Starting phenix.real_space_refine on Thu Mar 6 08:16:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8orm_17129/03_2025/8orm_17129.cif Found real_map, /net/cci-nas-00/data/ceres_data/8orm_17129/03_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_17129/03_2025/8orm_17129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8orm_17129/03_2025/8orm_17129.map" model { file = "/net/cci-nas-00/data/ceres_data/8orm_17129/03_2025/8orm_17129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8orm_17129/03_2025/8orm_17129.cif" } resolution = 1.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 32 5.16 5 Cl 1 4.86 5 C 3307 2.51 5 N 874 2.21 5 O 1127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5341 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "I" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2281 Unusual residues: {'ACE': 1} Classifications: {'peptide': 279, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Chain: "J" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2297 Classifications: {'peptide': 288} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 269} Chain breaks: 2 Chain: "J" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'V0G': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "I" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "J" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 112 Classifications: {'water': 112} Link IDs: {None: 111} Time building chain proxies: 4.04, per 1000 atoms: 0.76 Number of scatterers: 5341 At special positions: 0 Unit cell: (85.5, 93.3375, 68.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 32 16.00 O 1127 8.00 N 874 7.00 C 3307 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 655.1 milliseconds 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1200 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 3 sheets defined 62.3% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'H' and resid 262 through 275 removed outlier: 4.450A pdb=" N GLY H 267 " --> pdb=" O GLU H 264 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR H 271 " --> pdb=" O ARG H 268 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU H 272 " --> pdb=" O LEU H 269 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL H 275 " --> pdb=" O LEU H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 286 Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.872A pdb=" N ALA H 292 " --> pdb=" O THR H 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 4 Processing helix chain 'I' and resid 5 through 11 Processing helix chain 'I' and resid 15 through 38 Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 93 removed outlier: 3.914A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.532A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 127 Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.671A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 178 Processing helix chain 'I' and resid 183 through 186 removed outlier: 3.533A pdb=" N ILE I 186 " --> pdb=" O ASN I 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 183 through 186' Processing helix chain 'I' and resid 187 through 201 removed outlier: 3.792A pdb=" N THR I 201 " --> pdb=" O ARG I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 228 through 234 removed outlier: 3.530A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 240 Processing helix chain 'I' and resid 241 through 261 Processing helix chain 'I' and resid 266 through 283 Processing helix chain 'J' and resid 56 through 67 Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 110 through 131 Processing helix chain 'J' and resid 139 through 141 No H-bonds generated for 'chain 'J' and resid 139 through 141' Processing helix chain 'J' and resid 175 through 179 Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 192 through 209 removed outlier: 3.725A pdb=" N ALA J 198 " --> pdb=" O VAL J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 230 Processing helix chain 'J' and resid 239 through 243 Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 265 through 276 Processing helix chain 'J' and resid 285 through 291 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.774A pdb=" N SER J 296 " --> pdb=" O MET J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 307 Processing sheet with id=AA1, first strand: chain 'J' and resid 13 through 20 removed outlier: 7.382A pdb=" N LEU J 15 " --> pdb=" O ARG J 30 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ARG J 30 " --> pdb=" O LEU J 15 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N PHE J 17 " --> pdb=" O LYS J 28 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LYS J 28 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP J 79 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LEU J 77 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134 276 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.30 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 825 1.31 - 1.43: 1414 1.43 - 1.56: 2966 1.56 - 1.69: 0 1.69 - 1.81: 51 Bond restraints: 5256 Sorted by residual: bond pdb=" C11 V0G J 401 " pdb=" N10 V0G J 401 " ideal model delta sigma weight residual 1.358 1.460 -0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" C05 V0G J 401 " pdb=" N06 V0G J 401 " ideal model delta sigma weight residual 1.362 1.463 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" C17 V0G J 401 " pdb=" N16 V0G J 401 " ideal model delta sigma weight residual 1.363 1.464 -0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C32 V0G J 401 " pdb=" C33 V0G J 401 " ideal model delta sigma weight residual 1.450 1.532 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C15 V0G J 401 " pdb=" N16 V0G J 401 " ideal model delta sigma weight residual 1.391 1.470 -0.079 2.00e-02 2.50e+03 1.58e+01 ... (remaining 5251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 6955 1.57 - 3.15: 120 3.15 - 4.72: 31 4.72 - 6.30: 6 6.30 - 7.87: 2 Bond angle restraints: 7114 Sorted by residual: angle pdb=" C09 V0G J 401 " pdb=" N10 V0G J 401 " pdb=" C11 V0G J 401 " ideal model delta sigma weight residual 129.31 121.44 7.87 3.00e+00 1.11e-01 6.89e+00 angle pdb=" CB MET J 94 " pdb=" CG MET J 94 " pdb=" SD MET J 94 " ideal model delta sigma weight residual 112.70 119.92 -7.22 3.00e+00 1.11e-01 5.79e+00 angle pdb=" CA ILE I 186 " pdb=" CB ILE I 186 " pdb=" CG1 ILE I 186 " ideal model delta sigma weight residual 110.40 114.26 -3.86 1.70e+00 3.46e-01 5.15e+00 angle pdb=" CA TYR I 91 " pdb=" CB TYR I 91 " pdb=" CG TYR I 91 " ideal model delta sigma weight residual 113.90 109.95 3.95 1.80e+00 3.09e-01 4.82e+00 angle pdb=" C VAL J 173 " pdb=" N VAL J 174 " pdb=" CA VAL J 174 " ideal model delta sigma weight residual 121.97 125.54 -3.57 1.80e+00 3.09e-01 3.93e+00 ... (remaining 7109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 2803 17.97 - 35.93: 251 35.93 - 53.90: 83 53.90 - 71.86: 20 71.86 - 89.83: 10 Dihedral angle restraints: 3167 sinusoidal: 1314 harmonic: 1853 Sorted by residual: dihedral pdb=" CG ARG J 298 " pdb=" CD ARG J 298 " pdb=" NE ARG J 298 " pdb=" CZ ARG J 298 " ideal model delta sinusoidal sigma weight residual -90.00 -42.52 -47.48 2 1.50e+01 4.44e-03 1.16e+01 dihedral pdb=" CA TYR I 91 " pdb=" C TYR I 91 " pdb=" N LEU I 92 " pdb=" CA LEU I 92 " ideal model delta harmonic sigma weight residual 180.00 163.07 16.93 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CB GLU I 61 " pdb=" CG GLU I 61 " pdb=" CD GLU I 61 " pdb=" OE1 GLU I 61 " ideal model delta sinusoidal sigma weight residual 0.00 89.83 -89.83 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 3164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 450 0.026 - 0.052: 190 0.052 - 0.077: 79 0.077 - 0.103: 41 0.103 - 0.129: 17 Chirality restraints: 777 Sorted by residual: chirality pdb=" CA TYR I 91 " pdb=" N TYR I 91 " pdb=" C TYR I 91 " pdb=" CB TYR I 91 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA PRO J 238 " pdb=" N PRO J 238 " pdb=" C PRO J 238 " pdb=" CB PRO J 238 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA VAL J 210 " pdb=" N VAL J 210 " pdb=" C VAL J 210 " pdb=" CB VAL J 210 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 774 not shown) Planarity restraints: 910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP I 44 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO I 45 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO I 45 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO I 45 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 298 " 0.128 9.50e-02 1.11e+02 5.75e-02 2.40e+00 pdb=" NE ARG J 298 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG J 298 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG J 298 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG J 298 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP I 193 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.81e+00 pdb=" C ASP I 193 " -0.023 2.00e-02 2.50e+03 pdb=" O ASP I 193 " 0.009 2.00e-02 2.50e+03 pdb=" N PHE I 194 " 0.008 2.00e-02 2.50e+03 ... (remaining 907 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1083 2.77 - 3.30: 5459 3.30 - 3.83: 10169 3.83 - 4.37: 11999 4.37 - 4.90: 19503 Nonbonded interactions: 48213 Sorted by model distance: nonbonded pdb=" O GLU I 145 " pdb=" O HOH I 401 " model vdw 2.236 3.040 nonbonded pdb=" O ARG J 283 " pdb=" O HOH J 501 " model vdw 2.264 3.040 nonbonded pdb=" O HOH J 556 " pdb=" O HOH J 566 " model vdw 2.270 3.040 nonbonded pdb=" O HOH J 584 " pdb=" O HOH J 591 " model vdw 2.272 3.040 nonbonded pdb=" O HOH I 432 " pdb=" O HOH I 469 " model vdw 2.280 3.040 ... (remaining 48208 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.370 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 5256 Z= 0.301 Angle : 0.576 7.875 7114 Z= 0.282 Chirality : 0.040 0.129 777 Planarity : 0.005 0.058 910 Dihedral : 16.750 89.831 1967 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.61 % Favored : 98.23 % Rotamer: Outliers : 0.90 % Allowed : 14.39 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.33), residues: 620 helix: 1.92 (0.28), residues: 338 sheet: -0.24 (0.94), residues: 25 loop : 0.62 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 11 HIS 0.005 0.001 HIS H 274 PHE 0.015 0.002 PHE I 30 TYR 0.015 0.001 TYR I 91 ARG 0.011 0.001 ARG J 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.643 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 91 average time/residue: 1.5811 time to fit residues: 148.8196 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 : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 170 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 48 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN I 183 ASN I 247 GLN I 275 GLN J 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.174104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.150003 restraints weight = 3513.839| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 0.62 r_work: 0.3535 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work: 0.3332 rms_B_bonded: 3.67 restraints_weight: 0.1250 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.0523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5256 Z= 0.190 Angle : 0.535 5.255 7114 Z= 0.282 Chirality : 0.041 0.131 777 Planarity : 0.005 0.040 910 Dihedral : 7.373 71.508 714 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.26 % Allowed : 13.49 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.34), residues: 620 helix: 1.97 (0.28), residues: 345 sheet: 1.99 (1.32), residues: 15 loop : 0.48 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 132 HIS 0.005 0.001 HIS H 274 PHE 0.015 0.002 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.006 0.001 ARG J 298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.565 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 91 average time/residue: 1.4429 time to fit residues: 136.1116 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 : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 106 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 51 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 11 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 61 optimal weight: 0.0470 overall best weight: 0.5680 ------------------------------------------------------------------------------- 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 = 0.4009 r_free = 0.4009 target = 0.175960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.152287 restraints weight = 3549.805| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 0.69 r_work: 0.3538 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work: 0.3342 rms_B_bonded: 3.98 restraints_weight: 0.1250 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5256 Z= 0.144 Angle : 0.485 4.854 7114 Z= 0.255 Chirality : 0.039 0.130 777 Planarity : 0.005 0.038 910 Dihedral : 6.162 57.956 706 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.44 % Allowed : 13.67 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.34), residues: 620 helix: 2.19 (0.28), residues: 343 sheet: 2.03 (1.39), residues: 15 loop : 0.37 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 132 HIS 0.004 0.001 HIS H 274 PHE 0.014 0.001 PHE I 30 TYR 0.016 0.001 TYR I 91 ARG 0.008 0.001 ARG J 298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.628 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 94 average time/residue: 1.4943 time to fit residues: 145.6190 Evaluate side-chains 88 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 25 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.173063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.148378 restraints weight = 3593.803| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 0.64 r_work: 0.3510 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work: 0.3311 rms_B_bonded: 3.66 restraints_weight: 0.1250 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5256 Z= 0.253 Angle : 0.597 7.630 7114 Z= 0.311 Chirality : 0.042 0.137 777 Planarity : 0.005 0.050 910 Dihedral : 6.200 58.459 704 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.34), residues: 620 helix: 1.77 (0.28), residues: 345 sheet: -0.45 (0.97), residues: 26 loop : 0.48 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 237 HIS 0.007 0.002 HIS J 131 PHE 0.017 0.002 PHE I 13 TYR 0.020 0.002 TYR I 2 ARG 0.008 0.001 ARG J 298 *********************** 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: 9 poor density : 86 time to evaluate : 0.645 Fit side-chains REVERT: I 77 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6815 (ttm170) REVERT: J 245 ASP cc_start: 0.7699 (m-30) cc_final: 0.7446 (m-30) outliers start: 9 outliers final: 5 residues processed: 92 average time/residue: 1.5866 time to fit residues: 151.2263 Evaluate side-chains 88 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 106 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 16 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN I 183 ASN I 247 GLN I 275 GLN J 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.174264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.149830 restraints weight = 3522.505| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 0.63 r_work: 0.3530 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work: 0.3330 rms_B_bonded: 3.66 restraints_weight: 0.1250 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5256 Z= 0.195 Angle : 0.543 4.936 7114 Z= 0.284 Chirality : 0.041 0.136 777 Planarity : 0.005 0.039 910 Dihedral : 6.115 59.156 704 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.55 % Rotamer: Outliers : 1.26 % Allowed : 13.67 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.34), residues: 620 helix: 1.84 (0.28), residues: 345 sheet: -0.47 (0.98), residues: 26 loop : 0.45 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.006 0.001 ARG J 298 *********************** 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: 7 poor density : 88 time to evaluate : 0.640 Fit side-chains REVERT: J 245 ASP cc_start: 0.7669 (m-30) cc_final: 0.7397 (m-30) outliers start: 7 outliers final: 5 residues processed: 92 average time/residue: 1.6170 time to fit residues: 153.7851 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 : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain I residue 200 LEU 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 5 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 49 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4002 r_free = 0.4002 target = 0.175356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.151364 restraints weight = 3541.739| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 0.65 r_work: 0.3548 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work: 0.3341 rms_B_bonded: 3.79 restraints_weight: 0.1250 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5256 Z= 0.160 Angle : 0.510 4.856 7114 Z= 0.266 Chirality : 0.040 0.132 777 Planarity : 0.005 0.036 910 Dihedral : 6.004 59.341 704 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.99 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.34), residues: 620 helix: 2.00 (0.28), residues: 345 sheet: 1.55 (1.35), residues: 15 loop : 0.44 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 11 HIS 0.004 0.001 HIS H 274 PHE 0.015 0.002 PHE I 30 TYR 0.016 0.002 TYR I 91 ARG 0.006 0.001 ARG I 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.550 Fit side-chains REVERT: I 77 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6738 (ttm170) REVERT: J 94 MET cc_start: 0.8217 (mmm) cc_final: 0.7999 (mmm) REVERT: J 245 ASP cc_start: 0.7645 (m-30) cc_final: 0.7405 (m-30) outliers start: 6 outliers final: 4 residues processed: 91 average time/residue: 1.5237 time to fit residues: 143.5728 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 : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 106 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 0.2980 chunk 60 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.174675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.150626 restraints weight = 3545.052| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 0.66 r_work: 0.3538 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work: 0.3326 rms_B_bonded: 3.91 restraints_weight: 0.1250 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5256 Z= 0.181 Angle : 0.535 4.946 7114 Z= 0.278 Chirality : 0.040 0.133 777 Planarity : 0.005 0.061 910 Dihedral : 5.998 58.411 704 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.34), residues: 620 helix: 1.94 (0.28), residues: 345 sheet: 1.57 (1.37), residues: 15 loop : 0.46 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 132 HIS 0.005 0.001 HIS H 274 PHE 0.015 0.002 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.011 0.001 ARG J 298 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.578 Fit side-chains REVERT: I 77 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6718 (ttm170) REVERT: J 245 ASP cc_start: 0.7668 (m-30) cc_final: 0.7421 (m-30) outliers start: 7 outliers final: 4 residues processed: 89 average time/residue: 1.5795 time to fit residues: 145.3945 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 : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 106 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 46 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.172412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.147775 restraints weight = 3537.614| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 0.64 r_work: 0.3504 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work: 0.3296 rms_B_bonded: 3.74 restraints_weight: 0.1250 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5256 Z= 0.319 Angle : 0.667 9.953 7114 Z= 0.347 Chirality : 0.045 0.159 777 Planarity : 0.006 0.060 910 Dihedral : 6.086 56.117 704 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % Rotamer: Outliers : 1.80 % Allowed : 12.59 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.33), residues: 620 helix: 1.49 (0.27), residues: 345 sheet: -0.77 (0.90), residues: 26 loop : 0.38 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP J 237 HIS 0.008 0.002 HIS J 131 PHE 0.019 0.003 PHE I 13 TYR 0.023 0.003 TYR I 2 ARG 0.009 0.001 ARG J 298 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.571 Fit side-chains REVERT: I 77 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6845 (ttm170) REVERT: J 245 ASP cc_start: 0.7788 (m-30) cc_final: 0.7528 (m-30) outliers start: 10 outliers final: 4 residues processed: 94 average time/residue: 1.5420 time to fit residues: 150.1129 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 : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 281 GLN 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 45 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 chunk 29 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.9360 ------------------------------------------------------------------------------- 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 = 0.3991 r_free = 0.3991 target = 0.174447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.150820 restraints weight = 3541.701| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 0.64 r_work: 0.3543 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work: 0.3316 rms_B_bonded: 4.07 restraints_weight: 0.1250 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5256 Z= 0.187 Angle : 0.555 7.622 7114 Z= 0.288 Chirality : 0.041 0.137 777 Planarity : 0.005 0.052 910 Dihedral : 5.886 53.925 704 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.55 % Rotamer: Outliers : 0.90 % Allowed : 13.49 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.33), residues: 620 helix: 1.80 (0.28), residues: 345 sheet: -0.43 (0.98), residues: 25 loop : 0.41 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.005 0.001 HIS H 274 PHE 0.016 0.002 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.009 0.001 ARG J 298 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.579 Fit side-chains REVERT: I 77 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6722 (ttm170) REVERT: J 245 ASP cc_start: 0.7744 (m-30) cc_final: 0.7429 (m-30) outliers start: 5 outliers final: 4 residues processed: 90 average time/residue: 1.6112 time to fit residues: 149.9906 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 : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 281 GLN 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 14 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.173793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.151363 restraints weight = 3552.793| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 0.61 r_work: 0.3519 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work: 0.3323 rms_B_bonded: 3.71 restraints_weight: 0.1250 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 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 : 0.003 0.027 5256 Z= 0.220 Angle : 0.594 9.698 7114 Z= 0.308 Chirality : 0.042 0.156 777 Planarity : 0.005 0.052 910 Dihedral : 5.899 55.454 704 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.33), residues: 620 helix: 1.73 (0.28), residues: 345 sheet: -0.57 (0.96), residues: 25 loop : 0.41 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP J 132 HIS 0.006 0.002 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.019 0.002 TYR I 2 ARG 0.009 0.001 ARG J 298 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.649 Fit side-chains REVERT: I 77 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6793 (ttm170) REVERT: J 245 ASP cc_start: 0.7718 (m-30) cc_final: 0.7456 (m-30) outliers start: 5 outliers final: 4 residues processed: 89 average time/residue: 1.7275 time to fit residues: 159.0750 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 : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 281 GLN 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 34 optimal weight: 0.0370 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.6460 ------------------------------------------------------------------------------- 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 = 0.4005 r_free = 0.4005 target = 0.175717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.152118 restraints weight = 3562.733| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 0.64 r_work: 0.3563 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work: 0.3338 rms_B_bonded: 4.04 restraints_weight: 0.1250 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5256 Z= 0.167 Angle : 0.546 10.112 7114 Z= 0.281 Chirality : 0.040 0.146 777 Planarity : 0.005 0.047 910 Dihedral : 5.786 54.551 704 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.19 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.34), residues: 620 helix: 2.01 (0.28), residues: 343 sheet: -0.46 (1.00), residues: 25 loop : 0.29 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 11 HIS 0.004 0.001 HIS H 274 PHE 0.015 0.002 PHE I 110 TYR 0.015 0.002 TYR I 91 ARG 0.009 0.001 ARG J 298 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7536.94 seconds wall clock time: 129 minutes 24.15 seconds (7764.15 seconds total)