Starting phenix.real_space_refine on Thu Mar 6 09:00:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xcd_38240/03_2025/8xcd_38240.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xcd_38240/03_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_38240/03_2025/8xcd_38240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xcd_38240/03_2025/8xcd_38240.map" model { file = "/net/cci-nas-00/data/ceres_data/8xcd_38240/03_2025/8xcd_38240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xcd_38240/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.98, per 1000 atoms: 0.71 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: 1.43 Conformation dependent library (CDL) restraints added in 798.2 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: 1.62 Time building geometry restraints manager: 1.66 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.710 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.800 ------------------------------------------------------------------------------- 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 : 0.549 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: 0.1560 time to fit residues: 26.2426 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 : 0.630 ------------------------------------------------------------------------------- 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 = 0.142827 restraints weight = 6358.320| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.71 r_work: 0.3371 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 : 0.606 Fit side-chains REVERT: A 34 MET cc_start: 0.6928 (tpp) cc_final: 0.6133 (ttm) REVERT: A 122 MET cc_start: 0.7898 (mmt) cc_final: 0.7670 (mmt) REVERT: A 151 LYS cc_start: 0.8578 (ptpt) cc_final: 0.7677 (tmtt) REVERT: A 192 MET cc_start: 0.4050 (mmp) cc_final: 0.3565 (mmm) REVERT: H 3 GLN cc_start: 0.7322 (pt0) cc_final: 0.6900 (tt0) REVERT: H 80 TYR cc_start: 0.8220 (m-80) cc_final: 0.7876 (m-10) REVERT: H 109 MET cc_start: 0.7592 (ptp) cc_final: 0.7369 (ttp) REVERT: H 114 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7809 (mp) REVERT: H 124 LYS cc_start: 0.7107 (tttm) cc_final: 0.6739 (tppt) REVERT: L 80 GLU cc_start: 0.8082 (tp30) cc_final: 0.7607 (tt0) outliers start: 27 outliers final: 12 residues processed: 110 average time/residue: 0.1424 time to fit residues: 21.5724 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 : 0.617 ------------------------------------------------------------------------------- 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: 0.7980 chunk 16 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 70 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 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: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.185325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.134543 restraints weight = 6344.482| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.97 r_work: 0.3328 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5764 Z= 0.234 Angle : 0.621 8.086 7854 Z= 0.303 Chirality : 0.043 0.168 922 Planarity : 0.005 0.054 959 Dihedral : 6.877 74.919 927 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.96 % Allowed : 21.39 % 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: 0.65 (0.32), residues: 721 helix: 1.55 (0.34), residues: 243 sheet: 0.50 (0.36), residues: 226 loop : -0.66 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 162 HIS 0.003 0.001 HIS L 188 PHE 0.018 0.002 PHE H 155 TYR 0.013 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 97 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.878 Fit side-chains REVERT: A 79 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7091 (mt) REVERT: A 116 MET cc_start: 0.7844 (tpp) cc_final: 0.7414 (tpp) REVERT: A 192 MET cc_start: 0.4080 (mmp) cc_final: 0.3681 (mmm) REVERT: H 109 MET cc_start: 0.8063 (ptp) cc_final: 0.7816 (ttp) REVERT: H 124 LYS cc_start: 0.7019 (tttm) cc_final: 0.6771 (tppt) REVERT: L 77 MET cc_start: 0.6942 (tpp) cc_final: 0.6122 (ttt) REVERT: L 80 GLU cc_start: 0.8381 (tp30) cc_final: 0.7838 (tt0) REVERT: L 162 TRP cc_start: 0.7946 (m-90) cc_final: 0.7745 (m-90) REVERT: L 174 MET cc_start: 0.6656 (tpt) cc_final: 0.6268 (tpt) outliers start: 25 outliers final: 16 residues processed: 92 average time/residue: 0.2160 time to fit residues: 28.6635 Evaluate side-chains 85 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 87 THR Chi-restraints excluded: chain H residue 106 VAL 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 84 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 145 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.184878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.137032 restraints weight = 6449.330| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.84 r_work: 0.3315 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5764 Z= 0.212 Angle : 0.574 7.345 7854 Z= 0.282 Chirality : 0.042 0.130 922 Planarity : 0.004 0.055 959 Dihedral : 6.403 74.739 927 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.44 % Allowed : 21.39 % Favored : 74.17 % 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: 0.76 (0.32), residues: 721 helix: 1.62 (0.34), residues: 243 sheet: 0.59 (0.36), residues: 226 loop : -0.61 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 162 HIS 0.004 0.001 HIS L 88 PHE 0.016 0.002 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 94 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.490 Fit side-chains REVERT: A 277 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.7552 (pt0) REVERT: H 88 SER cc_start: 0.8908 (OUTLIER) cc_final: 0.8398 (p) REVERT: H 106 VAL cc_start: 0.7337 (OUTLIER) cc_final: 0.6992 (m) REVERT: L 7 SER cc_start: 0.8328 (m) cc_final: 0.7982 (p) REVERT: L 32 MET cc_start: 0.8471 (tpp) cc_final: 0.8204 (ttm) REVERT: L 77 MET cc_start: 0.7054 (tpp) cc_final: 0.6494 (ttt) outliers start: 28 outliers final: 20 residues processed: 92 average time/residue: 0.1365 time to fit residues: 17.7838 Evaluate side-chains 85 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 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 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 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 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 Chi-restraints excluded: chain L residue 164 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 43 optimal weight: 0.0470 chunk 31 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 61 optimal weight: 0.0000 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 0.0970 chunk 6 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.3280 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.187495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.142881 restraints weight = 6330.039| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.71 r_work: 0.3351 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5764 Z= 0.154 Angle : 0.542 7.253 7854 Z= 0.264 Chirality : 0.040 0.141 922 Planarity : 0.004 0.055 959 Dihedral : 6.170 74.873 927 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.80 % Allowed : 22.98 % Favored : 73.22 % 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: 0.93 (0.32), residues: 721 helix: 1.77 (0.34), residues: 243 sheet: 0.72 (0.37), residues: 220 loop : -0.55 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 162 HIS 0.004 0.001 HIS L 88 PHE 0.016 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 94 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.599 Fit side-chains REVERT: A 79 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7363 (mt) REVERT: A 192 MET cc_start: 0.4188 (mmp) cc_final: 0.3646 (mmm) REVERT: A 243 LEU cc_start: 0.6349 (tp) cc_final: 0.5571 (mt) REVERT: H 3 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.7155 (tt0) REVERT: H 106 VAL cc_start: 0.7307 (OUTLIER) cc_final: 0.7025 (m) REVERT: L 7 SER cc_start: 0.8239 (m) cc_final: 0.7966 (p) REVERT: L 77 MET cc_start: 0.7188 (tpp) cc_final: 0.6555 (ttt) REVERT: L 162 TRP cc_start: 0.8057 (m-90) cc_final: 0.7679 (m-90) outliers start: 24 outliers final: 19 residues processed: 91 average time/residue: 0.1345 time to fit residues: 17.2355 Evaluate side-chains 90 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 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 294 LEU Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 54 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 62 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 145 VAL 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: 0.8980 chunk 67 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 0.5980 chunk 51 optimal weight: 0.0570 chunk 46 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.192365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.147596 restraints weight = 6297.325| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.71 r_work: 0.3346 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5764 Z= 0.175 Angle : 0.555 8.837 7854 Z= 0.267 Chirality : 0.041 0.138 922 Planarity : 0.004 0.054 959 Dihedral : 6.121 75.212 927 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.91 % Allowed : 22.35 % 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: 0.94 (0.32), residues: 721 helix: 1.84 (0.34), residues: 243 sheet: 0.76 (0.38), residues: 205 loop : -0.57 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 0.004 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 104 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 73 time to evaluate : 0.557 Fit side-chains REVERT: A 146 TYR cc_start: 0.8908 (t80) cc_final: 0.8545 (t80) REVERT: A 243 LEU cc_start: 0.6372 (tp) cc_final: 0.5618 (mt) REVERT: A 247 ASN cc_start: 0.8556 (t0) cc_final: 0.8176 (t0) REVERT: H 3 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.7128 (tt0) REVERT: H 55 ASN cc_start: 0.8633 (t0) cc_final: 0.8317 (t0) REVERT: H 106 VAL cc_start: 0.7296 (OUTLIER) cc_final: 0.7032 (m) REVERT: L 7 SER cc_start: 0.8324 (m) cc_final: 0.8076 (p) REVERT: L 77 MET cc_start: 0.7159 (tpp) cc_final: 0.6497 (ttt) outliers start: 31 outliers final: 25 residues processed: 99 average time/residue: 0.1124 time to fit residues: 16.6112 Evaluate side-chains 96 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 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 219 THR 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.0670 chunk 24 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN A 293 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.182075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.139412 restraints weight = 6281.241| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.45 r_work: 0.3328 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.5463 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= 0.230 Angle : 0.581 9.331 7854 Z= 0.283 Chirality : 0.042 0.135 922 Planarity : 0.005 0.054 959 Dihedral : 6.288 75.112 927 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.75 % Allowed : 22.82 % Favored : 72.42 % 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: 1.76 (0.34), residues: 243 sheet: 0.58 (0.37), residues: 226 loop : -0.45 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 162 HIS 0.004 0.001 HIS L 88 PHE 0.019 0.002 PHE H 155 TYR 0.017 0.002 TYR H 154 ARG 0.004 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 104 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 0.589 Fit side-chains REVERT: A 79 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7979 (mp) REVERT: A 146 TYR cc_start: 0.8946 (t80) cc_final: 0.8613 (t80) REVERT: A 214 ILE cc_start: 0.6286 (OUTLIER) cc_final: 0.5938 (tt) REVERT: A 243 LEU cc_start: 0.6647 (tp) cc_final: 0.5820 (mt) REVERT: A 247 ASN cc_start: 0.8649 (t0) cc_final: 0.8197 (t0) REVERT: A 299 LEU cc_start: 0.8141 (mt) cc_final: 0.7603 (mt) REVERT: H 3 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.7046 (tt0) REVERT: H 55 ASN cc_start: 0.8697 (t0) cc_final: 0.8418 (t0) REVERT: H 88 SER cc_start: 0.8792 (OUTLIER) cc_final: 0.8475 (p) REVERT: H 106 VAL cc_start: 0.7246 (OUTLIER) cc_final: 0.7008 (m) REVERT: L 7 SER cc_start: 0.8553 (m) cc_final: 0.8286 (p) REVERT: L 77 MET cc_start: 0.6951 (tpp) cc_final: 0.6541 (ttm) REVERT: L 138 PHE cc_start: 0.8353 (p90) cc_final: 0.8065 (p90) REVERT: L 162 TRP cc_start: 0.8261 (m-90) cc_final: 0.7864 (m-90) outliers start: 30 outliers final: 24 residues processed: 101 average time/residue: 0.1190 time to fit residues: 17.3664 Evaluate side-chains 100 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 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 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: 7.9990 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 48 optimal weight: 0.0070 chunk 1 optimal weight: 0.9980 chunk 60 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 = 0.3986 r_free = 0.3986 target = 0.184452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 124)---------------| | r_work = 0.3490 r_free = 0.3490 target = 0.137014 restraints weight = 6280.759| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.47 r_work: 0.3373 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5764 Z= 0.172 Angle : 0.542 8.280 7854 Z= 0.263 Chirality : 0.040 0.141 922 Planarity : 0.004 0.054 959 Dihedral : 6.091 75.102 927 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.75 % Allowed : 22.66 % 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 (0.32), residues: 721 helix: 1.88 (0.34), residues: 243 sheet: 0.66 (0.38), residues: 206 loop : -0.57 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 162 HIS 0.004 0.001 HIS L 88 PHE 0.016 0.001 PHE H 155 TYR 0.015 0.001 TYR H 154 ARG 0.002 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 110 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.551 Fit side-chains REVERT: A 79 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7925 (mp) REVERT: A 146 TYR cc_start: 0.8913 (t80) cc_final: 0.8514 (t80) REVERT: A 192 MET cc_start: 0.4574 (mmp) cc_final: 0.4067 (mmm) REVERT: A 214 ILE cc_start: 0.6140 (OUTLIER) cc_final: 0.5794 (tt) REVERT: A 243 LEU cc_start: 0.6593 (tp) cc_final: 0.5775 (mt) REVERT: A 247 ASN cc_start: 0.8453 (t0) cc_final: 0.7974 (t0) REVERT: A 299 LEU cc_start: 0.8071 (mt) cc_final: 0.7531 (mt) REVERT: H 3 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.7007 (tt0) REVERT: H 55 ASN cc_start: 0.8719 (t0) cc_final: 0.8425 (t0) REVERT: H 106 VAL cc_start: 0.7269 (OUTLIER) cc_final: 0.7043 (m) REVERT: L 7 SER cc_start: 0.8459 (m) cc_final: 0.8248 (p) REVERT: L 77 MET cc_start: 0.6821 (tpp) cc_final: 0.6398 (ttt) REVERT: L 138 PHE cc_start: 0.8205 (p90) cc_final: 0.7879 (p90) outliers start: 30 outliers final: 25 residues processed: 105 average time/residue: 0.1219 time to fit residues: 18.2403 Evaluate side-chains 104 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 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 110 ASP 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 Chi-restraints excluded: chain L residue 164 ASP 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: 0.6980 chunk 26 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 63 optimal weight: 0.0570 chunk 24 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.184044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.136661 restraints weight = 6274.284| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.92 r_work: 0.3273 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.5788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5764 Z= 0.185 Angle : 0.547 8.698 7854 Z= 0.266 Chirality : 0.040 0.135 922 Planarity : 0.004 0.054 959 Dihedral : 6.100 75.053 927 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.91 % Allowed : 22.03 % Favored : 73.06 % 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: 1.01 (0.32), residues: 721 helix: 1.98 (0.34), residues: 237 sheet: 0.66 (0.38), residues: 206 loop : -0.43 (0.38), residues: 278 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 0.017 0.001 PHE H 155 TYR 0.017 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 109 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 78 time to evaluate : 0.615 Fit side-chains REVERT: A 79 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7955 (mp) REVERT: A 146 TYR cc_start: 0.8962 (t80) cc_final: 0.8598 (t80) REVERT: A 184 MET cc_start: 0.3587 (tpt) cc_final: 0.2237 (tpt) REVERT: A 192 MET cc_start: 0.4539 (mmp) cc_final: 0.4087 (mmm) REVERT: A 214 ILE cc_start: 0.6012 (OUTLIER) cc_final: 0.5673 (tt) REVERT: A 243 LEU cc_start: 0.6669 (tp) cc_final: 0.5780 (mt) REVERT: A 247 ASN cc_start: 0.8444 (t0) cc_final: 0.7963 (t0) REVERT: A 299 LEU cc_start: 0.8057 (mt) cc_final: 0.7724 (mt) REVERT: H 3 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.7200 (tt0) REVERT: H 55 ASN cc_start: 0.8844 (t0) cc_final: 0.8537 (t0) REVERT: H 106 VAL cc_start: 0.7413 (OUTLIER) cc_final: 0.7189 (m) REVERT: L 7 SER cc_start: 0.8570 (m) cc_final: 0.8347 (p) REVERT: L 77 MET cc_start: 0.7013 (tpp) cc_final: 0.6429 (ttt) REVERT: L 138 PHE cc_start: 0.8202 (p90) cc_final: 0.7922 (p90) REVERT: L 174 MET cc_start: 0.8081 (tpt) cc_final: 0.7284 (tpt) outliers start: 31 outliers final: 26 residues processed: 103 average time/residue: 0.1203 time to fit residues: 18.0318 Evaluate side-chains 103 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 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 110 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 30 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 7 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.181748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.136514 restraints weight = 6405.199| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.92 r_work: 0.3268 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.5954 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= 0.214 Angle : 0.567 8.840 7854 Z= 0.276 Chirality : 0.041 0.137 922 Planarity : 0.005 0.054 959 Dihedral : 6.132 74.903 927 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.07 % Allowed : 21.87 % Favored : 73.06 % 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: 1.00 (0.32), residues: 721 helix: 1.95 (0.35), residues: 237 sheet: 0.60 (0.37), residues: 211 loop : -0.39 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP L 162 HIS 0.004 0.001 HIS L 88 PHE 0.016 0.001 PHE H 155 TYR 0.017 0.001 TYR H 154 ARG 0.003 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 110 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 78 time to evaluate : 0.610 Fit side-chains REVERT: A 79 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8010 (mp) REVERT: A 146 TYR cc_start: 0.8942 (t80) cc_final: 0.8562 (t80) REVERT: A 184 MET cc_start: 0.3616 (tpt) cc_final: 0.2226 (tpt) REVERT: A 192 MET cc_start: 0.4636 (mmp) cc_final: 0.4169 (mmm) REVERT: A 214 ILE cc_start: 0.6041 (OUTLIER) cc_final: 0.5712 (tt) REVERT: A 243 LEU cc_start: 0.6695 (tp) cc_final: 0.5816 (mt) REVERT: A 247 ASN cc_start: 0.8325 (t0) cc_final: 0.7872 (t0) REVERT: A 299 LEU cc_start: 0.8097 (mt) cc_final: 0.7879 (mt) REVERT: H 3 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.7165 (tt0) REVERT: H 55 ASN cc_start: 0.8832 (t0) cc_final: 0.8536 (t0) REVERT: H 106 VAL cc_start: 0.7369 (OUTLIER) cc_final: 0.7155 (m) REVERT: L 7 SER cc_start: 0.8542 (m) cc_final: 0.8335 (p) REVERT: L 77 MET cc_start: 0.7050 (tpp) cc_final: 0.6520 (ttt) REVERT: L 162 TRP cc_start: 0.8256 (m-90) cc_final: 0.7879 (m-90) outliers start: 32 outliers final: 25 residues processed: 104 average time/residue: 0.1244 time to fit residues: 18.7815 Evaluate side-chains 106 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 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 110 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 30 optimal weight: 0.0970 chunk 13 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 chunk 0 optimal weight: 9.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.184477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.138757 restraints weight = 6291.969| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.67 r_work: 0.3340 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.6084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5764 Z= 0.166 Angle : 0.541 8.250 7854 Z= 0.263 Chirality : 0.040 0.145 922 Planarity : 0.004 0.054 959 Dihedral : 6.059 74.972 927 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.44 % Allowed : 22.50 % Favored : 73.06 % 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: 1.11 (0.33), residues: 721 helix: 2.08 (0.35), residues: 236 sheet: 0.73 (0.38), residues: 207 loop : -0.40 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP L 162 HIS 0.003 0.001 HIS L 88 PHE 0.016 0.001 PHE H 155 TYR 0.016 0.001 TYR H 154 ARG 0.001 0.000 ARG L 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3404.65 seconds wall clock time: 59 minutes 16.54 seconds (3556.54 seconds total)