Starting phenix.real_space_refine on Tue Jan 14 04:37:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xcd_38240/01_2025/8xcd_38240.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xcd_38240/01_2025/8xcd_38240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xcd_38240/01_2025/8xcd_38240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xcd_38240/01_2025/8xcd_38240.map" model { file = "/net/cci-nas-00/data/ceres_data/8xcd_38240/01_2025/8xcd_38240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xcd_38240/01_2025/8xcd_38240.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.035 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 50 5.16 5 C 3629 2.51 5 N 894 2.21 5 O 1053 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 5626 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2223 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 15, 'TRANS': 274} Chain: "H" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1693 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 208} Chain: "L" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1640 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 202} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'TCH': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.78, per 1000 atoms: 0.67 Number of scatterers: 5626 At special positions: 0 Unit cell: (72.08, 62.54, 137.8, 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 50 16.00 O 1053 8.00 N 894 7.00 C 3629 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS L 133 " - pdb=" SG CYS L 193 " 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: 1.41 Conformation dependent library (CDL) restraints added in 916.8 milliseconds 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1350 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 11 sheets defined 39.2% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 21 through 43 Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 59 through 71 Processing helix chain 'A' and resid 71 through 83 Processing helix chain 'A' and resid 86 through 99 Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.962A pdb=" N VAL A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 142 removed outlier: 3.588A pdb=" N ILE A 120 " --> pdb=" O MET A 116 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 155 through 160 removed outlier: 3.504A pdb=" N ILE A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 160' Processing helix chain 'A' and resid 163 through 180 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 186 through 216 removed outlier: 3.838A pdb=" N ILE A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASN A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 245 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 248 through 258 removed outlier: 3.657A pdb=" N ARG A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 removed outlier: 4.200A pdb=" N SER A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.641A pdb=" N ILE A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 280 " --> pdb=" O PRO A 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 275 through 280' Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 310 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.041A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 200 Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.917A pdb=" N ALA L 82 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 127 removed outlier: 3.522A pdb=" N LEU L 124 " --> pdb=" O SER L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 188 removed outlier: 3.683A pdb=" N HIS L 188 " --> pdb=" O GLU L 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.587A pdb=" N THR H 119 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL H 12 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR H 94 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN H 59 " --> pdb=" O GLU H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.587A pdb=" N THR H 119 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL H 12 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR H 94 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP H 102 " --> pdb=" O PHE H 107 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE H 107 " --> pdb=" O ASP H 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 129 through 133 removed outlier: 4.005A pdb=" N SER H 129 " --> pdb=" O LYS H 152 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY H 148 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL H 192 " --> pdb=" O VAL H 145 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS H 149 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER H 188 " --> pdb=" O CYS H 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 129 through 133 removed outlier: 4.005A pdb=" N SER H 129 " --> pdb=" O LYS H 152 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY H 148 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY H 153 " --> pdb=" O TYR H 184 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR H 184 " --> pdb=" O GLY H 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 160 through 161 Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.559A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL L 19 " --> pdb=" O ILE L 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 11 removed outlier: 5.917A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.900A pdb=" N GLN L 89 " --> pdb=" O THR L 96 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR L 96 " --> pdb=" O GLN L 89 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 115 through 117 removed outlier: 3.643A pdb=" N PHE L 117 " --> pdb=" O VAL L 132 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL L 132 " --> pdb=" O PHE L 117 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU L 135 " --> pdb=" O MET L 174 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N TYR L 172 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 152 through 153 284 hydrogen bonds defined for protein. 771 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: 1.65 Time building geometry restraints manager: 1.61 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: 1694 1.34 - 1.46: 1181 1.46 - 1.58: 2812 1.58 - 1.69: 1 1.69 - 1.81: 76 Bond restraints: 5764 Sorted by residual: bond pdb=" CB PRO H 127 " pdb=" CG PRO H 127 " ideal model delta sigma weight residual 1.492 1.662 -0.170 5.00e-02 4.00e+02 1.15e+01 bond pdb=" N PRO H 127 " pdb=" CD PRO H 127 " ideal model delta sigma weight residual 1.473 1.518 -0.045 1.40e-02 5.10e+03 1.04e+01 bond pdb=" CG PRO H 127 " pdb=" CD PRO H 127 " ideal model delta sigma weight residual 1.503 1.405 0.098 3.40e-02 8.65e+02 8.24e+00 bond pdb=" C VAL A 164 " pdb=" N PRO A 165 " ideal model delta sigma weight residual 1.337 1.355 -0.018 9.80e-03 1.04e+04 3.43e+00 bond pdb=" N PRO H 127 " pdb=" CA PRO H 127 " ideal model delta sigma weight residual 1.465 1.431 0.034 2.03e-02 2.43e+03 2.85e+00 ... (remaining 5759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 7816 3.27 - 6.53: 32 6.53 - 9.80: 2 9.80 - 13.06: 3 13.06 - 16.33: 1 Bond angle restraints: 7854 Sorted by residual: angle pdb=" CA PRO H 127 " pdb=" N PRO H 127 " pdb=" CD PRO H 127 " ideal model delta sigma weight residual 112.00 95.67 16.33 1.40e+00 5.10e-01 1.36e+02 angle pdb=" N PRO H 127 " pdb=" CD PRO H 127 " pdb=" CG PRO H 127 " ideal model delta sigma weight residual 103.20 95.31 7.89 1.50e+00 4.44e-01 2.77e+01 angle pdb=" CA PRO H 127 " pdb=" CB PRO H 127 " pdb=" CG PRO H 127 " ideal model delta sigma weight residual 104.50 96.85 7.65 1.90e+00 2.77e-01 1.62e+01 angle pdb=" CB MET A 34 " pdb=" CG MET A 34 " pdb=" SD MET A 34 " ideal model delta sigma weight residual 112.70 123.46 -10.76 3.00e+00 1.11e-01 1.29e+01 angle pdb=" N ILE A 145 " pdb=" CA ILE A 145 " pdb=" C ILE A 145 " ideal model delta sigma weight residual 112.96 109.71 3.25 1.00e+00 1.00e+00 1.06e+01 ... (remaining 7849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.04: 3223 24.04 - 48.08: 277 48.08 - 72.11: 30 72.11 - 96.15: 19 96.15 - 120.19: 7 Dihedral angle restraints: 3556 sinusoidal: 1449 harmonic: 2107 Sorted by residual: dihedral pdb=" C4 TCH A 401 " pdb=" C5 TCH A 401 " pdb=" C6 TCH A 401 " pdb=" C7 TCH A 401 " ideal model delta sinusoidal sigma weight residual 74.38 -165.43 -120.19 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" CB CYS H 149 " pdb=" SG CYS H 149 " pdb=" SG CYS H 204 " pdb=" CB CYS H 204 " ideal model delta sinusoidal sigma weight residual 93.00 59.47 33.53 1 1.00e+01 1.00e-02 1.60e+01 dihedral pdb=" C10 TCH A 401 " pdb=" C5 TCH A 401 " pdb=" C6 TCH A 401 " pdb=" C7 TCH A 401 " ideal model delta sinusoidal sigma weight residual -53.95 60.40 -114.35 1 3.00e+01 1.11e-03 1.51e+01 ... (remaining 3553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 725 0.046 - 0.092: 150 0.092 - 0.139: 45 0.139 - 0.185: 1 0.185 - 0.231: 1 Chirality restraints: 922 Sorted by residual: chirality pdb=" CA PRO H 127 " pdb=" N PRO H 127 " pdb=" C PRO H 127 " pdb=" CB PRO H 127 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C5 TCH A 401 " pdb=" C10 TCH A 401 " pdb=" C4 TCH A 401 " pdb=" C6 TCH A 401 " both_signs ideal model delta sigma weight residual False -2.45 -2.27 -0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" CA ILE L 47 " pdb=" N ILE L 47 " pdb=" C ILE L 47 " pdb=" CB ILE L 47 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 919 not shown) Planarity restraints: 959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 126 " 0.078 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO H 127 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO H 127 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO H 127 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 21 " -0.037 5.00e-02 4.00e+02 5.50e-02 4.85e+00 pdb=" N PRO A 22 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO H 127 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C PRO H 127 " -0.034 2.00e-02 2.50e+03 pdb=" O PRO H 127 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO H 128 " 0.011 2.00e-02 2.50e+03 ... (remaining 956 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 153 2.70 - 3.25: 5491 3.25 - 3.80: 8712 3.80 - 4.35: 10633 4.35 - 4.90: 18554 Nonbonded interactions: 43543 Sorted by model distance: nonbonded pdb=" OG1 THR H 28 " pdb=" OD1 ASN H 31 " model vdw 2.156 3.040 nonbonded pdb=" O PRO H 132 " pdb=" OG SER L 120 " model vdw 2.210 3.040 nonbonded pdb=" OE1 GLN H 6 " pdb=" OG1 THR H 116 " model vdw 2.239 3.040 nonbonded pdb=" OG SER A 99 " pdb=" O ASN A 262 " model vdw 2.244 3.040 nonbonded pdb=" OG SER H 211 " pdb=" OG1 THR H 213 " model vdw 2.247 3.040 ... (remaining 43538 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: 0.580 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: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.700 Find NCS groups from input model: 0.060 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 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 0.170 5764 Z= 0.325 Angle : 0.662 16.328 7854 Z= 0.344 Chirality : 0.042 0.231 922 Planarity : 0.005 0.107 959 Dihedral : 18.637 120.190 2194 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.32 % Allowed : 21.08 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.81 (0.33), residues: 721 helix: 1.57 (0.35), residues: 243 sheet: 0.55 (0.39), residues: 214 loop : -0.36 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 162 HIS 0.002 0.001 HIS A 54 PHE 0.021 0.001 PHE L 138 TYR 0.012 0.001 TYR H 184 ARG 0.003 0.000 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.475 Fit side-chains REVERT: A 151 LYS cc_start: 0.8340 (ptpt) cc_final: 0.7981 (tmtt) REVERT: A 269 ILE cc_start: 0.6364 (mm) cc_final: 0.5913 (mm) REVERT: A 303 MET cc_start: 0.7231 (mtt) cc_final: 0.6943 (mtt) outliers start: 2 outliers final: 1 residues processed: 126 average time/residue: 0.1572 time to fit residues: 26.3757 Evaluate side-chains 84 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 185 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 0.0470 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.187958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.142850 restraints weight = 6358.323| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.71 r_work: 0.3370 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5764 Z= 0.234 Angle : 0.668 8.161 7854 Z= 0.319 Chirality : 0.046 0.303 922 Planarity : 0.005 0.056 959 Dihedral : 8.454 75.432 928 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.28 % Allowed : 19.18 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 721 helix: 1.49 (0.34), residues: 243 sheet: 0.63 (0.37), residues: 223 loop : -0.62 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 162 HIS 0.004 0.001 HIS L 188 PHE 0.031 0.002 PHE H 155 TYR 0.010 0.001 TYR L 35 ARG 0.004 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.611 Fit side-chains REVERT: A 34 MET cc_start: 0.6929 (tpp) cc_final: 0.6134 (ttm) REVERT: A 122 MET cc_start: 0.7897 (mmt) cc_final: 0.7668 (mmt) REVERT: A 151 LYS cc_start: 0.8579 (ptpt) cc_final: 0.7679 (tmtt) REVERT: A 192 MET cc_start: 0.4050 (mmp) cc_final: 0.3565 (mmm) REVERT: H 3 GLN cc_start: 0.7323 (pt0) cc_final: 0.6901 (tt0) REVERT: H 80 TYR cc_start: 0.8222 (m-80) cc_final: 0.7877 (m-10) REVERT: H 109 MET cc_start: 0.7591 (ptp) cc_final: 0.7368 (ttp) REVERT: H 114 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7811 (mp) REVERT: H 124 LYS cc_start: 0.7106 (tttm) cc_final: 0.6739 (tppt) REVERT: L 80 GLU cc_start: 0.8079 (tp30) cc_final: 0.7606 (tt0) outliers start: 27 outliers final: 12 residues processed: 110 average time/residue: 0.1533 time to fit residues: 23.0804 Evaluate side-chains 92 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 145 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 54 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 50 optimal weight: 30.0000 chunk 70 optimal weight: 8.9990 chunk 29 optimal weight: 0.4980 chunk 62 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.185621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.141014 restraints weight = 6344.227| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.86 r_work: 0.3319 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5764 Z= 0.228 Angle : 0.622 8.274 7854 Z= 0.305 Chirality : 0.043 0.162 922 Planarity : 0.005 0.054 959 Dihedral : 6.715 74.813 927 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.65 % Allowed : 21.71 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.66 (0.32), residues: 721 helix: 1.53 (0.34), residues: 244 sheet: 0.50 (0.36), residues: 226 loop : -0.62 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 162 HIS 0.003 0.001 HIS L 188 PHE 0.019 0.002 PHE H 155 TYR 0.015 0.002 TYR H 154 ARG 0.003 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.606 Fit side-chains REVERT: A 79 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7223 (mt) REVERT: A 116 MET cc_start: 0.7827 (tpp) cc_final: 0.7427 (tpp) REVERT: H 124 LYS cc_start: 0.7071 (tttm) cc_final: 0.6848 (tppt) REVERT: L 77 MET cc_start: 0.7022 (tpp) cc_final: 0.6260 (ttt) REVERT: L 80 GLU cc_start: 0.8411 (tp30) cc_final: 0.7902 (tt0) REVERT: L 174 MET cc_start: 0.6758 (tpt) cc_final: 0.6449 (tpt) outliers start: 23 outliers final: 14 residues processed: 88 average time/residue: 0.1474 time to fit residues: 18.0471 Evaluate side-chains 80 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 96 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 0.1980 chunk 52 optimal weight: 0.0470 chunk 14 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.188440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.143807 restraints weight = 6442.258| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.83 r_work: 0.3330 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5764 Z= 0.166 Angle : 0.547 6.803 7854 Z= 0.269 Chirality : 0.041 0.132 922 Planarity : 0.004 0.055 959 Dihedral : 6.341 74.932 927 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.96 % Allowed : 21.71 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.87 (0.32), residues: 721 helix: 1.70 (0.34), residues: 243 sheet: 0.71 (0.37), residues: 220 loop : -0.58 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 162 HIS 0.004 0.001 HIS L 88 PHE 0.017 0.001 PHE H 155 TYR 0.012 0.001 TYR H 154 ARG 0.004 0.000 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.636 Fit side-chains REVERT: H 3 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.7187 (tt0) REVERT: H 106 VAL cc_start: 0.7288 (OUTLIER) cc_final: 0.6961 (m) REVERT: L 7 SER cc_start: 0.8156 (m) cc_final: 0.7836 (p) REVERT: L 77 MET cc_start: 0.7006 (tpp) cc_final: 0.6358 (ttt) outliers start: 25 outliers final: 20 residues processed: 93 average time/residue: 0.1321 time to fit residues: 17.2367 Evaluate side-chains 87 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 145 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 43 optimal weight: 0.0020 chunk 31 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.189786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.145182 restraints weight = 6315.610| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.78 r_work: 0.3316 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5764 Z= 0.198 Angle : 0.565 7.059 7854 Z= 0.275 Chirality : 0.041 0.130 922 Planarity : 0.004 0.054 959 Dihedral : 6.189 74.801 927 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.91 % Allowed : 20.29 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 721 helix: 1.80 (0.34), residues: 243 sheet: 0.63 (0.36), residues: 225 loop : -0.52 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 162 HIS 0.004 0.001 HIS L 88 PHE 0.015 0.001 PHE H 155 TYR 0.012 0.001 TYR H 154 ARG 0.003 0.000 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 69 time to evaluate : 0.602 Fit side-chains REVERT: A 146 TYR cc_start: 0.8960 (t80) cc_final: 0.8538 (t80) REVERT: A 277 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.7649 (pt0) REVERT: H 88 SER cc_start: 0.8874 (OUTLIER) cc_final: 0.8389 (p) REVERT: H 106 VAL cc_start: 0.7334 (OUTLIER) cc_final: 0.7032 (m) REVERT: H 144 MET cc_start: 0.5030 (pmm) cc_final: 0.4661 (mmm) REVERT: L 7 SER cc_start: 0.8289 (m) cc_final: 0.8005 (p) REVERT: L 77 MET cc_start: 0.7199 (tpp) cc_final: 0.6503 (ttt) outliers start: 31 outliers final: 24 residues processed: 97 average time/residue: 0.1291 time to fit residues: 17.7546 Evaluate side-chains 94 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 67 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain L residue 164 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 39 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 67 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 chunk 51 optimal weight: 0.0870 chunk 46 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.184961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.3485 r_free = 0.3485 target = 0.136709 restraints weight = 6308.950| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.75 r_work: 0.3346 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5764 Z= 0.184 Angle : 0.539 7.026 7854 Z= 0.264 Chirality : 0.041 0.136 922 Planarity : 0.004 0.054 959 Dihedral : 6.145 75.253 927 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.07 % Allowed : 21.55 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.91 (0.32), residues: 721 helix: 1.83 (0.34), residues: 243 sheet: 0.69 (0.38), residues: 207 loop : -0.55 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 162 HIS 0.004 0.001 HIS L 88 PHE 0.014 0.001 PHE H 155 TYR 0.011 0.001 TYR H 154 ARG 0.002 0.000 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 77 time to evaluate : 0.589 Fit side-chains REVERT: A 79 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7781 (mp) REVERT: A 146 TYR cc_start: 0.8931 (t80) cc_final: 0.8475 (t80) REVERT: A 192 MET cc_start: 0.4082 (mmp) cc_final: 0.3660 (mmm) REVERT: A 214 ILE cc_start: 0.6069 (OUTLIER) cc_final: 0.5713 (tt) REVERT: A 243 LEU cc_start: 0.6430 (tp) cc_final: 0.5673 (mt) REVERT: A 247 ASN cc_start: 0.8450 (t0) cc_final: 0.8010 (t0) REVERT: A 277 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.7656 (pt0) REVERT: A 299 LEU cc_start: 0.8006 (mt) cc_final: 0.7504 (mt) REVERT: H 3 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.7055 (tt0) REVERT: H 55 ASN cc_start: 0.8657 (t0) cc_final: 0.8337 (t0) REVERT: H 106 VAL cc_start: 0.7254 (OUTLIER) cc_final: 0.6982 (m) REVERT: L 7 SER cc_start: 0.8388 (m) cc_final: 0.8165 (p) REVERT: L 77 MET cc_start: 0.7197 (tpp) cc_final: 0.6447 (ttt) REVERT: L 174 MET cc_start: 0.7401 (tpt) cc_final: 0.6484 (tpt) outliers start: 32 outliers final: 25 residues processed: 106 average time/residue: 0.1348 time to fit residues: 20.1736 Evaluate side-chains 101 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain L residue 164 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.183009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.134369 restraints weight = 6301.785| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.78 r_work: 0.3316 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.5413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5764 Z= 0.221 Angle : 0.577 9.952 7854 Z= 0.279 Chirality : 0.041 0.134 922 Planarity : 0.005 0.054 959 Dihedral : 6.186 75.130 927 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.39 % Allowed : 21.71 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 721 helix: 1.81 (0.34), residues: 243 sheet: 0.52 (0.36), residues: 225 loop : -0.40 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 162 HIS 0.004 0.001 HIS L 88 PHE 0.015 0.001 PHE H 155 TYR 0.024 0.001 TYR H 154 ARG 0.003 0.000 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 73 time to evaluate : 0.624 Fit side-chains REVERT: A 79 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7955 (mp) REVERT: A 146 TYR cc_start: 0.8955 (t80) cc_final: 0.8565 (t80) REVERT: A 214 ILE cc_start: 0.6275 (OUTLIER) cc_final: 0.5921 (tt) REVERT: A 243 LEU cc_start: 0.6610 (tp) cc_final: 0.5771 (mt) REVERT: A 247 ASN cc_start: 0.8620 (t0) cc_final: 0.8171 (t0) REVERT: A 277 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.7628 (pt0) REVERT: A 299 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7585 (mt) REVERT: H 3 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.7064 (tt0) REVERT: H 55 ASN cc_start: 0.8683 (t0) cc_final: 0.8392 (t0) REVERT: H 88 SER cc_start: 0.8779 (OUTLIER) cc_final: 0.8445 (p) REVERT: H 106 VAL cc_start: 0.7299 (OUTLIER) cc_final: 0.7035 (m) REVERT: L 7 SER cc_start: 0.8486 (m) cc_final: 0.8266 (p) REVERT: L 77 MET cc_start: 0.6934 (tpp) cc_final: 0.6479 (ttt) outliers start: 34 outliers final: 27 residues processed: 102 average time/residue: 0.1227 time to fit residues: 18.1222 Evaluate side-chains 106 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 72 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain L residue 164 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 71 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 60 optimal weight: 0.0170 chunk 51 optimal weight: 0.0010 overall best weight: 0.4624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.185297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.137674 restraints weight = 6265.544| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.90 r_work: 0.3329 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5764 Z= 0.160 Angle : 0.542 8.736 7854 Z= 0.263 Chirality : 0.040 0.139 922 Planarity : 0.004 0.054 959 Dihedral : 6.090 75.212 927 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.75 % Allowed : 22.50 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.32), residues: 721 helix: 1.94 (0.34), residues: 243 sheet: 0.73 (0.38), residues: 207 loop : -0.48 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 162 HIS 0.004 0.001 HIS L 88 PHE 0.015 0.001 PHE H 155 TYR 0.021 0.001 TYR H 154 ARG 0.003 0.000 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.594 Fit side-chains REVERT: A 79 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7895 (mp) REVERT: A 146 TYR cc_start: 0.8959 (t80) cc_final: 0.8526 (t80) REVERT: A 192 MET cc_start: 0.4460 (mmp) cc_final: 0.4012 (mmm) REVERT: A 214 ILE cc_start: 0.5957 (OUTLIER) cc_final: 0.5624 (tt) REVERT: A 243 LEU cc_start: 0.6544 (tp) cc_final: 0.5658 (mt) REVERT: A 247 ASN cc_start: 0.8353 (t0) cc_final: 0.7856 (t0) REVERT: A 277 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.7640 (pt0) REVERT: A 299 LEU cc_start: 0.8018 (mt) cc_final: 0.7467 (mt) REVERT: H 3 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.7113 (tt0) REVERT: H 55 ASN cc_start: 0.8688 (t0) cc_final: 0.8359 (t0) REVERT: H 88 SER cc_start: 0.8833 (OUTLIER) cc_final: 0.8552 (p) REVERT: H 106 VAL cc_start: 0.7319 (OUTLIER) cc_final: 0.7053 (m) REVERT: L 7 SER cc_start: 0.8560 (m) cc_final: 0.8290 (p) REVERT: L 77 MET cc_start: 0.6992 (tpp) cc_final: 0.6153 (ttt) REVERT: L 174 MET cc_start: 0.7461 (tpt) cc_final: 0.6679 (tpt) outliers start: 30 outliers final: 24 residues processed: 103 average time/residue: 0.1263 time to fit residues: 18.7980 Evaluate side-chains 102 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 145 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 19 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 66 optimal weight: 20.0000 chunk 68 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN L 197 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.180874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.135856 restraints weight = 6353.379| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.93 r_work: 0.3249 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.5860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5764 Z= 0.238 Angle : 0.594 9.967 7854 Z= 0.288 Chirality : 0.042 0.142 922 Planarity : 0.005 0.053 959 Dihedral : 6.200 74.905 927 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.39 % Allowed : 21.87 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.99 (0.33), residues: 721 helix: 1.92 (0.35), residues: 236 sheet: 0.49 (0.36), residues: 224 loop : -0.28 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP L 162 HIS 0.004 0.001 HIS L 88 PHE 0.015 0.002 PHE H 155 TYR 0.021 0.001 TYR H 154 ARG 0.005 0.000 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 78 time to evaluate : 0.601 Fit side-chains REVERT: A 79 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8104 (mp) REVERT: A 146 TYR cc_start: 0.8989 (t80) cc_final: 0.8584 (t80) REVERT: A 214 ILE cc_start: 0.6077 (OUTLIER) cc_final: 0.5734 (tt) REVERT: A 243 LEU cc_start: 0.6732 (tp) cc_final: 0.5835 (mt) REVERT: A 247 ASN cc_start: 0.8451 (t0) cc_final: 0.8036 (t0) REVERT: A 277 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.7725 (pt0) REVERT: A 299 LEU cc_start: 0.8188 (mt) cc_final: 0.7955 (mt) REVERT: H 3 GLN cc_start: 0.7399 (OUTLIER) cc_final: 0.7123 (tt0) REVERT: H 55 ASN cc_start: 0.8823 (t0) cc_final: 0.8536 (t0) REVERT: H 88 SER cc_start: 0.8851 (OUTLIER) cc_final: 0.8585 (p) REVERT: H 106 VAL cc_start: 0.7375 (OUTLIER) cc_final: 0.7119 (m) REVERT: L 7 SER cc_start: 0.8607 (m) cc_final: 0.8336 (p) REVERT: L 77 MET cc_start: 0.7104 (tpp) cc_final: 0.6851 (ttm) outliers start: 34 outliers final: 27 residues processed: 107 average time/residue: 0.1303 time to fit residues: 20.0438 Evaluate side-chains 110 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain L residue 164 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 30 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.179901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.135148 restraints weight = 6442.250| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.83 r_work: 0.3260 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.6098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5764 Z= 0.248 Angle : 0.591 9.524 7854 Z= 0.288 Chirality : 0.042 0.137 922 Planarity : 0.005 0.054 959 Dihedral : 6.198 74.647 927 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.07 % Allowed : 22.35 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.91 (0.33), residues: 721 helix: 1.87 (0.35), residues: 236 sheet: 0.47 (0.36), residues: 224 loop : -0.37 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP L 162 HIS 0.005 0.001 HIS L 88 PHE 0.016 0.002 PHE H 155 TYR 0.017 0.001 TYR H 154 ARG 0.005 0.000 ARG L 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 0.577 Fit side-chains REVERT: A 79 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8108 (mp) REVERT: A 146 TYR cc_start: 0.8974 (t80) cc_final: 0.8644 (t80) REVERT: A 184 MET cc_start: 0.3629 (tpt) cc_final: 0.2269 (tpt) REVERT: A 192 MET cc_start: 0.4725 (mmp) cc_final: 0.4193 (mmm) REVERT: A 214 ILE cc_start: 0.6170 (OUTLIER) cc_final: 0.5831 (tt) REVERT: A 243 LEU cc_start: 0.6771 (tp) cc_final: 0.5928 (mt) REVERT: A 247 ASN cc_start: 0.8468 (t0) cc_final: 0.8053 (t0) REVERT: A 277 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.7713 (pt0) REVERT: A 299 LEU cc_start: 0.8128 (mt) cc_final: 0.7910 (mt) REVERT: H 3 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.7067 (tt0) REVERT: H 55 ASN cc_start: 0.8823 (t0) cc_final: 0.8532 (t0) REVERT: H 88 SER cc_start: 0.8797 (OUTLIER) cc_final: 0.8566 (p) REVERT: H 106 VAL cc_start: 0.7419 (OUTLIER) cc_final: 0.7163 (m) REVERT: L 7 SER cc_start: 0.8573 (m) cc_final: 0.8324 (p) REVERT: L 77 MET cc_start: 0.7111 (tpp) cc_final: 0.6792 (ttt) REVERT: L 174 MET cc_start: 0.8158 (tpt) cc_final: 0.7618 (tpt) outliers start: 32 outliers final: 24 residues processed: 108 average time/residue: 0.1214 time to fit residues: 18.9125 Evaluate side-chains 106 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 145 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 20 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.181790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.136488 restraints weight = 6328.897| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.65 r_work: 0.3326 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.6195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5764 Z= 0.193 Angle : 0.565 9.134 7854 Z= 0.276 Chirality : 0.041 0.139 922 Planarity : 0.005 0.054 959 Dihedral : 6.154 74.814 927 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.60 % Allowed : 22.50 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.98 (0.32), residues: 721 helix: 1.94 (0.35), residues: 236 sheet: 0.64 (0.37), residues: 211 loop : -0.44 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP L 162 HIS 0.004 0.001 HIS L 88 PHE 0.015 0.001 PHE H 155 TYR 0.016 0.001 TYR H 154 ARG 0.004 0.000 ARG L 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3167.66 seconds wall clock time: 57 minutes 3.58 seconds (3423.58 seconds total)