Starting phenix.real_space_refine on Thu Mar 6 09:21:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jqt_61741/03_2025/9jqt_61741.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jqt_61741/03_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_61741/03_2025/9jqt_61741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jqt_61741/03_2025/9jqt_61741.map" model { file = "/net/cci-nas-00/data/ceres_data/9jqt_61741/03_2025/9jqt_61741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jqt_61741/03_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-5624/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: 4.50, per 1000 atoms: 0.79 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: 1.35 Conformation dependent library (CDL) restraints added in 694.2 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: 0.99 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: 2.17 Time building geometry restraints manager: 1.62 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: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 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: 18.810 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:14.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.230 ------------------------------------------------------------------------------- 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 : 0.655 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: 1.1871 time to fit residues: 120.9039 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 : 0.634 ------------------------------------------------------------------------------- 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 = 0.136574 restraints weight = 5376.900| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.43 r_work: 0.3511 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 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 : 0.702 Fit side-chains REVERT: A 66 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8505 (t0) REVERT: A 101 LYS cc_start: 0.8183 (mttt) cc_final: 0.7912 (mptm) REVERT: B 19 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8319 (tttt) REVERT: B 30 GLU cc_start: 0.7653 (pt0) cc_final: 0.6964 (pm20) REVERT: B 57 LYS cc_start: 0.7463 (mttt) cc_final: 0.7246 (mmmm) REVERT: B 59 ASN cc_start: 0.8191 (m-40) cc_final: 0.7988 (m110) REVERT: C 168 LYS cc_start: 0.7541 (mttt) cc_final: 0.7157 (ttpp) REVERT: D 92 ASP cc_start: 0.7518 (m-30) cc_final: 0.7292 (m-30) outliers start: 18 outliers final: 7 residues processed: 93 average time/residue: 1.2588 time to fit residues: 122.2700 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 : 0.616 ------------------------------------------------------------------------------- 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: 0.8980 chunk 5 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.188853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.132485 restraints weight = 5379.686| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.45 r_work: 0.3462 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 5815 Z= 0.312 Angle : 0.569 8.612 7910 Z= 0.296 Chirality : 0.043 0.160 863 Planarity : 0.005 0.053 1014 Dihedral : 4.622 16.905 778 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.99 % Allowed : 14.17 % Favored : 82.83 % 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: 0.56 (0.32), residues: 706 helix: 0.98 (1.06), residues: 21 sheet: 0.50 (0.27), residues: 343 loop : 0.35 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 47 HIS 0.004 0.001 HIS A 123 PHE 0.021 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 106 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.565 Fit side-chains REVERT: A 66 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8523 (t0) REVERT: A 101 LYS cc_start: 0.8170 (mttt) cc_final: 0.7818 (mptm) REVERT: A 149 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7491 (pt0) REVERT: B 19 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8331 (tttt) REVERT: B 30 GLU cc_start: 0.7612 (pt0) cc_final: 0.6946 (pm20) REVERT: B 59 ASN cc_start: 0.8290 (m-40) cc_final: 0.8032 (m110) REVERT: B 210 LYS cc_start: 0.7666 (tttt) cc_final: 0.7029 (tptm) REVERT: C 80 GLU cc_start: 0.8363 (pm20) cc_final: 0.8015 (pm20) REVERT: C 168 LYS cc_start: 0.7549 (mttt) cc_final: 0.7074 (ttpp) REVERT: D 92 ASP cc_start: 0.7584 (m-30) cc_final: 0.7313 (m-30) outliers start: 19 outliers final: 11 residues processed: 99 average time/residue: 1.3660 time to fit residues: 140.8094 Evaluate side-chains 98 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 155 THR 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: 9.9990 chunk 68 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 19 optimal weight: 0.0060 chunk 25 optimal weight: 0.0050 chunk 53 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.4812 ------------------------------------------------------------------------------- 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 = 0.4154 r_free = 0.4154 target = 0.193194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.138093 restraints weight = 5431.294| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.47 r_work: 0.3529 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5815 Z= 0.162 Angle : 0.482 6.035 7910 Z= 0.252 Chirality : 0.041 0.141 863 Planarity : 0.004 0.056 1014 Dihedral : 4.218 14.249 778 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.46 % Allowed : 14.17 % 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: 0.70 (0.32), residues: 706 helix: 1.39 (1.11), residues: 21 sheet: 0.53 (0.28), residues: 343 loop : 0.51 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 47 HIS 0.002 0.001 HIS A 123 PHE 0.013 0.001 PHE D 49 TYR 0.009 0.001 TYR A 189 ARG 0.003 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 108 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.668 Fit side-chains REVERT: A 66 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.8447 (t0) REVERT: A 101 LYS cc_start: 0.8153 (mttt) cc_final: 0.7801 (mptm) REVERT: A 149 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7392 (pt0) REVERT: B 30 GLU cc_start: 0.7611 (pt0) cc_final: 0.6942 (pm20) REVERT: B 210 LYS cc_start: 0.7644 (tttt) cc_final: 0.7072 (tptm) REVERT: C 106 LYS cc_start: 0.8096 (tttt) cc_final: 0.7895 (tttm) outliers start: 22 outliers final: 11 residues processed: 100 average time/residue: 1.3729 time to fit residues: 143.4633 Evaluate side-chains 91 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 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 85 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 35 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 32 optimal weight: 0.1980 chunk 45 optimal weight: 0.4980 chunk 59 optimal weight: 0.5980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.4147 r_free = 0.4147 target = 0.192484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136713 restraints weight = 5356.966| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.45 r_work: 0.3296 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5815 Z= 0.189 Angle : 0.496 6.736 7910 Z= 0.258 Chirality : 0.041 0.147 863 Planarity : 0.005 0.056 1014 Dihedral : 4.206 14.430 778 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.09 % Allowed : 14.33 % Favored : 81.57 % 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: 0.76 (0.32), residues: 706 helix: 1.53 (1.14), residues: 21 sheet: 0.56 (0.27), residues: 343 loop : 0.56 (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 0.002 PHE D 49 TYR 0.009 0.001 TYR D 97 ARG 0.004 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 110 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.617 Fit side-chains REVERT: A 66 ASN cc_start: 0.8666 (OUTLIER) cc_final: 0.8431 (t0) REVERT: A 101 LYS cc_start: 0.8129 (mttt) cc_final: 0.7736 (mptm) REVERT: A 149 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7417 (pt0) REVERT: B 19 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8322 (tttt) REVERT: B 30 GLU cc_start: 0.7639 (pt0) cc_final: 0.6925 (pm20) REVERT: B 210 LYS cc_start: 0.7627 (tttt) cc_final: 0.7026 (tptm) REVERT: C 80 GLU cc_start: 0.8360 (pm20) cc_final: 0.7818 (pm20) REVERT: C 168 LYS cc_start: 0.7635 (ttmt) cc_final: 0.6769 (ttpp) REVERT: D 40 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7760 (ptp-170) outliers start: 26 outliers final: 11 residues processed: 100 average time/residue: 1.3049 time to fit residues: 135.9993 Evaluate side-chains 95 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN 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 90 TRP Chi-restraints excluded: chain C residue 99 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 33 optimal weight: 0.0270 chunk 19 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 0.0040 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 0.0270 overall best weight: 0.2508 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.196738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.142259 restraints weight = 5338.334| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.43 r_work: 0.3599 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5815 Z= 0.131 Angle : 0.454 5.619 7910 Z= 0.237 Chirality : 0.040 0.135 863 Planarity : 0.004 0.057 1014 Dihedral : 3.956 12.912 778 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.36 % Allowed : 16.06 % Favored : 81.57 % 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: 0.97 (0.32), residues: 706 helix: 1.83 (1.18), residues: 21 sheet: 0.67 (0.28), residues: 343 loop : 0.72 (0.36), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 90 HIS 0.002 0.001 HIS A 181 PHE 0.010 0.001 PHE D 49 TYR 0.009 0.001 TYR A 189 ARG 0.005 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 105 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.645 Fit side-chains REVERT: A 101 LYS cc_start: 0.8163 (mttt) cc_final: 0.7831 (mptm) REVERT: A 149 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7406 (pt0) REVERT: B 19 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8279 (tttt) REVERT: B 30 GLU cc_start: 0.7558 (pt0) cc_final: 0.6909 (pm20) REVERT: B 119 SER cc_start: 0.7988 (p) cc_final: 0.7769 (m) REVERT: B 210 LYS cc_start: 0.7623 (tttt) cc_final: 0.7044 (tptm) REVERT: C 80 GLU cc_start: 0.8336 (pm20) cc_final: 0.7940 (pm20) REVERT: C 168 LYS cc_start: 0.7748 (ttmt) cc_final: 0.6903 (ttpp) outliers start: 15 outliers final: 7 residues processed: 102 average time/residue: 1.2396 time to fit residues: 132.0121 Evaluate side-chains 95 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 19 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 180 LEU 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: 0.0050 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 = 0.4159 r_free = 0.4159 target = 0.193371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137672 restraints weight = 5419.661| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.46 r_work: 0.3550 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1677 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= 0.190 Angle : 0.483 6.765 7910 Z= 0.251 Chirality : 0.041 0.149 863 Planarity : 0.005 0.056 1014 Dihedral : 4.121 14.018 778 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.83 % Allowed : 16.22 % Favored : 80.94 % 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: 0.90 (0.32), residues: 706 helix: 1.77 (1.17), residues: 21 sheet: 0.66 (0.27), residues: 343 loop : 0.63 (0.36), 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 0.002 PHE D 49 TYR 0.009 0.001 TYR C 85 ARG 0.006 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 101 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.679 Fit side-chains REVERT: A 101 LYS cc_start: 0.8125 (mttt) cc_final: 0.7762 (mptm) REVERT: A 149 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7415 (pt0) REVERT: B 19 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8298 (tttt) REVERT: B 30 GLU cc_start: 0.7484 (pt0) cc_final: 0.6828 (pm20) REVERT: B 210 LYS cc_start: 0.7620 (tttt) cc_final: 0.7034 (tptm) REVERT: C 80 GLU cc_start: 0.8348 (pm20) cc_final: 0.7991 (pm20) REVERT: C 148 LYS cc_start: 0.7527 (mmtp) cc_final: 0.7232 (mptp) REVERT: C 168 LYS cc_start: 0.7727 (ttmt) cc_final: 0.6872 (ttpp) outliers start: 18 outliers final: 11 residues processed: 94 average time/residue: 1.3174 time to fit residues: 129.4610 Evaluate side-chains 95 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 127 THR 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 71 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 63 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 37 optimal weight: 0.0670 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 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 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 = 0.4166 r_free = 0.4166 target = 0.194140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.139642 restraints weight = 5323.190| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.40 r_work: 0.3323 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1718 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= 0.177 Angle : 0.478 6.180 7910 Z= 0.249 Chirality : 0.041 0.147 863 Planarity : 0.004 0.056 1014 Dihedral : 4.117 13.846 778 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.52 % Allowed : 16.69 % Favored : 80.79 % 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: 0.94 (0.32), residues: 706 helix: 1.80 (1.18), residues: 21 sheet: 0.67 (0.27), residues: 343 loop : 0.68 (0.36), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 D 97 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 96 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.673 Fit side-chains REVERT: A 101 LYS cc_start: 0.8111 (mttt) cc_final: 0.7718 (mptm) REVERT: A 133 GLN cc_start: 0.6454 (mm-40) cc_final: 0.6077 (mm110) REVERT: A 149 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7434 (pt0) REVERT: B 19 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8299 (tttt) REVERT: B 30 GLU cc_start: 0.7474 (pt0) cc_final: 0.6817 (pm20) REVERT: B 210 LYS cc_start: 0.7600 (tttt) cc_final: 0.6992 (tptm) REVERT: C 80 GLU cc_start: 0.8297 (pm20) cc_final: 0.7887 (pm20) REVERT: C 168 LYS cc_start: 0.7597 (ttmt) cc_final: 0.6724 (ttpp) outliers start: 16 outliers final: 13 residues processed: 91 average time/residue: 1.4574 time to fit residues: 138.5296 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 : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 0.8980 chunk 21 optimal weight: 1.9990 chunk 37 optimal weight: 0.0670 chunk 66 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.191134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.135125 restraints weight = 5398.195| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.43 r_work: 0.3504 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1677 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= 0.244 Angle : 0.517 7.378 7910 Z= 0.268 Chirality : 0.042 0.155 863 Planarity : 0.005 0.056 1014 Dihedral : 4.341 14.967 778 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.83 % Allowed : 16.85 % 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: 0.88 (0.32), residues: 706 helix: 1.75 (1.19), residues: 21 sheet: 0.64 (0.27), residues: 343 loop : 0.63 (0.36), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.003 0.001 HIS A 123 PHE 0.017 0.002 PHE D 49 TYR 0.010 0.001 TYR C 48 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 100 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.607 Fit side-chains REVERT: A 101 LYS cc_start: 0.8177 (mttt) cc_final: 0.7769 (mptm) REVERT: A 133 GLN cc_start: 0.6519 (mm-40) cc_final: 0.6181 (mm110) REVERT: A 149 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7450 (pt0) REVERT: B 19 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8294 (tttt) REVERT: B 30 GLU cc_start: 0.7426 (pt0) cc_final: 0.6822 (pm20) REVERT: B 210 LYS cc_start: 0.7647 (tttt) cc_final: 0.7069 (tptm) REVERT: C 80 GLU cc_start: 0.8380 (pm20) cc_final: 0.7968 (pm20) REVERT: C 168 LYS cc_start: 0.7690 (ttmt) cc_final: 0.6844 (ttpp) outliers start: 18 outliers final: 12 residues processed: 94 average time/residue: 1.2545 time to fit residues: 123.1785 Evaluate side-chains 95 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 73 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.188684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.132404 restraints weight = 5447.248| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.41 r_work: 0.3456 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 5815 Z= 0.378 Angle : 0.599 9.993 7910 Z= 0.309 Chirality : 0.044 0.172 863 Planarity : 0.005 0.059 1014 Dihedral : 4.748 17.112 778 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.83 % Allowed : 17.01 % 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: 0.62 (0.32), residues: 706 helix: 1.58 (1.18), residues: 21 sheet: 0.47 (0.27), residues: 347 loop : 0.44 (0.36), residues: 338 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 0.022 0.002 PHE D 49 TYR 0.013 0.002 TYR C 48 ARG 0.007 0.001 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 102 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.637 Fit side-chains REVERT: A 101 LYS cc_start: 0.8256 (mttt) cc_final: 0.7900 (mptm) REVERT: B 19 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8341 (tttt) REVERT: B 30 GLU cc_start: 0.7496 (pt0) cc_final: 0.6897 (pm20) REVERT: B 210 LYS cc_start: 0.7690 (tttt) cc_final: 0.7066 (tptm) REVERT: C 80 GLU cc_start: 0.8416 (pm20) cc_final: 0.7912 (pm20) REVERT: C 104 GLU cc_start: 0.8162 (tt0) cc_final: 0.7806 (tt0) REVERT: C 168 LYS cc_start: 0.7659 (ttmt) cc_final: 0.6828 (ttpp) outliers start: 18 outliers final: 13 residues processed: 96 average time/residue: 1.3439 time to fit residues: 134.4394 Evaluate side-chains 95 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 127 THR 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 30 SER 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 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: 0.9990 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN 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 = 0.4110 r_free = 0.4110 target = 0.188773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.132810 restraints weight = 5491.981| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.46 r_work: 0.3501 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 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 : 0.004 0.055 5815 Z= 0.241 Angle : 0.521 6.642 7910 Z= 0.272 Chirality : 0.042 0.152 863 Planarity : 0.005 0.058 1014 Dihedral : 4.507 16.267 778 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.68 % Allowed : 17.17 % 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: 0.67 (0.32), residues: 706 helix: 1.73 (1.20), residues: 21 sheet: 0.46 (0.27), residues: 348 loop : 0.54 (0.36), residues: 337 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 0.017 0.002 PHE D 49 TYR 0.011 0.002 TYR C 85 ARG 0.006 0.000 ARG C 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6034.70 seconds wall clock time: 105 minutes 38.02 seconds (6338.02 seconds total)