chain breaks: 1 Chain: "B" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1557 Classifications: {'peptide': 206} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 193} Chain breaks: 2 Chain: "C" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1603 Classifications: {'peptide': 208} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 194} Chain: "D" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 910 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Time building chain proxies: 3.81, per 1000 atoms: 0.67 Number of scatterers: 5669 At special positions: 0 Unit cell: (80.864, 85.918, 113.354, 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 23 16.00 O 1102 8.00 N 963 7.00 C 3581 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 102 " - pdb=" SG CYS A 115 " distance=2.03 Simple disulfide: pdb=" SG CYS A 182 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 200 " distance=2.04 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 87 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 193 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 98 " distance=2.03 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: 1.19 Conformation dependent library (CDL) restraints added in 531.6 milliseconds 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1354 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 18 sheets defined 8.3% alpha, 49.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 75 through 79 removed outlier: 3.615A pdb=" N SER A 78 " --> pdb=" O ASN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 122 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.537A pdb=" N THR B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 191 through 193 No H-bonds generated for 'chain 'B' and resid 191 through 193' Processing helix chain 'B' and resid 205 through 208 Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.647A pdb=" N PHE C 82 " --> pdb=" O PRO C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 127 Processing helix chain 'C' and resid 182 through 188 removed outlier: 3.871A pdb=" N HIS C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 34 removed outlier: 4.175A pdb=" N ARG D 33 " --> pdb=" O THR D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 108 removed outlier: 6.601A pdb=" N LEU A 106 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE A 153 " --> pdb=" O CYS A 62 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL A 64 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 101 Processing sheet with id=AA3, first strand: chain 'A' and resid 158 through 163 removed outlier: 4.428A pdb=" N LEU A 160 " --> pdb=" O ASN A 173 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN A 173 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU A 162 " --> pdb=" O GLU A 171 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLU A 171 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 202 Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.530A pdb=" N GLU B 10 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.530A pdb=" N GLU B 10 " --> pdb=" O THR B 114 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 128 removed outlier: 5.927A pdb=" N TYR B 180 " --> pdb=" O ASP B 148 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 124 through 128 removed outlier: 5.927A pdb=" N TYR B 180 " --> pdb=" O ASP B 148 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 155 through 158 Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.015A pdb=" N LEU C 11 " --> pdb=" O GLU C 104 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TRP C 34 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.015A pdb=" N LEU C 11 " --> pdb=" O GLU C 104 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR C 96 " --> pdb=" O GLN C 89 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 113 through 117 removed outlier: 5.626A pdb=" N TYR C 172 " --> pdb=" O ASN C 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 152 through 154 removed outlier: 4.648A pdb=" N TRP C 147 " --> pdb=" O GLN C 154 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 7 through 9 Processing sheet with id=AB8, first strand: chain 'D' and resid 60 through 62 removed outlier: 6.672A pdb=" N TRP D 38 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL D 52 " --> pdb=" O MET D 36 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N MET D 36 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA D 35 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR D 112 " --> pdb=" O ILE D 100 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 60 through 62 removed outlier: 6.672A pdb=" N TRP D 38 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL D 52 " --> pdb=" O MET D 36 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N MET D 36 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA D 35 " --> pdb=" O ASP D 101 " (cutoff:3.500A) 262 hydrogen bonds defined for protein. 627 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: 1.81 Time building geometry restraints manager: 1.39 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: 1822 1.34 - 1.46: 1422 1.46 - 1.58: 2541 1.58 - 1.70: 0 1.70 - 1.82: 30 Bond restraints: 5815 Sorted by residual: bond pdb=" N VAL A 223 " pdb=" CA VAL A 223 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.18e-02 7.18e+03 1.00e+01 bond pdb=" N GLY D 116 " pdb=" CA GLY D 116 " ideal model delta sigma weight residual 1.446 1.476 -0.030 1.02e-02 9.61e+03 8.91e+00 bond pdb=" N VAL B 146 " pdb=" CA VAL B 146 " ideal model delta sigma weight residual 1.460 1.492 -0.033 1.10e-02 8.26e+03 8.85e+00 bond pdb=" N VAL B 125 " pdb=" CA VAL B 125 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.24e-02 6.50e+03 8.62e+00 bond pdb=" N VAL A 187 " pdb=" CA VAL A 187 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.52e+00 ... (remaining 5810 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 7431 1.35 - 2.70: 387 2.70 - 4.05: 75 4.05 - 5.40: 10 5.40 - 6.76: 7 Bond angle restraints: 7910 Sorted by residual: angle pdb=" CA GLY D 116 " pdb=" C GLY D 116 " pdb=" O GLY D 116 " ideal model delta sigma weight residual 122.23 118.37 3.86 6.90e-01 2.10e+00 3.13e+01 angle pdb=" CA GLY B 49 " pdb=" C GLY B 49 " pdb=" O GLY B 49 " ideal model delta sigma weight residual 121.60 118.12 3.48 9.70e-01 1.06e+00 1.28e+01 angle pdb=" N TYR B 106 " pdb=" CA TYR B 106 " pdb=" CB TYR B 106 " ideal model delta sigma weight residual 110.69 104.95 5.74 1.61e+00 3.86e-01 1.27e+01 angle pdb=" CA ASP B 52 " pdb=" CB ASP B 52 " pdb=" CG ASP B 52 " ideal model delta sigma weight residual 112.60 116.13 -3.53 1.00e+00 1.00e+00 1.25e+01 angle pdb=" N PRO A 229 " pdb=" CA PRO A 229 " pdb=" CB PRO A 229 " ideal model delta sigma weight residual 102.60 99.00 3.60 1.10e+00 8.26e-01 1.07e+01 ... (remaining 7905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3162 17.94 - 35.88: 229 35.88 - 53.82: 56 53.82 - 71.77: 9 71.77 - 89.71: 4 Dihedral angle restraints: 3460 sinusoidal: 1357 harmonic: 2103 Sorted by residual: dihedral pdb=" CB CYS B 144 " pdb=" SG CYS B 144 " pdb=" SG CYS B 200 " pdb=" CB CYS B 200 " ideal model delta sinusoidal sigma weight residual 93.00 54.27 38.73 1 1.00e+01 1.00e-02 2.11e+01 dihedral pdb=" CA ASN A 228 " pdb=" C ASN A 228 " pdb=" N PRO A 229 " pdb=" CA PRO A 229 " ideal model delta harmonic sigma weight residual 0.00 -20.52 20.52 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 87 " pdb=" CB CYS C 87 " ideal model delta sinusoidal sigma weight residual 93.00 63.50 29.50 1 1.00e+01 1.00e-02 1.24e+01 ... (remaining 3457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 711 0.060 - 0.120: 129 0.120 - 0.179: 19 0.179 - 0.239: 2 0.239 - 0.299: 2 Chirality restraints: 863 Sorted by residual: chirality pdb=" CA ILE D 31 " pdb=" N ILE D 31 " pdb=" C ILE D 31 " pdb=" CB ILE D 31 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA VAL C 145 " pdb=" N VAL C 145 " pdb=" C VAL C 145 " pdb=" CB VAL C 145 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA VAL B 146 " pdb=" N VAL B 146 " pdb=" C VAL B 146 " pdb=" CB VAL B 146 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 860 not shown) Planarity restraints: 1014 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 78 " -0.037 5.00e-02 4.00e+02 5.63e-02 5.06e+00 pdb=" N PRO C 79 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 79 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 79 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 50 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C THR C 50 " -0.034 2.00e-02 2.50e+03 pdb=" O THR C 50 " 0.013 2.00e-02 2.50e+03 pdb=" N SER C 51 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 61 " 0.028 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO B 62 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 62 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 62 " 0.024 5.00e-02 4.00e+02 ... (remaining 1011 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 507 2.75 - 3.29: 5054 3.29 - 3.82: 9534 3.82 - 4.36: 12193 4.36 - 4.90: 20589 Nonbonded interactions: 47877 Sorted by model distance: nonbonded pdb=" O PHE B 102 " pdb=" OD1 ASP B 105 " model vdw 2.209 3.040 nonbonded pdb=" OD1 ASN A 150 " pdb=" OG SER A 233 " model vdw 2.224 3.040 nonbonded pdb=" OD1 ASP B 73 " pdb=" OG SER B 75 " model vdw 2.260 3.040 nonbonded pdb=" NH1 ARG D 40 " pdb=" OD1 ASP D 92 " model vdw 2.306 3.120 nonbonded pdb=" O PRO A 157 " pdb=" OG SER A 241 " model vdw 2.309 3.040 ... (remaining 47872 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.060 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.810 Find NCS groups from input model: 0.080 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:13.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5878 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 : 0.005 0.037 5815 Z= 0.329 Angle : 0.717 6.756 7910 Z= 0.449 Chirality : 0.050 0.299 863 Planarity : 0.005 0.063 1014 Dihedral : 13.514 89.707 2085 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.31 % Allowed : 12.60 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.32), residues: 706 helix: 0.65 (1.11), residues: 21 sheet: 0.47 (0.28), residues: 323 loop : 0.34 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 47 HIS 0.006 0.001 HIS C 197 PHE 0.014 0.002 PHE C 138 TYR 0.010 0.001 TYR C 48 ARG 0.003 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.664 Fit side-chains REVERT: A 101 LYS cc_start: 0.7565 (mttt) cc_final: 0.7243 (mptm) REVERT: B 30 GLU cc_start: 0.6940 (pt0) cc_final: 0.6120 (pm20) REVERT: B 59 ASN cc_start: 0.7210 (m-40) cc_final: 0.6879 (m110) REVERT: C 168 LYS cc_start: 0.6680 (mttt) cc_final: 0.6369 (ttpp) outliers start: 2 outliers final: 1 residues processed: 97 average time/residue: 1.1792 time to fit residues: 120.2242 Evaluate side-chains 82 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN B 201 ASN C 93 ASN D 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.191431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.136576 restraints weight = 5376.900| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.43 r_work: 0.3510 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5815 Z= 0.217 Angle : 0.525 7.398 7910 Z= 0.275 Chirality : 0.042 0.152 863 Planarity : 0.005 0.051 1014 Dihedral : 4.390 15.420 779 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.83 % Allowed : 13.07 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.32), residues: 706 helix: 1.03 (1.06), residues: 21 sheet: 0.44 (0.27), residues: 343 loop : 0.53 (0.36), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.005 0.001 HIS B 35 PHE 0.015 0.002 PHE D 49 TYR 0.009 0.001 TYR A 189 ARG 0.003 0.000 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.580 Fit side-chains REVERT: A 66 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.8503 (t0) REVERT: A 101 LYS cc_start: 0.8181 (mttt) cc_final: 0.7909 (mptm) REVERT: B 19 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8316 (tttt) REVERT: B 30 GLU cc_start: 0.7653 (pt0) cc_final: 0.6962 (pm20) REVERT: B 57 LYS cc_start: 0.7461 (mttt) cc_final: 0.7244 (mmmm) REVERT: B 59 ASN cc_start: 0.8189 (m-40) cc_final: 0.7985 (m110) REVERT: C 168 LYS cc_start: 0.7538 (mttt) cc_final: 0.7155 (ttpp) REVERT: D 92 ASP cc_start: 0.7516 (m-30) cc_final: 0.7290 (m-30) outliers start: 18 outliers final: 7 residues processed: 93 average time/residue: 1.3430 time to fit residues: 130.2093 Evaluate side-chains 88 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 73 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 60 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 33 optimal weight: 0.0770 chunk 40 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 88 HIS B 201 ASN C 93 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.189880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.133844 restraints weight = 5382.588| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.45 r_work: 0.3477 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5815 Z= 0.270 Angle : 0.546 7.836 7910 Z= 0.284 Chirality : 0.043 0.157 863 Planarity : 0.005 0.053 1014 Dihedral : 4.509 16.321 778 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.83 % Allowed : 13.86 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.32), residues: 706 helix: 1.08 (1.06), residues: 21 sheet: 0.48 (0.27), residues: 343 loop : 0.45 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.004 0.001 HIS A 123 PHE 0.019 0.002 PHE D 49 TYR 0.010 0.002 TYR C 48 ARG 0.003 0.000 ARG D 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.550 Fit side-chains REVERT: A 66 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8495 (t0) REVERT: A 101 LYS cc_start: 0.8152 (mttt) cc_final: 0.7826 (mptm) REVERT: A 149 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7460 (pt0) REVERT: B 19 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8315 (tttt) REVERT: B 30 GLU cc_start: 0.7608 (pt0) cc_final: 0.6924 (pm20) REVERT: B 59 ASN cc_start: 0.8256 (m-40) cc_final: 0.7985 (m110) REVERT: B 210 LYS cc_start: 0.7649 (tttt) cc_final: 0.7050 (tptm) REVERT: C 80 GLU cc_start: 0.8345 (pm20) cc_final: 0.7749 (pm20) REVERT: C 168 LYS cc_start: 0.7494 (mttt) cc_final: 0.7029 (ttpp) REVERT: D 92 ASP cc_start: 0.7580 (m-30) cc_final: 0.7321 (m-30) outliers start: 18 outliers final: 10 residues processed: 98 average time/residue: 1.3525 time to fit residues: 137.8853 Evaluate side-chains 96 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 90 TRP Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 73 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 37 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 0.0050 chunk 25 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 201 ASN C 93 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.192216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136827 restraints weight = 5438.027| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.47 r_work: 0.3530 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5815 Z= 0.187 Angle : 0.494 6.234 7910 Z= 0.257 Chirality : 0.041 0.146 863 Planarity : 0.005 0.056 1014 Dihedral : 4.258 14.769 778 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.78 % Allowed : 13.86 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.32), residues: 706 helix: 1.37 (1.10), residues: 21 sheet: 0.53 (0.28), residues: 343 loop : 0.49 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 HIS 0.003 0.001 HIS A 123 PHE 0.014 0.001 PHE D 49 TYR 0.009 0.001 TYR A 189 ARG 0.002 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.681 Fit side-chains REVERT: A 66 ASN cc_start: 0.8683 (OUTLIER) cc_final: 0.8467 (t0) REVERT: A 101 LYS cc_start: 0.8157 (mttt) cc_final: 0.7807 (mptm) REVERT: A 149 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7404 (pt0) REVERT: B 19 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8307 (tttt) REVERT: B 30 GLU cc_start: 0.7632 (pt0) cc_final: 0.6956 (pm20) REVERT: B 59 ASN cc_start: 0.8268 (m-40) cc_final: 0.8066 (m110) REVERT: B 210 LYS cc_start: 0.7657 (tttt) cc_final: 0.7084 (tptm) outliers start: 24 outliers final: 12 residues processed: 100 average time/residue: 1.3067 time to fit residues: 136.2259 Evaluate side-chains 94 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 90 TRP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 85 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 47 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 32 optimal weight: 0.3980 chunk 45 optimal weight: 0.7980 chunk 59 optimal weight: 0.4980 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 201 ASN C 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.192206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.136570 restraints weight = 5352.592| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.43 r_work: 0.3528 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5815 Z= 0.195 Angle : 0.498 6.758 7910 Z= 0.259 Chirality : 0.041 0.148 863 Planarity : 0.005 0.056 1014 Dihedral : 4.237 14.511 778 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.62 % Allowed : 14.49 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.32), residues: 706 helix: 1.49 (1.13), residues: 21 sheet: 0.54 (0.27), residues: 343 loop : 0.53 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 HIS 0.003 0.001 HIS A 123 PHE 0.015 0.002 PHE D 49 TYR 0.009 0.001 TYR C 85 ARG 0.005 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.618 Fit side-chains REVERT: A 66 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8444 (t0) REVERT: A 101 LYS cc_start: 0.8117 (mttt) cc_final: 0.7733 (mptm) REVERT: A 149 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7395 (pt0) REVERT: B 30 GLU cc_start: 0.7561 (pt0) cc_final: 0.6874 (pm20) REVERT: B 59 ASN cc_start: 0.8258 (m-40) cc_final: 0.8039 (m110) REVERT: B 210 LYS cc_start: 0.7646 (tttt) cc_final: 0.7071 (tptm) REVERT: C 80 GLU cc_start: 0.8381 (pm20) cc_final: 0.7927 (pm20) REVERT: C 168 LYS cc_start: 0.7721 (ttmt) cc_final: 0.6853 (ttpp) outliers start: 23 outliers final: 10 residues processed: 98 average time/residue: 1.2916 time to fit residues: 132.0413 Evaluate side-chains 93 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 90 TRP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 85 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 0.0050 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 0.0060 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.7812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 ASN C 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.192316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.137280 restraints weight = 5317.467| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.39 r_work: 0.3287 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5815 Z= 0.214 Angle : 0.506 7.199 7910 Z= 0.262 Chirality : 0.042 0.151 863 Planarity : 0.005 0.057 1014 Dihedral : 4.291 14.872 778 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.09 % Allowed : 14.17 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.32), residues: 706 helix: 1.62 (1.15), residues: 21 sheet: 0.54 (0.27), residues: 343 loop : 0.55 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 HIS 0.003 0.001 HIS A 123 PHE 0.016 0.002 PHE D 49 TYR 0.009 0.001 TYR D 97 ARG 0.003 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.611 Fit side-chains REVERT: A 66 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.8445 (t0) REVERT: A 101 LYS cc_start: 0.8167 (mttt) cc_final: 0.7754 (mptm) REVERT: A 149 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7509 (pt0) REVERT: B 19 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8331 (tttt) REVERT: B 23 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7933 (tttm) REVERT: B 30 GLU cc_start: 0.7605 (pt0) cc_final: 0.6899 (pm20) REVERT: B 59 ASN cc_start: 0.8298 (m-40) cc_final: 0.8040 (m110) REVERT: B 210 LYS cc_start: 0.7639 (tttt) cc_final: 0.7041 (tptm) REVERT: C 80 GLU cc_start: 0.8373 (pm20) cc_final: 0.7907 (pm20) REVERT: C 168 LYS cc_start: 0.7618 (ttmt) cc_final: 0.6749 (ttpp) REVERT: D 40 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7768 (ptt180) outliers start: 26 outliers final: 12 residues processed: 100 average time/residue: 1.3282 time to fit residues: 138.5557 Evaluate side-chains 98 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 90 TRP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 85 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 36 optimal weight: 0.0970 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 0.0030 chunk 65 optimal weight: 0.0980 chunk 1 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 ASN C 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.194929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.139997 restraints weight = 5410.291| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.45 r_work: 0.3579 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5815 Z= 0.147 Angle : 0.462 5.887 7910 Z= 0.242 Chirality : 0.041 0.139 863 Planarity : 0.004 0.057 1014 Dihedral : 4.060 13.382 778 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.31 % Allowed : 14.96 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.32), residues: 706 helix: 1.82 (1.18), residues: 21 sheet: 0.60 (0.27), residues: 344 loop : 0.62 (0.36), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 90 HIS 0.002 0.001 HIS A 123 PHE 0.012 0.001 PHE D 49 TYR 0.010 0.001 TYR D 97 ARG 0.004 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.655 Fit side-chains REVERT: A 66 ASN cc_start: 0.8620 (OUTLIER) cc_final: 0.8399 (t0) REVERT: A 101 LYS cc_start: 0.8152 (mttt) cc_final: 0.7801 (mptm) REVERT: A 149 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7423 (pt0) REVERT: B 19 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8297 (tttt) REVERT: B 30 GLU cc_start: 0.7449 (pt0) cc_final: 0.6818 (pm20) REVERT: B 59 ASN cc_start: 0.8289 (m-40) cc_final: 0.8088 (m110) REVERT: B 210 LYS cc_start: 0.7624 (tttt) cc_final: 0.7044 (tptm) REVERT: C 80 GLU cc_start: 0.8366 (pm20) cc_final: 0.8033 (pm20) REVERT: C 168 LYS cc_start: 0.7724 (ttmt) cc_final: 0.6871 (ttpp) REVERT: D 40 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7702 (ptt180) outliers start: 21 outliers final: 13 residues processed: 99 average time/residue: 1.4117 time to fit residues: 145.5425 Evaluate side-chains 97 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 90 TRP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 85 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 63 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 19 optimal weight: 0.0030 chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 ASN C 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.192680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.136871 restraints weight = 5321.405| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.43 r_work: 0.3533 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5815 Z= 0.201 Angle : 0.494 7.212 7910 Z= 0.257 Chirality : 0.041 0.151 863 Planarity : 0.005 0.056 1014 Dihedral : 4.210 14.398 778 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.83 % Allowed : 16.54 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.32), residues: 706 helix: 1.79 (1.19), residues: 21 sheet: 0.59 (0.27), residues: 344 loop : 0.62 (0.36), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 HIS 0.003 0.001 HIS A 123 PHE 0.014 0.002 PHE D 49 TYR 0.009 0.001 TYR C 48 ARG 0.005 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.659 Fit side-chains REVERT: A 66 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8435 (t0) REVERT: A 101 LYS cc_start: 0.8133 (mttt) cc_final: 0.7732 (mptm) REVERT: A 149 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7383 (pt0) REVERT: B 19 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8281 (tttt) REVERT: B 30 GLU cc_start: 0.7472 (pt0) cc_final: 0.6816 (pm20) REVERT: B 59 ASN cc_start: 0.8273 (m-40) cc_final: 0.8044 (m110) REVERT: B 210 LYS cc_start: 0.7608 (tttt) cc_final: 0.7018 (tptm) REVERT: C 80 GLU cc_start: 0.8377 (pm20) cc_final: 0.8031 (pm20) REVERT: C 168 LYS cc_start: 0.7650 (ttmt) cc_final: 0.6786 (ttpp) REVERT: D 40 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7753 (ptt180) outliers start: 18 outliers final: 12 residues processed: 93 average time/residue: 1.3271 time to fit residues: 128.6474 Evaluate side-chains 96 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 90 TRP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 85 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 59 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 42 optimal weight: 0.2980 chunk 9 optimal weight: 0.2980 chunk 4 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 ASN C 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.193688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.138150 restraints weight = 5365.929| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.43 r_work: 0.3551 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5815 Z= 0.173 Angle : 0.476 6.091 7910 Z= 0.248 Chirality : 0.041 0.146 863 Planarity : 0.005 0.056 1014 Dihedral : 4.128 13.882 778 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.99 % Allowed : 17.01 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.32), residues: 706 helix: 1.85 (1.21), residues: 21 sheet: 0.64 (0.27), residues: 344 loop : 0.68 (0.36), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 47 HIS 0.002 0.001 HIS A 123 PHE 0.013 0.001 PHE D 49 TYR 0.010 0.001 TYR D 97 ARG 0.006 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.686 Fit side-chains REVERT: A 66 ASN cc_start: 0.8630 (OUTLIER) cc_final: 0.8426 (t0) REVERT: A 101 LYS cc_start: 0.8092 (mttt) cc_final: 0.7698 (mptm) REVERT: A 149 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7384 (pt0) REVERT: B 19 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8263 (tttt) REVERT: B 30 GLU cc_start: 0.7368 (pt0) cc_final: 0.6756 (pm20) REVERT: B 59 ASN cc_start: 0.8266 (m-40) cc_final: 0.8033 (m110) REVERT: B 210 LYS cc_start: 0.7591 (tttt) cc_final: 0.7001 (tptm) REVERT: C 80 GLU cc_start: 0.8365 (pm20) cc_final: 0.8087 (pm20) REVERT: D 40 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7738 (ptt180) outliers start: 19 outliers final: 12 residues processed: 94 average time/residue: 1.2471 time to fit residues: 122.6110 Evaluate side-chains 94 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 90 TRP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 85 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 13 optimal weight: 0.2980 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 32 optimal weight: 0.4980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 ASN C 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.190801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.134815 restraints weight = 5425.232| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.42 r_work: 0.3482 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5815 Z= 0.276 Angle : 0.539 8.034 7910 Z= 0.279 Chirality : 0.042 0.159 863 Planarity : 0.005 0.070 1014 Dihedral : 4.440 15.511 778 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.99 % Allowed : 16.69 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.32), residues: 706 helix: 1.75 (1.21), residues: 21 sheet: 0.52 (0.27), residues: 351 loop : 0.54 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.004 0.001 HIS A 123 PHE 0.018 0.002 PHE D 49 TYR 0.011 0.002 TYR C 48 ARG 0.008 0.000 ARG C 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.585 Fit side-chains REVERT: A 66 ASN cc_start: 0.8703 (OUTLIER) cc_final: 0.8490 (t0) REVERT: A 101 LYS cc_start: 0.8177 (mttt) cc_final: 0.7846 (mptm) REVERT: A 149 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7435 (pt0) REVERT: B 19 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8305 (tttt) REVERT: B 30 GLU cc_start: 0.7438 (pt0) cc_final: 0.6836 (pm20) REVERT: B 59 ASN cc_start: 0.8327 (m-40) cc_final: 0.8053 (m110) REVERT: B 210 LYS cc_start: 0.7647 (tttt) cc_final: 0.7066 (tptm) REVERT: C 80 GLU cc_start: 0.8389 (pm20) cc_final: 0.8044 (pm20) REVERT: C 99 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7439 (mp10) REVERT: C 122 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6579 (mt-10) REVERT: C 168 LYS cc_start: 0.7634 (ttmt) cc_final: 0.6813 (ttpp) REVERT: D 40 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7920 (ptt180) outliers start: 19 outliers final: 11 residues processed: 95 average time/residue: 1.3394 time to fit residues: 132.8113 Evaluate side-chains 98 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 90 TRP Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 85 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 6 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 ASN C 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.189603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.133871 restraints weight = 5416.133| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.42 r_work: 0.3500 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5815 Z= 0.282 Angle : 0.544 7.809 7910 Z= 0.281 Chirality : 0.043 0.158 863 Planarity : 0.005 0.062 1014 Dihedral : 4.505 15.881 778 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.31 % Allowed : 16.54 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.32), residues: 706 helix: 1.70 (1.21), residues: 21 sheet: 0.50 (0.27), residues: 351 loop : 0.51 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.004 0.001 HIS A 123 PHE 0.018 0.002 PHE D 49 TYR 0.011 0.002 TYR C 48 ARG 0.009 0.000 ARG C 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5589.42 seconds wall clock time: 99 minutes 53.39 seconds (5993.39 seconds total)