Starting phenix.real_space_refine on Thu Jul 2 01:44:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8orm_17129/07_2026/8orm_17129.cif Found real_map, /net/cci-nas-00/data/ceres_data/8orm_17129/07_2026/8orm_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 { model { file = "/net/cci-nas-00/data/ceres_data/8orm_17129/07_2026/8orm_17129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8orm_17129/07_2026/8orm_17129.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8orm_17129/07_2026/8orm_17129.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8orm_17129/07_2026/8orm_17129.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8orm_17129/07_2026/8orm_17129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8orm_17129/07_2026/8orm_17129.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 0.92, per 1000 atoms: 0.17 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: 0.40 Conformation dependent library (CDL) restraints added in 137.9 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: 0.13 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: 0.70 Time building geometry restraints manager: 0.52 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: 2799 17.97 - 35.93: 251 35.93 - 53.90: 83 53.90 - 71.86: 20 71.86 - 89.83: 10 Dihedral angle restraints: 3163 sinusoidal: 1310 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 3160 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: 3.470 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.290 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:5.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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= 0.224 Angle : 0.576 7.875 7114 Z= 0.282 Chirality : 0.040 0.129 777 Planarity : 0.005 0.058 910 Dihedral : 16.765 89.831 1963 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 are 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/Z covalent geometry : bond 0.00446 / 0.22 ( 5256) covalent geometry : angle 0.57562 / 0.28 ( 7114) hydrogen bonds : bond 0.13443 / 8.25 ( 276) hydrogen bonds : angle 5.74457 / 4.05 ( 762) Misc. bond : bond 0.03341 / 1.76 ( 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 : 0.124 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 91 average time/residue: 0.5764 time to fit residues: 54.2131 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 : 0.168 ------------------------------------------------------------------------------- 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... 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 = 0.4003 r_free = 0.4003 target = 0.175367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.151224 restraints weight = 3585.118| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 0.63 r_work: 0.3551 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work: 0.3346 rms_B_bonded: 3.78 restraints_weight: 0.1250 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.0581 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= 0.119 Angle : 0.504 4.855 7114 Z= 0.265 Chirality : 0.040 0.128 777 Planarity : 0.005 0.037 910 Dihedral : 7.317 74.432 710 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.55 % Rotamer: Outliers : 1.44 % Allowed : 13.13 % 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 are not related in a simple way. whole: 2.11 (0.34), residues: 620 helix: 2.11 (0.28), residues: 345 sheet: 2.07 (1.34), residues: 15 loop : 0.50 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 0.004 0.001 HIS H 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 ( 5256) covalent geometry : angle 0.50365 / 0.27 ( 7114) hydrogen bonds : bond 0.04940 / 3.17 ( 276) hydrogen bonds : angle 4.60512 / 3.22 ( 762) Misc. bond : bond 0.00045 / 0.02 ( 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 97 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.128 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 94 average time/residue: 0.5124 time to fit residues: 49.9557 Evaluate side-chains 87 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 57 optimal weight: 0.9990 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: 0.9990 chunk 59 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3974 r_free = 0.3974 target = 0.172667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.148306 restraints weight = 3509.834| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 0.62 r_work: 0.3511 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work: 0.3301 rms_B_bonded: 3.79 restraints_weight: 0.1250 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.0685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5257 Z= 0.191 Angle : 0.610 6.259 7114 Z= 0.320 Chirality : 0.043 0.138 777 Planarity : 0.005 0.046 910 Dihedral : 6.297 58.893 700 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.38 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 are not related in a simple way. whole: 1.57 (0.33), residues: 620 helix: 1.70 (0.28), residues: 345 sheet: -0.47 (0.95), residues: 26 loop : 0.42 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 132 HIS 0.007 0.002 HIS J 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 ( 5256) covalent geometry : angle 0.60984 / 0.32 ( 7114) hydrogen bonds : bond 0.05907 / 3.73 ( 276) hydrogen bonds : angle 4.82338 / 3.38 ( 762) Misc. bond : bond 0.00037 / 0.02 ( 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 98 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.209 Fit side-chains REVERT: I 62 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7504 (mmtp) outliers start: 9 outliers final: 4 residues processed: 96 average time/residue: 0.5773 time to fit residues: 57.3418 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 : 0.131 ------------------------------------------------------------------------------- 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 53 ASP 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: 2.9990 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 0.0570 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4003 r_free = 0.4003 target = 0.175421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.151521 restraints weight = 3560.584| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 0.65 r_work: 0.3551 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work: 0.3348 rms_B_bonded: 3.73 restraints_weight: 0.1250 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5257 Z= 0.115 Angle : 0.499 4.827 7114 Z= 0.262 Chirality : 0.040 0.133 777 Planarity : 0.005 0.038 910 Dihedral : 6.043 58.058 700 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.34), residues: 620 helix: 2.04 (0.28), residues: 345 sheet: 1.32 (1.37), residues: 16 loop : 0.44 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 298 TYR 0.016 0.002 TYR I 91 PHE 0.016 0.002 PHE I 30 TRP 0.008 0.001 TRP I 11 HIS 0.004 0.001 HIS I 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 5256) covalent geometry : angle 0.49903 / 0.26 ( 7114) hydrogen bonds : bond 0.04656 / 2.98 ( 276) hydrogen bonds : angle 4.49686 / 3.14 ( 762) Misc. bond : bond 0.00033 / 0.02 ( 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 95 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.131 Fit side-chains REVERT: I 62 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7509 (mmtp) REVERT: I 77 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6716 (ttm170) outliers start: 8 outliers final: 3 residues processed: 91 average time/residue: 0.5549 time to fit residues: 52.2919 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 : 0.194 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3975 r_free = 0.3975 target = 0.172828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.148339 restraints weight = 3568.878| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 0.63 r_work: 0.3510 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work: 0.3312 rms_B_bonded: 3.64 restraints_weight: 0.1250 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.0774 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 : 0.603 6.865 7114 Z= 0.316 Chirality : 0.043 0.138 777 Planarity : 0.005 0.058 910 Dihedral : 6.180 58.910 700 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.55 % Rotamer: Outliers : 1.44 % Allowed : 13.49 % 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 are not related in a simple way. whole: 1.56 (0.33), residues: 620 helix: 1.68 (0.28), residues: 345 sheet: -0.52 (0.96), residues: 26 loop : 0.44 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 298 TYR 0.021 0.002 TYR I 2 PHE 0.017 0.002 PHE I 30 TRP 0.010 0.002 TRP J 132 HIS 0.007 0.002 HIS J 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 ( 5256) covalent geometry : angle 0.60348 / 0.32 ( 7114) hydrogen bonds : bond 0.05764 / 3.64 ( 276) hydrogen bonds : angle 4.76304 / 3.33 ( 762) Misc. bond : bond 0.00045 / 0.02 ( 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 93 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.205 Fit side-chains REVERT: I 62 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7497 (mmtp) REVERT: I 77 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.6786 (ttm170) outliers start: 8 outliers final: 3 residues processed: 90 average time/residue: 0.5600 time to fit residues: 52.1581 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 : 0.146 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 27 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.0040 chunk 2 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 0.0670 chunk 51 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.4730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.176310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.152065 restraints weight = 3632.874| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 0.64 r_work: 0.3562 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work: 0.3356 rms_B_bonded: 3.82 restraints_weight: 0.1250 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.0842 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= 0.107 Angle : 0.491 4.828 7114 Z= 0.257 Chirality : 0.039 0.132 777 Planarity : 0.004 0.039 910 Dihedral : 5.947 58.955 700 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.08 % Allowed : 13.67 % 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 are not related in a simple way. whole: 2.04 (0.34), residues: 620 helix: 2.07 (0.28), residues: 345 sheet: 1.73 (1.44), residues: 15 loop : 0.45 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 298 TYR 0.015 0.001 TYR I 91 PHE 0.015 0.002 PHE I 30 TRP 0.008 0.001 TRP I 11 HIS 0.004 0.001 HIS I 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 ( 5256) covalent geometry : angle 0.49146 / 0.26 ( 7114) hydrogen bonds : bond 0.04422 / 2.84 ( 276) hydrogen bonds : angle 4.42121 / 3.08 ( 762) Misc. bond : bond 0.00037 / 0.02 ( 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: 6 poor density : 86 time to evaluate : 0.152 Fit side-chains REVERT: I 62 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7511 (mmtp) REVERT: I 77 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6740 (ttm170) REVERT: J 28 LYS cc_start: 0.7419 (tttt) cc_final: 0.7211 (tttm) outliers start: 6 outliers final: 4 residues processed: 89 average time/residue: 0.6085 time to fit residues: 55.9413 Evaluate side-chains 89 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.125 ------------------------------------------------------------------------------- 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 18 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3981 r_free = 0.3981 target = 0.173341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.148699 restraints weight = 3594.128| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 0.64 r_work: 0.3515 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work: 0.3306 rms_B_bonded: 3.90 restraints_weight: 0.1250 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5257 Z= 0.179 Angle : 0.599 9.461 7114 Z= 0.311 Chirality : 0.042 0.135 777 Planarity : 0.005 0.040 910 Dihedral : 6.038 55.005 700 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % Rotamer: Outliers : 1.44 % Allowed : 13.13 % 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 are not related in a simple way. whole: 1.65 (0.33), residues: 620 helix: 1.76 (0.28), residues: 345 sheet: -0.48 (0.99), residues: 26 loop : 0.46 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 298 TYR 0.020 0.002 TYR I 2 PHE 0.016 0.002 PHE I 13 TRP 0.010 0.002 TRP J 237 HIS 0.007 0.002 HIS J 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 ( 5256) covalent geometry : angle 0.59905 / 0.31 ( 7114) hydrogen bonds : bond 0.05620 / 3.55 ( 276) hydrogen bonds : angle 4.70868 / 3.30 ( 762) Misc. bond : bond 0.00051 / 0.03 ( 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 94 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.194 Fit side-chains REVERT: I 62 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7552 (mmtp) REVERT: I 77 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.6832 (ttm170) REVERT: J 245 ASP cc_start: 0.7725 (m-30) cc_final: 0.7460 (m-30) outliers start: 8 outliers final: 5 residues processed: 91 average time/residue: 0.5341 time to fit residues: 50.2836 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 : 0.193 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 22 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 57 optimal weight: 0.0970 chunk 15 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4003 r_free = 0.4003 target = 0.175502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.151640 restraints weight = 3555.501| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 0.65 r_work: 0.3554 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work: 0.3340 rms_B_bonded: 3.93 restraints_weight: 0.1250 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5257 Z= 0.115 Angle : 0.516 6.395 7114 Z= 0.268 Chirality : 0.040 0.134 777 Planarity : 0.005 0.059 910 Dihedral : 5.895 53.098 700 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.26 % Allowed : 13.31 % 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 are not related in a simple way. whole: 1.87 (0.34), residues: 620 helix: 2.00 (0.28), residues: 345 sheet: -0.37 (1.03), residues: 25 loop : 0.46 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 298 TYR 0.016 0.002 TYR I 91 PHE 0.015 0.002 PHE I 30 TRP 0.008 0.001 TRP I 11 HIS 0.004 0.001 HIS H 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 ( 5256) covalent geometry : angle 0.51591 / 0.27 ( 7114) hydrogen bonds : bond 0.04632 / 2.96 ( 276) hydrogen bonds : angle 4.47491 / 3.12 ( 762) Misc. bond : bond 0.00044 / 0.02 ( 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 93 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.122 Fit side-chains REVERT: I 62 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7541 (mmtp) REVERT: I 77 ARG cc_start: 0.7014 (OUTLIER) cc_final: 0.6723 (ttm170) REVERT: J 28 LYS cc_start: 0.7443 (tttt) cc_final: 0.7240 (tttm) REVERT: J 245 ASP cc_start: 0.7681 (m-30) cc_final: 0.7417 (m-30) outliers start: 7 outliers final: 4 residues processed: 90 average time/residue: 0.5821 time to fit residues: 54.0909 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 : 0.125 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 1 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 59 optimal weight: 0.2980 chunk 56 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3979 r_free = 0.3979 target = 0.173249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.148807 restraints weight = 3561.082| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 0.63 r_work: 0.3518 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work: 0.3317 rms_B_bonded: 3.68 restraints_weight: 0.1250 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.0856 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= 0.178 Angle : 0.607 9.513 7114 Z= 0.316 Chirality : 0.043 0.156 777 Planarity : 0.005 0.057 910 Dihedral : 5.969 55.876 700 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.55 % Rotamer: Outliers : 1.44 % Allowed : 13.13 % 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 are not related in a simple way. whole: 1.63 (0.33), residues: 620 helix: 1.73 (0.28), residues: 345 sheet: -0.42 (1.00), residues: 25 loop : 0.45 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 298 TYR 0.020 0.002 TYR I 2 PHE 0.016 0.002 PHE I 30 TRP 0.010 0.002 TRP J 237 HIS 0.007 0.002 HIS J 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 ( 5256) covalent geometry : angle 0.60678 / 0.32 ( 7114) hydrogen bonds : bond 0.05615 / 3.54 ( 276) hydrogen bonds : angle 4.71463 / 3.30 ( 762) Misc. bond : bond 0.00060 / 0.03 ( 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 93 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.126 Fit side-chains REVERT: I 62 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7509 (mmtp) REVERT: I 77 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.6811 (ttm170) REVERT: J 245 ASP cc_start: 0.7739 (m-30) cc_final: 0.7463 (m-30) outliers start: 8 outliers final: 4 residues processed: 90 average time/residue: 0.5346 time to fit residues: 49.8222 Evaluate side-chains 89 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 28 optimal weight: 9.9990 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4000 r_free = 0.4000 target = 0.175221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.152878 restraints weight = 3598.772| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 0.61 r_work: 0.3539 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work: 0.3340 rms_B_bonded: 3.78 restraints_weight: 0.1250 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.0826 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= 0.126 Angle : 0.542 9.503 7114 Z= 0.282 Chirality : 0.041 0.157 777 Planarity : 0.005 0.051 910 Dihedral : 5.834 54.334 700 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.09 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 are not related in a simple way. whole: 1.83 (0.34), residues: 620 helix: 1.97 (0.28), residues: 345 sheet: -0.51 (1.00), residues: 25 loop : 0.44 (0.39), residues: 250 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 0.015 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/Z covalent geometry : bond 0.00264 / 0.13 ( 5256) covalent geometry : angle 0.54203 / 0.28 ( 7114) hydrogen bonds : bond 0.04784 / 3.06 ( 276) hydrogen bonds : angle 4.52006 / 3.16 ( 762) Misc. bond : bond 0.00052 / 0.03 ( 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 92 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.185 Fit side-chains REVERT: I 62 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7503 (mmtp) REVERT: I 77 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6754 (ttm170) REVERT: J 28 LYS cc_start: 0.7426 (tttt) cc_final: 0.7225 (tttm) REVERT: J 245 ASP cc_start: 0.7672 (m-30) cc_final: 0.7422 (m-30) outliers start: 6 outliers final: 4 residues processed: 89 average time/residue: 0.5742 time to fit residues: 52.8134 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 : 0.218 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3979 r_free = 0.3979 target = 0.173236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.148763 restraints weight = 3574.833| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 0.63 r_work: 0.3516 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work: 0.3313 rms_B_bonded: 3.66 restraints_weight: 0.1250 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5257 Z= 0.185 Angle : 0.625 11.777 7114 Z= 0.324 Chirality : 0.043 0.179 777 Planarity : 0.005 0.054 910 Dihedral : 5.916 56.112 700 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.68 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 are not related in a simple way. whole: 1.56 (0.33), residues: 620 helix: 1.69 (0.28), residues: 345 sheet: -0.64 (0.95), residues: 25 loop : 0.44 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 298 TYR 0.020 0.002 TYR I 2 PHE 0.016 0.002 PHE I 30 TRP 0.011 0.002 TRP J 237 HIS 0.007 0.002 HIS J 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 ( 5256) covalent geometry : angle 0.62464 / 0.32 ( 7114) hydrogen bonds : bond 0.05687 / 3.59 ( 276) hydrogen bonds : angle 4.73680 / 3.32 ( 762) Misc. bond : bond 0.00067 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2695.41 seconds wall clock time: 46 minutes 26.30 seconds (2786.30 seconds total)