Starting phenix.real_space_refine on Tue Feb 11 11:39:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8orm_17129/02_2025/8orm_17129.cif Found real_map, /net/cci-nas-00/data/ceres_data/8orm_17129/02_2025/8orm_17129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8orm_17129/02_2025/8orm_17129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8orm_17129/02_2025/8orm_17129.map" model { file = "/net/cci-nas-00/data/ceres_data/8orm_17129/02_2025/8orm_17129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8orm_17129/02_2025/8orm_17129.cif" } resolution = 1.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 32 5.16 5 Cl 1 4.86 5 C 3307 2.51 5 N 874 2.21 5 O 1127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5341 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "I" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2281 Unusual residues: {'ACE': 1} Classifications: {'peptide': 279, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Chain: "J" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2297 Classifications: {'peptide': 288} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 269} Chain breaks: 2 Chain: "J" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'V0G': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "I" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "J" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 112 Classifications: {'water': 112} Link IDs: {None: 111} Time building chain proxies: 4.15, per 1000 atoms: 0.78 Number of scatterers: 5341 At special positions: 0 Unit cell: (85.5, 93.3375, 68.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 32 16.00 O 1127 8.00 N 874 7.00 C 3307 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 750.1 milliseconds 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1200 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 3 sheets defined 62.3% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'H' and resid 262 through 275 removed outlier: 4.450A pdb=" N GLY H 267 " --> pdb=" O GLU H 264 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR H 271 " --> pdb=" O ARG H 268 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU H 272 " --> pdb=" O LEU H 269 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL H 275 " --> pdb=" O LEU H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 286 Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.872A pdb=" N ALA H 292 " --> pdb=" O THR H 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 4 Processing helix chain 'I' and resid 5 through 11 Processing helix chain 'I' and resid 15 through 38 Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 93 removed outlier: 3.914A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.532A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 127 Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.671A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 178 Processing helix chain 'I' and resid 183 through 186 removed outlier: 3.533A pdb=" N ILE I 186 " --> pdb=" O ASN I 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 183 through 186' Processing helix chain 'I' and resid 187 through 201 removed outlier: 3.792A pdb=" N THR I 201 " --> pdb=" O ARG I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 228 through 234 removed outlier: 3.530A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 240 Processing helix chain 'I' and resid 241 through 261 Processing helix chain 'I' and resid 266 through 283 Processing helix chain 'J' and resid 56 through 67 Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 110 through 131 Processing helix chain 'J' and resid 139 through 141 No H-bonds generated for 'chain 'J' and resid 139 through 141' Processing helix chain 'J' and resid 175 through 179 Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 192 through 209 removed outlier: 3.725A pdb=" N ALA J 198 " --> pdb=" O VAL J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 230 Processing helix chain 'J' and resid 239 through 243 Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 265 through 276 Processing helix chain 'J' and resid 285 through 291 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.774A pdb=" N SER J 296 " --> pdb=" O MET J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 307 Processing sheet with id=AA1, first strand: chain 'J' and resid 13 through 20 removed outlier: 7.382A pdb=" N LEU J 15 " --> pdb=" O ARG J 30 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ARG J 30 " --> pdb=" O LEU J 15 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N PHE J 17 " --> pdb=" O LYS J 28 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LYS J 28 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP J 79 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LEU J 77 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134 276 hydrogen bonds defined for protein. 762 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: 1.44 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 825 1.31 - 1.43: 1414 1.43 - 1.56: 2966 1.56 - 1.69: 0 1.69 - 1.81: 51 Bond restraints: 5256 Sorted by residual: bond pdb=" C11 V0G J 401 " pdb=" N10 V0G J 401 " ideal model delta sigma weight residual 1.358 1.460 -0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" C05 V0G J 401 " pdb=" N06 V0G J 401 " ideal model delta sigma weight residual 1.362 1.463 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" C17 V0G J 401 " pdb=" N16 V0G J 401 " ideal model delta sigma weight residual 1.363 1.464 -0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C32 V0G J 401 " pdb=" C33 V0G J 401 " ideal model delta sigma weight residual 1.450 1.532 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C15 V0G J 401 " pdb=" N16 V0G J 401 " ideal model delta sigma weight residual 1.391 1.470 -0.079 2.00e-02 2.50e+03 1.58e+01 ... (remaining 5251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 6955 1.57 - 3.15: 120 3.15 - 4.72: 31 4.72 - 6.30: 6 6.30 - 7.87: 2 Bond angle restraints: 7114 Sorted by residual: angle pdb=" C09 V0G J 401 " pdb=" N10 V0G J 401 " pdb=" C11 V0G J 401 " ideal model delta sigma weight residual 129.31 121.44 7.87 3.00e+00 1.11e-01 6.89e+00 angle pdb=" CB MET J 94 " pdb=" CG MET J 94 " pdb=" SD MET J 94 " ideal model delta sigma weight residual 112.70 119.92 -7.22 3.00e+00 1.11e-01 5.79e+00 angle pdb=" CA ILE I 186 " pdb=" CB ILE I 186 " pdb=" CG1 ILE I 186 " ideal model delta sigma weight residual 110.40 114.26 -3.86 1.70e+00 3.46e-01 5.15e+00 angle pdb=" CA TYR I 91 " pdb=" CB TYR I 91 " pdb=" CG TYR I 91 " ideal model delta sigma weight residual 113.90 109.95 3.95 1.80e+00 3.09e-01 4.82e+00 angle pdb=" C VAL J 173 " pdb=" N VAL J 174 " pdb=" CA VAL J 174 " ideal model delta sigma weight residual 121.97 125.54 -3.57 1.80e+00 3.09e-01 3.93e+00 ... (remaining 7109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 2803 17.97 - 35.93: 251 35.93 - 53.90: 83 53.90 - 71.86: 20 71.86 - 89.83: 10 Dihedral angle restraints: 3167 sinusoidal: 1314 harmonic: 1853 Sorted by residual: dihedral pdb=" CG ARG J 298 " pdb=" CD ARG J 298 " pdb=" NE ARG J 298 " pdb=" CZ ARG J 298 " ideal model delta sinusoidal sigma weight residual -90.00 -42.52 -47.48 2 1.50e+01 4.44e-03 1.16e+01 dihedral pdb=" CA TYR I 91 " pdb=" C TYR I 91 " pdb=" N LEU I 92 " pdb=" CA LEU I 92 " ideal model delta harmonic sigma weight residual 180.00 163.07 16.93 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CB GLU I 61 " pdb=" CG GLU I 61 " pdb=" CD GLU I 61 " pdb=" OE1 GLU I 61 " ideal model delta sinusoidal sigma weight residual 0.00 89.83 -89.83 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 3164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 450 0.026 - 0.052: 190 0.052 - 0.077: 79 0.077 - 0.103: 41 0.103 - 0.129: 17 Chirality restraints: 777 Sorted by residual: chirality pdb=" CA TYR I 91 " pdb=" N TYR I 91 " pdb=" C TYR I 91 " pdb=" CB TYR I 91 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA PRO J 238 " pdb=" N PRO J 238 " pdb=" C PRO J 238 " pdb=" CB PRO J 238 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA VAL J 210 " pdb=" N VAL J 210 " pdb=" C VAL J 210 " pdb=" CB VAL J 210 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 774 not shown) Planarity restraints: 910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP I 44 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO I 45 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO I 45 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO I 45 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 298 " 0.128 9.50e-02 1.11e+02 5.75e-02 2.40e+00 pdb=" NE ARG J 298 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG J 298 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG J 298 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG J 298 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP I 193 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.81e+00 pdb=" C ASP I 193 " -0.023 2.00e-02 2.50e+03 pdb=" O ASP I 193 " 0.009 2.00e-02 2.50e+03 pdb=" N PHE I 194 " 0.008 2.00e-02 2.50e+03 ... (remaining 907 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1083 2.77 - 3.30: 5459 3.30 - 3.83: 10169 3.83 - 4.37: 11999 4.37 - 4.90: 19503 Nonbonded interactions: 48213 Sorted by model distance: nonbonded pdb=" O GLU I 145 " pdb=" O HOH I 401 " model vdw 2.236 3.040 nonbonded pdb=" O ARG J 283 " pdb=" O HOH J 501 " model vdw 2.264 3.040 nonbonded pdb=" O HOH J 556 " pdb=" O HOH J 566 " model vdw 2.270 3.040 nonbonded pdb=" O HOH J 584 " pdb=" O HOH J 591 " model vdw 2.272 3.040 nonbonded pdb=" O HOH I 432 " pdb=" O HOH I 469 " model vdw 2.280 3.040 ... (remaining 48208 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.770 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 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 : 0.004 0.102 5256 Z= 0.301 Angle : 0.576 7.875 7114 Z= 0.282 Chirality : 0.040 0.129 777 Planarity : 0.005 0.058 910 Dihedral : 16.750 89.831 1967 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.61 % Favored : 98.23 % Rotamer: Outliers : 0.90 % Allowed : 14.39 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.88 (0.33), residues: 620 helix: 1.92 (0.28), residues: 338 sheet: -0.24 (0.94), residues: 25 loop : 0.62 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 11 HIS 0.005 0.001 HIS H 274 PHE 0.015 0.002 PHE I 30 TYR 0.015 0.001 TYR I 91 ARG 0.011 0.001 ARG J 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.609 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 91 average time/residue: 1.5938 time to fit residues: 150.0568 Evaluate side-chains 90 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 170 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 48 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN I 183 ASN I 247 GLN I 275 GLN J 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.174104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.150003 restraints weight = 3513.839| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 0.62 r_work: 0.3534 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work: 0.3328 rms_B_bonded: 3.73 restraints_weight: 0.1250 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.0523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5256 Z= 0.190 Angle : 0.535 5.255 7114 Z= 0.282 Chirality : 0.041 0.131 777 Planarity : 0.005 0.040 910 Dihedral : 7.373 71.508 714 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.26 % Allowed : 13.49 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.98 (0.34), residues: 620 helix: 1.97 (0.28), residues: 345 sheet: 1.99 (1.32), residues: 15 loop : 0.48 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 132 HIS 0.005 0.001 HIS H 274 PHE 0.015 0.002 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.006 0.001 ARG J 298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.616 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 91 average time/residue: 1.5537 time to fit residues: 146.3245 Evaluate side-chains 87 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 106 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 51 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN I 183 ASN I 247 GLN I 275 GLN J 148 ASN J 306 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.172644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.151000 restraints weight = 3522.364| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 0.60 r_work: 0.3514 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work: 0.3308 rms_B_bonded: 3.72 restraints_weight: 0.1250 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5256 Z= 0.248 Angle : 0.587 5.901 7114 Z= 0.309 Chirality : 0.042 0.139 777 Planarity : 0.005 0.048 910 Dihedral : 6.401 59.013 706 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % Rotamer: Outliers : 1.98 % Allowed : 12.95 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.68 (0.33), residues: 620 helix: 1.70 (0.28), residues: 345 sheet: 1.64 (1.30), residues: 15 loop : 0.41 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.006 0.002 HIS H 274 PHE 0.017 0.002 PHE I 30 TYR 0.020 0.002 TYR I 2 ARG 0.008 0.001 ARG J 298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.678 Fit side-chains REVERT: I 62 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7511 (mmtp) REVERT: I 77 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6745 (ttm170) outliers start: 11 outliers final: 3 residues processed: 96 average time/residue: 1.6262 time to fit residues: 161.4158 Evaluate side-chains 89 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 106 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN I 183 ASN I 247 GLN I 275 GLN J 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.173911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.152794 restraints weight = 3623.061| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 0.59 r_work: 0.3535 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work: 0.3331 rms_B_bonded: 3.64 restraints_weight: 0.1250 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5256 Z= 0.190 Angle : 0.535 4.958 7114 Z= 0.281 Chirality : 0.041 0.135 777 Planarity : 0.005 0.038 910 Dihedral : 6.110 59.456 704 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.45 % Favored : 98.39 % Rotamer: Outliers : 1.44 % Allowed : 13.85 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.82 (0.33), residues: 620 helix: 1.85 (0.28), residues: 345 sheet: 1.70 (1.38), residues: 15 loop : 0.40 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.005 0.001 HIS H 274 PHE 0.017 0.002 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.006 0.001 ARG I 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.607 Fit side-chains REVERT: I 62 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7484 (mmtp) outliers start: 8 outliers final: 4 residues processed: 95 average time/residue: 1.5892 time to fit residues: 156.1751 Evaluate side-chains 88 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 106 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 16 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN I 183 ASN I 247 GLN I 275 GLN J 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.174184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.150171 restraints weight = 3519.961| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 0.65 r_work: 0.3533 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work: 0.3325 rms_B_bonded: 3.73 restraints_weight: 0.1250 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.0740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5256 Z= 0.191 Angle : 0.542 6.817 7114 Z= 0.283 Chirality : 0.041 0.135 777 Planarity : 0.005 0.039 910 Dihedral : 6.058 59.277 704 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.80 % Allowed : 12.95 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.79 (0.33), residues: 620 helix: 1.84 (0.28), residues: 345 sheet: 1.07 (1.39), residues: 16 loop : 0.41 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 132 HIS 0.005 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.006 0.001 ARG I 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.624 Fit side-chains REVERT: I 62 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7498 (mmtp) REVERT: I 77 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6722 (ttm170) outliers start: 10 outliers final: 5 residues processed: 94 average time/residue: 1.6370 time to fit residues: 159.0497 Evaluate side-chains 91 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 106 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN I 183 ASN I 247 GLN I 275 GLN J 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.175028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.151088 restraints weight = 3536.372| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 0.65 r_work: 0.3542 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work: 0.3338 rms_B_bonded: 3.73 restraints_weight: 0.1250 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.0783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5256 Z= 0.171 Angle : 0.527 8.460 7114 Z= 0.272 Chirality : 0.040 0.133 777 Planarity : 0.004 0.038 910 Dihedral : 5.970 57.719 704 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.45 % Favored : 98.39 % Rotamer: Outliers : 1.44 % Allowed : 12.95 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.89 (0.33), residues: 620 helix: 1.93 (0.28), residues: 345 sheet: 1.46 (1.38), residues: 15 loop : 0.43 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 132 HIS 0.004 0.001 HIS H 274 PHE 0.015 0.002 PHE I 30 TYR 0.016 0.002 TYR I 91 ARG 0.004 0.001 ARG I 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.511 Fit side-chains REVERT: I 62 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7485 (mmtp) REVERT: I 77 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6763 (ttm170) REVERT: J 28 LYS cc_start: 0.7423 (tttt) cc_final: 0.7217 (tttm) outliers start: 8 outliers final: 4 residues processed: 95 average time/residue: 1.6750 time to fit residues: 164.3751 Evaluate side-chains 92 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 106 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN I 183 ASN I 247 GLN I 275 GLN J 148 ASN J 306 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.173364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.149393 restraints weight = 3529.135| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 0.64 r_work: 0.3523 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work: 0.3309 rms_B_bonded: 3.82 restraints_weight: 0.1250 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5256 Z= 0.238 Angle : 0.596 10.236 7114 Z= 0.309 Chirality : 0.042 0.136 777 Planarity : 0.005 0.055 910 Dihedral : 6.004 53.865 704 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.26 % Allowed : 13.13 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.59 (0.33), residues: 620 helix: 1.70 (0.28), residues: 345 sheet: -0.40 (0.98), residues: 25 loop : 0.43 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 132 HIS 0.007 0.002 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.020 0.002 TYR I 2 ARG 0.009 0.001 ARG J 298 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.584 Fit side-chains REVERT: I 62 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7503 (mmtp) REVERT: I 77 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.6801 (ttm170) outliers start: 7 outliers final: 4 residues processed: 91 average time/residue: 1.6365 time to fit residues: 154.0094 Evaluate side-chains 91 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 106 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 52 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN I 183 ASN I 247 GLN I 275 GLN J 148 ASN J 306 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.173458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.148944 restraints weight = 3572.517| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 0.64 r_work: 0.3519 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work: 0.3314 rms_B_bonded: 3.73 restraints_weight: 0.1250 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5256 Z= 0.236 Angle : 0.600 11.729 7114 Z= 0.309 Chirality : 0.042 0.136 777 Planarity : 0.005 0.064 910 Dihedral : 5.965 53.841 704 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.80 % Allowed : 12.95 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.53 (0.33), residues: 620 helix: 1.65 (0.27), residues: 345 sheet: -0.57 (0.95), residues: 25 loop : 0.43 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 132 HIS 0.006 0.002 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.019 0.002 TYR I 2 ARG 0.010 0.001 ARG J 298 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.487 Fit side-chains REVERT: I 62 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7509 (mmtp) REVERT: I 77 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6733 (ttm170) outliers start: 10 outliers final: 5 residues processed: 95 average time/residue: 1.5997 time to fit residues: 157.2806 Evaluate side-chains 94 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 106 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN I 183 ASN I 247 GLN I 275 GLN J 148 ASN J 306 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.173844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149879 restraints weight = 3523.386| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 0.64 r_work: 0.3533 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work: 0.3310 rms_B_bonded: 3.95 restraints_weight: 0.1250 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5256 Z= 0.223 Angle : 0.597 13.115 7114 Z= 0.308 Chirality : 0.042 0.138 777 Planarity : 0.005 0.063 910 Dihedral : 5.920 53.641 704 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.62 % Allowed : 13.31 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.66 (0.33), residues: 620 helix: 1.69 (0.28), residues: 345 sheet: 1.24 (1.35), residues: 15 loop : 0.42 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 132 HIS 0.006 0.002 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.018 0.002 TYR I 2 ARG 0.010 0.001 ARG J 298 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.602 Fit side-chains REVERT: I 62 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7515 (mmtp) REVERT: I 77 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6760 (ttm170) outliers start: 9 outliers final: 6 residues processed: 92 average time/residue: 1.6156 time to fit residues: 153.8428 Evaluate side-chains 93 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 106 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN I 183 ASN I 247 GLN I 275 GLN J 148 ASN J 306 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.174283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.149877 restraints weight = 3548.945| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 0.63 r_work: 0.3532 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work: 0.3324 rms_B_bonded: 3.81 restraints_weight: 0.1250 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5256 Z= 0.205 Angle : 0.592 14.302 7114 Z= 0.304 Chirality : 0.042 0.152 777 Planarity : 0.005 0.062 910 Dihedral : 5.865 53.373 704 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.55 % Rotamer: Outliers : 1.44 % Allowed : 13.67 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.63 (0.33), residues: 620 helix: 1.76 (0.28), residues: 345 sheet: -0.55 (0.99), residues: 25 loop : 0.44 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 132 HIS 0.005 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.019 0.002 TYR I 59 ARG 0.011 0.001 ARG J 298 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.619 Fit side-chains REVERT: I 62 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7507 (mmtp) REVERT: I 77 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6796 (ttm170) outliers start: 8 outliers final: 6 residues processed: 90 average time/residue: 1.6345 time to fit residues: 152.1169 Evaluate side-chains 92 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 106 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.0470 chunk 16 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN I 183 ASN I 247 GLN I 275 GLN J 148 ASN J 306 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.174187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.149805 restraints weight = 3549.425| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 0.63 r_work: 0.3530 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work: 0.3328 rms_B_bonded: 3.69 restraints_weight: 0.1250 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5256 Z= 0.209 Angle : 0.596 14.035 7114 Z= 0.306 Chirality : 0.042 0.151 777 Planarity : 0.005 0.064 910 Dihedral : 5.850 53.453 704 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.62 % Allowed : 13.67 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.62 (0.33), residues: 620 helix: 1.74 (0.28), residues: 345 sheet: -0.57 (0.98), residues: 25 loop : 0.44 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 132 HIS 0.006 0.002 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.018 0.002 TYR I 2 ARG 0.011 0.001 ARG J 298 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7097.13 seconds wall clock time: 125 minutes 37.56 seconds (7537.56 seconds total)