Starting phenix.real_space_refine on Fri Aug 22 15:59:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8orm_17129/08_2025/8orm_17129.cif Found real_map, /net/cci-nas-00/data/ceres_data/8orm_17129/08_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_17129/08_2025/8orm_17129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8orm_17129/08_2025/8orm_17129.map" model { file = "/net/cci-nas-00/data/ceres_data/8orm_17129/08_2025/8orm_17129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8orm_17129/08_2025/8orm_17129.cif" } resolution = 1.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.61, per 1000 atoms: 0.30 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: 0.54 Conformation dependent library (CDL) restraints added in 206.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.17 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: 0.85 Time building geometry restraints manager: 0.66 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: 3.920 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.300 Find NCS groups from input model: 0.030 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:8.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.050 ------------------------------------------------------------------------------- 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 5257 Z= 0.225 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.001 ARG J 298 TYR 0.015 0.001 TYR I 91 PHE 0.015 0.002 PHE I 30 TRP 0.009 0.001 TRP I 11 HIS 0.005 0.001 HIS H 274 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 5256) covalent geometry : angle 0.57585 ( 7114) hydrogen bonds : bond 0.13443 ( 276) hydrogen bonds : angle 5.74457 ( 762) Misc. bond : bond 0.03341 ( 1) *********************** 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 : 0.238 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 91 average time/residue: 0.8624 time to fit residues: 80.9014 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 : 0.212 ------------------------------------------------------------------------------- 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 54 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 32 optimal weight: 0.0040 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 = 0.4002 r_free = 0.4002 target = 0.175269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.151110 restraints weight = 3583.369| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 0.63 r_work: 0.3547 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work: 0.3344 rms_B_bonded: 3.80 restraints_weight: 0.1250 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.0559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5257 Z= 0.121 Angle : 0.506 4.854 7114 Z= 0.266 Chirality : 0.040 0.128 777 Planarity : 0.005 0.037 910 Dihedral : 7.305 74.163 714 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.62 % Allowed : 13.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.34), residues: 620 helix: 2.10 (0.28), residues: 345 sheet: 2.06 (1.33), residues: 15 loop : 0.50 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 298 TYR 0.016 0.002 TYR I 91 PHE 0.014 0.002 PHE I 30 TRP 0.007 0.001 TRP J 132 HIS 0.005 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 5256) covalent geometry : angle 0.50565 ( 7114) hydrogen bonds : bond 0.04981 ( 276) hydrogen bonds : angle 4.62436 ( 762) Misc. bond : bond 0.00049 ( 1) *********************** 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 98 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.217 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 94 average time/residue: 0.7554 time to fit residues: 73.4365 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 : 0.284 ------------------------------------------------------------------------------- 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 11 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.172205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.147802 restraints weight = 3504.901| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 0.63 r_work: 0.3503 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work: 0.3299 rms_B_bonded: 3.67 restraints_weight: 0.1250 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.0719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5257 Z= 0.213 Angle : 0.638 6.612 7114 Z= 0.335 Chirality : 0.044 0.142 777 Planarity : 0.006 0.047 910 Dihedral : 6.470 59.093 706 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.98 % Allowed : 12.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.33), residues: 620 helix: 1.60 (0.28), residues: 345 sheet: -0.60 (0.92), residues: 26 loop : 0.40 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 298 TYR 0.022 0.003 TYR I 2 PHE 0.017 0.003 PHE I 30 TRP 0.012 0.002 TRP J 237 HIS 0.007 0.002 HIS H 274 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 5256) covalent geometry : angle 0.63817 ( 7114) hydrogen bonds : bond 0.06157 ( 276) hydrogen bonds : angle 4.89295 ( 762) Misc. bond : bond 0.00037 ( 1) *********************** 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 101 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.224 Fit side-chains REVERT: I 62 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7514 (mmtp) REVERT: I 77 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6810 (ttm170) outliers start: 11 outliers final: 3 residues processed: 98 average time/residue: 0.8424 time to fit residues: 85.0018 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 : 0.220 ------------------------------------------------------------------------------- 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 12 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 0.3980 chunk 26 optimal weight: 0.1980 chunk 2 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.174248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.150058 restraints weight = 3553.233| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 0.63 r_work: 0.3537 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work: 0.3333 rms_B_bonded: 3.69 restraints_weight: 0.1250 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.0737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5257 Z= 0.130 Angle : 0.525 4.894 7114 Z= 0.276 Chirality : 0.040 0.136 777 Planarity : 0.005 0.038 910 Dihedral : 6.097 59.279 704 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 : 1.26 % Allowed : 13.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.34), residues: 620 helix: 1.87 (0.28), residues: 345 sheet: -0.35 (1.00), residues: 26 loop : 0.44 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 298 TYR 0.017 0.002 TYR I 91 PHE 0.017 0.002 PHE I 30 TRP 0.010 0.001 TRP J 132 HIS 0.005 0.001 HIS H 274 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 5256) covalent geometry : angle 0.52501 ( 7114) hydrogen bonds : bond 0.04994 ( 276) hydrogen bonds : angle 4.59430 ( 762) Misc. bond : bond 0.00040 ( 1) *********************** 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 96 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.226 Fit side-chains REVERT: I 62 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7487 (mmtp) outliers start: 7 outliers final: 3 residues processed: 94 average time/residue: 0.7107 time to fit residues: 68.9573 Evaluate side-chains 88 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 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 31 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 7 optimal weight: 0.0370 chunk 45 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.172545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.148008 restraints weight = 3583.814| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 0.63 r_work: 0.3508 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work: 0.3309 rms_B_bonded: 3.62 restraints_weight: 0.1250 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 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 : 0.004 0.034 5257 Z= 0.187 Angle : 0.602 6.109 7114 Z= 0.316 Chirality : 0.043 0.141 777 Planarity : 0.005 0.042 910 Dihedral : 6.162 57.951 704 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.80 % Allowed : 12.77 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.33), residues: 620 helix: 1.60 (0.28), residues: 345 sheet: -0.60 (0.94), residues: 26 loop : 0.41 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 28 TYR 0.021 0.002 TYR I 2 PHE 0.017 0.002 PHE I 30 TRP 0.011 0.002 TRP J 132 HIS 0.007 0.002 HIS H 274 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 5256) covalent geometry : angle 0.60189 ( 7114) hydrogen bonds : bond 0.05805 ( 276) hydrogen bonds : angle 4.78824 ( 762) Misc. bond : bond 0.00046 ( 1) *********************** 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 95 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.175 Fit side-chains REVERT: I 62 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7498 (mmtp) REVERT: I 77 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6774 (ttm170) outliers start: 10 outliers final: 4 residues processed: 92 average time/residue: 0.7531 time to fit residues: 71.4770 Evaluate side-chains 90 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 27 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN I 183 ASN I 247 GLN I 275 GLN J 148 ASN J 297 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.175067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.150658 restraints weight = 3610.038| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 0.64 r_work: 0.3545 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work: 0.3340 rms_B_bonded: 3.75 restraints_weight: 0.1250 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5257 Z= 0.121 Angle : 0.512 4.870 7114 Z= 0.269 Chirality : 0.040 0.136 777 Planarity : 0.004 0.039 910 Dihedral : 5.963 56.684 704 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.55 % Rotamer: Outliers : 0.90 % Allowed : 13.67 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.34), residues: 620 helix: 1.93 (0.28), residues: 345 sheet: 1.09 (1.40), residues: 16 loop : 0.44 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 28 TYR 0.016 0.002 TYR I 91 PHE 0.016 0.002 PHE I 30 TRP 0.009 0.001 TRP J 132 HIS 0.004 0.001 HIS H 274 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 5256) covalent geometry : angle 0.51249 ( 7114) hydrogen bonds : bond 0.04779 ( 276) hydrogen bonds : angle 4.52219 ( 762) Misc. bond : bond 0.00041 ( 1) *********************** 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 92 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.220 Fit side-chains REVERT: I 62 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7514 (mmtp) outliers start: 5 outliers final: 4 residues processed: 90 average time/residue: 0.7781 time to fit residues: 72.3356 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 : 0.267 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.172624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.148555 restraints weight = 3597.270| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 0.68 r_work: 0.3491 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work: 0.3292 rms_B_bonded: 3.90 restraints_weight: 0.1250 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5257 Z= 0.198 Angle : 0.622 6.649 7114 Z= 0.326 Chirality : 0.043 0.140 777 Planarity : 0.005 0.056 910 Dihedral : 6.039 54.248 704 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.62 % Allowed : 12.95 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.33), residues: 620 helix: 1.59 (0.27), residues: 345 sheet: -0.46 (0.94), residues: 25 loop : 0.41 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 298 TYR 0.022 0.002 TYR I 2 PHE 0.017 0.002 PHE I 30 TRP 0.011 0.002 TRP J 237 HIS 0.007 0.002 HIS H 274 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 5256) covalent geometry : angle 0.62208 ( 7114) hydrogen bonds : bond 0.05874 ( 276) hydrogen bonds : angle 4.79269 ( 762) Misc. bond : bond 0.00057 ( 1) *********************** 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 95 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.260 Fit side-chains REVERT: I 62 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7510 (mmtp) REVERT: I 77 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6848 (ttm170) outliers start: 9 outliers final: 4 residues processed: 92 average time/residue: 0.7829 time to fit residues: 74.3947 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 : 0.220 ------------------------------------------------------------------------------- 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 22 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.174567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.153097 restraints weight = 3544.669| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 0.59 r_work: 0.3540 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work: 0.3336 rms_B_bonded: 3.72 restraints_weight: 0.1250 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5257 Z= 0.131 Angle : 0.542 6.904 7114 Z= 0.283 Chirality : 0.041 0.138 777 Planarity : 0.005 0.057 910 Dihedral : 5.880 52.966 704 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.55 % Rotamer: Outliers : 1.08 % Allowed : 13.49 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.33), residues: 620 helix: 1.84 (0.28), residues: 345 sheet: 1.48 (1.39), residues: 15 loop : 0.42 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 298 TYR 0.016 0.002 TYR I 91 PHE 0.016 0.002 PHE I 30 TRP 0.009 0.001 TRP J 132 HIS 0.005 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 5256) covalent geometry : angle 0.54194 ( 7114) hydrogen bonds : bond 0.04963 ( 276) hydrogen bonds : angle 4.57218 ( 762) Misc. bond : bond 0.00048 ( 1) *********************** 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 92 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.226 Fit side-chains REVERT: I 62 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7512 (mmtp) outliers start: 6 outliers final: 4 residues processed: 90 average time/residue: 0.7735 time to fit residues: 71.8444 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 : 0.216 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 25 optimal weight: 0.0060 chunk 39 optimal weight: 5.9990 chunk 42 optimal weight: 0.0670 chunk 59 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 overall best weight: 0.5334 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.176284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.152325 restraints weight = 3589.651| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 0.66 r_work: 0.3563 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work: 0.3351 rms_B_bonded: 3.89 restraints_weight: 0.1250 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5257 Z= 0.112 Angle : 0.516 6.917 7114 Z= 0.268 Chirality : 0.040 0.136 777 Planarity : 0.005 0.054 910 Dihedral : 5.773 52.461 704 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.55 % Rotamer: Outliers : 0.90 % Allowed : 13.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.34), residues: 620 helix: 2.10 (0.28), residues: 343 sheet: 1.41 (1.40), residues: 15 loop : 0.30 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 298 TYR 0.014 0.002 TYR I 91 PHE 0.016 0.002 PHE I 110 TRP 0.008 0.001 TRP I 11 HIS 0.004 0.001 HIS H 274 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 5256) covalent geometry : angle 0.51596 ( 7114) hydrogen bonds : bond 0.04472 ( 276) hydrogen bonds : angle 4.43215 ( 762) Misc. bond : bond 0.00045 ( 1) *********************** 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 90 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.186 Fit side-chains REVERT: I 62 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7551 (mmtp) outliers start: 5 outliers final: 4 residues processed: 88 average time/residue: 0.7580 time to fit residues: 68.7701 Evaluate side-chains 87 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.153 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 0.0870 chunk 51 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 183 ASN I 247 GLN I 275 GLN J 148 ASN J 306 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.173618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.149054 restraints weight = 3567.027| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 0.63 r_work: 0.3521 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work: 0.3315 rms_B_bonded: 3.68 restraints_weight: 0.1250 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5257 Z= 0.176 Angle : 0.635 16.442 7114 Z= 0.324 Chirality : 0.043 0.141 777 Planarity : 0.005 0.064 910 Dihedral : 5.860 53.740 704 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % Rotamer: Outliers : 0.90 % Allowed : 14.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.33), residues: 620 helix: 1.76 (0.28), residues: 345 sheet: -0.45 (0.97), residues: 25 loop : 0.41 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 298 TYR 0.019 0.002 TYR I 2 PHE 0.016 0.002 PHE I 13 TRP 0.010 0.002 TRP J 132 HIS 0.007 0.002 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 5256) covalent geometry : angle 0.63541 ( 7114) hydrogen bonds : bond 0.05567 ( 276) hydrogen bonds : angle 4.69275 ( 762) Misc. bond : bond 0.00066 ( 1) ********************** 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 89 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.220 Fit side-chains REVERT: I 62 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7511 (mmtp) REVERT: J 245 ASP cc_start: 0.7690 (m-30) cc_final: 0.7411 (m-30) outliers start: 5 outliers final: 4 residues processed: 87 average time/residue: 0.7033 time to fit residues: 63.2775 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 : 0.178 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 32 optimal weight: 0.0980 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 42 optimal weight: 0.0870 chunk 39 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 183 ASN I 247 GLN I 275 GLN J 148 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.176746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.152791 restraints weight = 3592.848| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 0.66 r_work: 0.3570 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work: 0.3359 rms_B_bonded: 3.91 restraints_weight: 0.1250 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5257 Z= 0.111 Angle : 0.531 10.581 7114 Z= 0.273 Chirality : 0.040 0.144 777 Planarity : 0.005 0.054 910 Dihedral : 5.713 52.813 704 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 0.90 % Allowed : 14.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.34), residues: 620 helix: 2.14 (0.28), residues: 343 sheet: -0.49 (0.99), residues: 25 loop : 0.34 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 298 TYR 0.014 0.002 TYR I 60 PHE 0.016 0.002 PHE I 110 TRP 0.009 0.001 TRP I 11 HIS 0.004 0.001 HIS H 274 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 5256) covalent geometry : angle 0.53070 ( 7114) hydrogen bonds : bond 0.04389 ( 276) hydrogen bonds : angle 4.40830 ( 762) Misc. bond : bond 0.00047 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3636.65 seconds wall clock time: 62 minutes 29.10 seconds (3749.10 seconds total)